OLD_NRSP8: National Animal Genome Research Program

(National Research Support Project Summary)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[03/03/2004] [03/16/2006] [03/18/2005] [05/27/2008]

Date of Annual Report: 03/03/2004

Report Information

Annual Meeting Dates: 01/10/2004 - 01/12/2004
Period the Report Covers: 01/01/2003 - 12/01/2003

Participants

Overall attendance to the NRSP-8 species workshops: 65 (Aquaculture), 56(Cattle & sheep), 51 (Horse), (Poultry), 97 (Swine).

Brief Summary of Minutes

I Approval of minutes: Minutes of the January 2003 meeting were distributed. Deb Hammernik moved the approval of minutes. Motion was seconded by Max Rothschild and unanimously approved.

II. Old Business

Cattle: Jim Womack presented the annual report of the species activities. The highlights included active support by the coordinator, NRSP8 participants and the cattle community developed a white paper and generated financial support for sequencing the cattle genome. The sequencing program was officially initiated in December 2003, and the first set of sequence data is expected to be made available by February/March 2004. The coordinator continues to maintain the RH-analysis website but has transferred other bovine genome database responsibilities to Database coordinator Jim Reecy at Iowa State University. DNA from the 5,000 and 12,000 rad panels is being distributed by the coordinator to all researchers interested in developing fine physical maps. Additionally, bovine BAC libraries, DNA from somatic cell hybrid panel, and DNA from the International Bovine Reference family panel (IBRP) are also being made available to scientists needing these mapping resources.

Cattle administrative advisor Colin Kaltenbach lauded the efforts and industry representative Elizabeth Dressler promised continuous support and interest of the industry in enhancing research strengths of the group.

Sheep: Noelle Cockett reported the progress currently being made through the coordinator?s funds to develop, analyze and distribute the ovine radiation hybrid panel. Efforts are underway to develop a framework map for the sheep genome with ~2,500 loci. A memorandum of understanding has been signed with Peter de Jong (BACPAC resources) to acquire the sheep BAC library, make copies and develop high density filters for distribution to the sheep gene mapping community. Progress on the BAC end sequencing and fingerprinting was reported. Currently end sequencing of 150,000 to 200,000 BACs is being carried out at INRA (France) and Roslin Institute (UK) in conjunction with NRSP8 sheep coordinator. A seed grant from Utah State University is currently being used to end sequence some (unspecified number) ovine BACs. Sheep administrative advisor Colin Kaltenbach commended the work of the sheep group and described them as strong and highly regarded internationally.

Equine: Ernie Bailey provided an overview of the equine workshop. The invited presentations focused on bioinformatics and MHC. He elaborated the coordinated progress of the equine group in the areas of RH and linkage mapping and defined the goals agreed upon by the community for the next year. Publication of the first generation RH map in horse was a highlight. Progress made at the Havermeyer International Equine Genomics meeting in South Africa was also briefly mentioned. Coordinator funds were used for development and distribution of resources (reference family material, genome scan panel, etc.), and for travel support to technical committee members and a graduate student for PAGXII. Horse administrative advisor Bill Trumble pointed out that despite a late start, the horse group has done an amazing job.

Poultry: Jerry Dodgson reported that the PAG XII chicken workshop was the best the group ever had. The first generation physical map was ready in December; the 2nd generation map will probably be obsolete with the sequence information being made available soon. The current focus of the chicken community is primarily on the sequencing project ? mainly getting the finished sequence data. The linkage map generated up till now was reported to be well used. He emphasized the importance of NRSP8 in getting the sequencing efforts on track, making the East Lansing International reference family DNA, primer pair kits, BAC libraries filters and PCR-screenable pooled DNA (superpools) and other resources to several laboratories around the world. He also mentioned the availability of chicken microarray from FHCRC (Jeff Delrow and Paul Neiman). The Poultry Genome News letter supported through NRSP8 is constantly providing updates and details on research activities to researchers around the world. On behalf of the poultry administrative advisor, Margaret Dentine greatly appreciated the efforts of the poultry gene mapping group.

Pig: Max Rothschild reported that the swine genome workshop had the biggest crowd compared to earlier meetings (~120 people). Several developments were reported including: active use of markers by the swine industry, constant rapid expansion of the maps, availability of 2 RH panels (one from MN/INRA and the other from Reno, Nevada), etc. Intense efforts being made by Larry Schook and the entire pig community to get funding for sequencing the pig genome was a major activity of the group. Submission of the white paper was mentioned. Efforts made by the entire pig community to generate funds to the tune of $20 million were stated. This includes requests made to the Pork Board. Further, the importance of NRSP8 in facilitating database activities, distribution of various resources/materials including the Pig Genome Update, and providing travel and meeting support were acknowledged. Swine administrative advisor Margaret Dentine was very supportive of the intense efforts made by the swine genomics group in development of a high resolution map and sequencing.

With permission from the Chair, Larry Schook requested to discuss about the critical situation pig researchers are facing for generating matching funds required for getting the pig genome sequencing on track. On behalf of the Swine sequencing committee, Schook requested for ?support and endorsement from the NRSP8 group to empower USDA/NRI to provide financial support because it is in the best interest of the entire animal genome community?. The motion was moved for approval.

Jim Womack (TAMU) supported the motion stating that the window of opportunity is narrow and all efforts must be made to capitalize on what is available. He requested the group to embrace the pig genome sequencing efforts.

Noelle Cockett (U of Utah) wanted to know the current status regarding the availability of funds for sequencing (primarily the amount that has been committed) and how much would be needed.

Larry Schook replied that $20M needs to be generated by October 1. He mentioned about some international commitments and various steps (not specified) that are being taken to achieve the target.

Max Rothschild clarified that the pig community has at least $10M and is reasonably comfortable to raise another $5M for whole genome sequencing. It is the remaining $5M that needs to be obtained from some source.

Chris Biddwell wanted to know whether support of the motion automatically implies availability of lesser federal (USDA/NRI) funds for competitive proposals.

It was finally suggested that the Chair of the meeting (F. Abel Ponce de León) will draft a letter of support and circulate it to chairs of different species committees, get a consensus and then send it to USDA/NRI-CREES.

Finally, Max Rothschild (ISU) suggested adoption of two motions:

Motion 1: NRSP8 group is supportive of efforts for sequencing the swine genome

Motion 2: The group is also supportive of the efforts by the USDA to find additional financial resources to support the swine sequencing effort.

Questions were raised whether this will authorize USDA to provide financial support to the pig group (Noelle Cockett, U of Utah). There were propositions that other agencies like DOE must be approached. Schook said that the possibility to get funds from DOE is bleak.

At the end of the discussion, the motion: ?The NRSP8 group is supportive of the efforts for sequencing the swine genome, and the group recommends USDA to make efforts to find financial resources supporting the sequencing project?. Deb Hamernik clarified that this does not bind USDA in anyway to commit financial resources to the pig genome sequencing project.

The motion was carried unanimously with Max Rothschild moving it and Jim Womack seconding it.

Database: James Reecy summarized about the presentations he made to different species workshops. He reiterated his eagerness to hear from species coordinators and participants regarding the database needs of individual groups.

Aquaculture: John Liu reported that the rather newly formed aquaculture group is very diverse with 6 different species. This year?s workshop organized by Tom Kocher was very strong in science. International participation was strong, especially by Tilapia researchers. Prospects of sequencing salmon in the near future were discussed.

Administrators reports:

Lead Administrative advisor Margaret Dentine reported about the new five year cycle for NRSP8 program. She welcomed the aquaculture group within the fold of the program. The participants were informed about the setting up of a database that is expected to provide detailed information about the project. All participants (~72, with 6 new from Beltsville) were asked to fulfill their reporting commitments on time because documentation of progress is important for the project. The new members were requested to provide complete addresses and e-mails, and current members were requested to update their e-mail addresses (if changed). Margaret said that the NRSP8 project is indeed in good shape and the progress made is excellent.

Program Leader Muquarrab Qureshi introduced himself to the NRSP8 community and provided an overview of CSREES activities. A summary of National Public Funding and the latest NRI funding was given. Stating that these are exciting times for genomics, he said that he will take the message regarding various developments to Washington DC, in particular the developments relating to sequencing efforts currently underway in chicken and cattle. He provided a brief overview of the ?Discover? conference, thanked species coordinators for providing impact statements for the new CSREES website, and mentioned about the current stand of USDA regarding consumption of cloned and genetically engineered food. Muquarrab expressed great enthusiasm to be a part of the NRSP8 community. He looked forward to regularly receiving constructive comments and suggestions for improvement in the program.

III New business

1. Meeting day and time for 2005: It was agreed that in January 2005, the executive committee of NRSP8 will meet at noon (instead of early morning; as has been the case in the past). Further, it was also unanimously agreed that in January 2005, the NRSP8 annual meeting will be held on Sunday, one day before the start of the PAG meeting, from 4:30 to 6:00 PM (instead of late evening or night). These changes will be reviewed after 2005 PAG meeting.

2. Election of officers for 2004: Tom Kocher (New Hampshire) was nominated and unanimously elected Secretary of the NRSP8 Animal Genome Technical Committee for 2004-2005. Current Chair Abel Ponce de León thanked everyone present for participation and fruitful discussions and handed over the responsibilities for the next year to current secretary Bhanu Chowdhary.

3. Selection of next meeting location and date: The next NRSP8 meeting will be held in conjunction with PAGXIV.

IV Adjournment: The meeting was adjourned at 8:45 P.M. with a vote of thanks to F. Abel Ponce de León for a very successful organization of the meeting.

Accomplishments

Progress Toward Objective 1: Aquaculture: Catfish ? AL has constructed a genetic linkage map for catfish containing 418 AFLP markers. This work has been published (see below under publications). EST project has now 4,103 gene-associated microsatellites and 145 gene-associated SNP markers. Rainbow trout - NCCCWA have developed more microsatellite and single nucleotide polymorphism markers for mapping in salmonid and Morone species. A high-density genetic map for rainbow trout is expected to be continued through 2004. Tilapia - NHAES has completed a genetic linkage map for tilapia containing more than 550 microsatellite and gene-based markers. A physical map based on the restriction fingerprints of 35,000 BAC clones (5x genome coverage) has also been completed (http//:www at hcgs.unh.edu) Oysters (Crassostrea virginica and C. gigas) - NJ has generated AFLP-based linkage maps for the eastern and Pacific oysters. VIMS and DE have analyzed inheritance of a set of microsatellite markers in the eastern oyster observing a high incidence of null alleles and distorted segregation ratios. Clams ? VA have initiated work on genetic improvement of the hard clam Mercenaria mercenaria. To date, four microsatellite libraries have been developed. Efforts have begun at VIMS to develop a set of Type I SNP markers for the hard clam. Of the 8 loci screened to date in a panel of clams from diverse commercial stocks, six have shown polymorphisms, with several containing more than two alleles. Cattle: Collaboration between TX and IL has produced a second-generation 5000 rad radiation hybrid (RH) EST map of the cattle genome covering gaps in the existing cattle-human comparative map as well as sparsely populated map intervals. A cattle-human comparative map containing 1463 comparative anchor points has been created using human genome sequence coordinates for paired orthologs to define boundaries of conserved chromosome segments. Approximately 312,000 BAC end sequences are in the public domain as a result of this collaborative effort, and a minimal tiling path of BACs for the bovine genome-sequencing project has been generated by an international consortium (including TX, IL, USDA-ARS). The class IIB and class III regions of the bovine MHC have been sequenced (TX). Future plans include development of a 1MB resolution comparative map (TX, IL), a bovine HapMap (TX) and finished sequence for the class IIB and class III regions of the bovine MHC (TX). The bovine genome is currently being sequenced making sequence annotation and integration with map data a high priority. Horse: The latest reiteration (MN, CA, Japan Laboratory of Racing Chemistry) and England Animal Health Trust, Newmarket) of the horse linkage map includes 801 markers and covers all autosomes with an average spacing of 6.8 cM. A radiation hybrid map (TX) now includes over 2000 markers. BAC libraries are being characterized and new markers being developed at TX, MN, France and Germany. A BAC contig has been developed (TX, NY) as well. Efforts are underway to utilize conserved, heterologous or horse-specific primers to generate 1-5 Mb marker density on selected equine chromosomes. Poultry: Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples on three international reference crosses, the Compton population, the East Lansing population and the Wageningen population. The consensus map includes 1965 markers, placed into 50 linkage groups, covering around 4000 cM. Several laboratories have cooperated to generate a second generation BAC contig map comprised of about 280 contigs, two-thirds of which have been anchored to the genetic linkage/chromosome map. The Washington U. Genome Sequencing Center (WUGSC) has completed ~6X sequencing of the chicken genome (primarily whole genome shotgun) and this is now being assembled. Sheep: An ovine whole-genome radiation hybrid (RH) panel of 5,000 rad has been constructed (TX, UT). The resulting ovine framework/comparative map will contain about 500 microsatellite markers previously assigned to ovine and bovine linkage maps and about 500 ovine ESTs with known human map locations. A 10-fold redundant BAC library has been purchased from BACPAC Resources (AgResearch (New Zealand), the National Meat and Livestock Board (Australia), the USDA/ARS Meat Animal Research Center (Nebraska), and the NRSP-8 Sheep Coordinator, UT). Swine: Physical and genetic maps of the pig genome continue to be enhanced (BARC, IA, MI, NC, WA, MN, NE, and NV) through mapping of candidate genes, EST, SNP, and microsatellite markers using RH mapping panels, FISH, and reference population resources. Significant milestones toward the completion of Objective 1 include detailed comparative maps focusing on swine chromosomes 3 and 4, description of a second generation map of the IMpRH7000Rad RH mapping panel with an estimated 98% coverage of the human genome, and identification of polymorphisms within several new genes that may be important QTL. Progress Toward Objective 2: Aquaculture: Catfish ? AL has continued to produce expressed sequence tags in channel catfish and blue catfish. Over 37,000 ESTs representing 25,334 unique sequences have been generated. These ESTs have been all deposited to GenBank. Using the EST resource, researchers have characterized expression of chemokine CXCL10 and CXCL8 in catfish with different resistance, both before and after infection. Rainbow trout - NCCCWA has continued to identify expressed sequence tags in rainbow trout for identification of functional candidate genes affecting aquaculture production traits and the development of microarrays for functional genomics. Tilapia - Sex linked markers have been identified on two linkage groups in Nile tilapia and blue tilapia. The locus on LG1 is an XY (male heterogametic) system. The locus on LG3 is a WZ (female heterogametic) system. Both loci segregated in a single family of blue tilapia. Work is underway to positionally clone these sex-determining genes. Oyster ?SC led a successful effort to develop BAC libraries for both the eastern and Pacific oyster, receiving funding from NIH (National Human Genome Research Institute). NJ obtained 500+ sequences from suppression subtractive hybridization (SSH) libraries built to identify up-regulated genes in eastern oysters infected by Dermo and MSX (two parasitic pathogens). Analysis of these sequences has led to the identification of about 170 unique genes. Cattle: A first generation bovine adipose tissue microarray (OSU) comprised of 1100 unique cDNAs has been generated. A second bovine microarray has been constructed (IA) that includes 10,604 unique bovine cDNAs from the BOV1-4 cDNA libraries. QTL mapping for various traits is underway (TX, WI, IL, CA). A new ovulation rate QTL was found (WI) on chromosome 14. Two regions show evidence of QTL segregation for ovulation rate or twinning rate in multiple families, and strong support for a previously reported BTA5 QTL \was found in a combined analysis of four related families. An F2 resource population (Bos taurus x Bos indicus) to investigate maternal reproductive traits is being developed (TX). Males will be used for feed efficiency experiments. A number of candidate genes for growth, disease resistance and reproduction have been evaluated in association studies (TX, NM). Mapping and identification of QTL provide the precursors for a better understanding of biological traits. Horse: About 11,000 high-quality, well characterized ESTs from stimulated and non-stimulated leukocytes were developed (GA) http://fungen.org/. ESTs (ca 14,000) from articular cartilage are being developed (KY) for the purpose of generating a microarray to study transcriptional changes in equine chondrocytes in osteoarthritis and other arthropathies. Additional ESTs are being developed at (MA, TX, NY). The use of genome mapping, comparative biochemistry and pathology and candidate gene evaluation resulted in the identification (MN) of a genetic change associated with glycogen storage disease IV (GBE1), a fatal disease in Quarter Horses. Sheep: The high growth (hg) mouse mutation is a 460 Kb deletion of mouse chromosome 10 which causes a 30-50% increase in growth in the homozygous animal. The research group (CA) has observed that the effect of hg can be modified dependent on the genetic background. They propose that the hg phenotype is influenced by genetic interactions between members of the Gh signaling pathway as a result of the absence of the SOCS-2 protein. A core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18A have been identified (UT, IN, USDA/ARS, and University of Liége). The callipyge (CLPG) mutation enhances the expression of genes in this core cluster when it is inherited in cis. Interval mapping (LA) in an F2 population [Gulf Coast Native (resistant) and Suffolk (susceptible)] generated to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites revealed a putative QTL localized on the central region of chromosome 1. Swine: IA, IL, MI reported progress toward the identification of QTL influencing the genetic regulation of meat quality traits. Also, BARC, IA, IN, MI, NC are using differential gene expression to identify genes controlling physiological traits of economic importance. Based on a microarray experiment NE identified approximately 100 genes putatively differentially expressed between reproductive selection lines. A number of QTL influencing meat quality traits have been identified, and fine mapping of causative genes is currently underway. Results from initial gene expression studies have identified gene expression patterns associated with muscle growth and development, immune responses, and tissue specificity. Additionally, the porcine long oligo microarray is being validated and will rapidly be put to use investigating a variety of experimental models. Progress Toward Objective 3: Aquaculture: Catfish - A web-based EST database for catfish is under construction. Data mining of EST databases has generated large numbers of type I molecular markers. Tilapia ? NHAES has developed WWW-based software for comparing the tilapia map with the linkage maps of medaka and zebrafish, and with the sequence scaffolds of pufferfish. The tilapia genetic and physical linkage maps are available in these browsers at hcgs.unh.edu Cattle: Two groups have begun to implement QTL databases on the web for bovine QTL data (CA,TX). One strategy has been to use the Generic Genome Browser (http://www.gmod.org) as the front end for a MySQL database. The other strategy has been to use the RatMap QTL browser (http://ratmap.org/qtler/) as the basis for an improved interface. Both databases will contain public domain QTL data and one of them will feature password protected log on for investigators to edit or submit QTL data prior to publication. Horse: The website at the University of Kentucky (http://www.uky.edu/Ag/Horsemap/) continues to be maintained and provides information describing workshop efforts, significant developments for the horse gene map. This site also provides links to other databases and communal resources. A graphic map viewer (HorseMap Viewer) is in final stages of development (CA) and will be also available to investigators. Swine: MN, NV, WA provided updates on their ongoing efforts to establish integrated database systems for multiple types of data relating to pig genes.

Publications

Aquaculture: Argue, B., Liu, Z.J., and Dunham, R.A. 2003. Dress-out and fillet yields of channel catfish, Ictalurus punctatus, blue catfish, I. furcatus, and their F1, F2 and backcross hybrids. Aquaculture 228, 81-90. Cnaani A, Lee B-Y, Ron M, Hulata G, Kocher TD, and Seroussi E. 2003. Linkage mapping of major histocompatibilty complex class I loci in tilapia (Oreochromis spp.). Animal Genetics 34:390-391. He, C., Chen, L., Simmons, M., Li, P., Kim, S., and Liu, Z.J. 2003. Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis. Animal Genetics 34, 445-448. Jenny, M. J., A. H. Ringwood, et al. (2002). "Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica." Marine Biotechnology 4: 81-93. Lee B-Y, Penman, DJ and Kocher TD. 2003. Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis. Animal Genetics 34(5): 379-383. Li, L. and X. Guo. 2003. AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology, in press. Liu, Z.J. 2003. A review of catfish genomics: progress and perspectives. Comparative and Functional Genomics 4, 259-265. Liu, Z.J., Karsi, A., Li, P., Cao, D., and R. Dunham. 2003. An AFLP-Based Genetic Linkage Map of Channel catfish (Ictalurus punctatus) Constructed by Using an Interspecific Hybrid Resource Family. Genetics 165, 687-694. Mickett, K., Morton, C., Feng, J., Li, P., Simmons, M., Dunham, R.A., Cao, D., and Liu, Z.J. 2003. Assessing genetic diversity of domestic populations of channel catfish (Ictalurus punctatus) in Alabama using AFLP markers. Aquaculture 228, 91-105. Patterson, A., Karsi, A., Feng, J., and Liu, Z. J. 2003. Translational Machinery of Channel Catfish: II. Complementary DNA and Expression of the Complete Set of 47 60S Ribosomal Proteins. Gene 305, 151-160. Reece, K.S, Ribeiro, W.L., Gaffney, P.M., Carnegie, R.B. and Allen, S.K. Jr. Microsatellite marker development and analysis in the eastern oyster, Crassostrea virginica: Confirmation of null alleles and non-Mendelian segregation ratios. J. Heredity (in press). Streelman, J.T. and T.D. Kocher. 2002. Microsatellite length variation is associated with prolactin expression and growth response of salt-challenged tilapia. Physiological Genomics 9:1-4. Yu, Z. and X. Guo. 2003. Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. Biol. Bull. 204: 327?338. Cattle: Adelson, D.L., Cam, G.R., DeSilva, U. and Franklin, I.R. (2004) Gene Expression in Sheep Skin and Wool (Hair).Genomics 83 (1): 95-105. Agca, C., C.A. Bidwell, and S.S. Donkin. (In Press) Cloning of bovine pyruvate carboxylase and 5‘‘‘‘ untranslated region variants. Animal Biotechnology. Ashwell, M. S., D. W. Heyen, T. S. Sonstergard, C. P. Van Tassell, Y. Da, P. M. Van Raden and H. A. Lewin. 2004. Detection of quantitative trait loci affecting female fertility and milk production in ten Dairy Bull DNA Repository families. J. Dairy Sci. (In press) Brunner, R.M., Sanftleben, H., Goldammer, T., Kühn, C., Weikard, R., Kata, S.R., Womack, J.E., and Schwerin, M.: The telomeric region of BTA18 containing a potential QTL region for health in cattle exhibits high similarity to the HSA19q region in humans. Genomics, 81:270-278, 2003. Chowdhary, B.P., Raudsepp, T., Kata, S.R., Goh, G., Millon, L.V., Allan, V., Piumi, F., Guérin, G., Swinburne, J., Binns, M., Lear, T.L.. Mickelson, J., Murray, J., Antczak, D.F., Womack, J.E., and Skow, L.C.: The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genome. Genome Research, 1:742-751, 2003. Denniston, D.J., M.G. Thomas, K.K. Kane, C.N. Roybal, L. Canales, D.M. Hallford, M.D. Remmenga, and D.E. Hawkins. 2003. Effect of Neuropeptide Y on GnRH-induced LH release from bovine anterior pituitary cell cultures derived from heifers in a follicular, luteal, or ovariectomized state. Anim. Reprod. Sci. 78:25-31. DeSilva, U, I.R. Franklin, B. van Hest, J.F. Maddox and D.L. Adelson Systematic screening of sheep skin cDNA libraries for microsatellite sequences. J. Cytogenetics and Genome Research (in press). Eun-Joon Lee, Terje Raudsepp, Srinivas R. Kata, David L. Adelson, James E. Womack, Loren C. Skow, Bhanu P. Chowdhary. A 1.4 Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genome Research (In press). Farber, C.R. and J. F. Medrano 2003. In silico anchoring of ESTs, genes and genomic sequence to bovine, porcine and chicken genome maps using SSLP markers. Animal Genetics 34:11-18. Farber, C.R. and J.F. Medrano 2004. Identification of putative homology between horse microsatellite flanking sequences and cross-species ESTs, mRNAs and genomic sequences. Animal Genetics (In press) Hamernik DL, Adelson DL (2003) USDA stakeholder workshop on animal bioinformatics: summary and recommendations. Comparative And Functional Genomics, 4 (2): 271-274. Hamernik, D. L., H. A. Lewin, and L. B. Schook. 2003. Allerton III. Beyond Livestock Genomics. Animal Biotechnology 14:77-82. Kim, K.-S., J.M. Reecy, W.H. Hsu, L.L. Anderson, and M.F. Rothschild. 2003. Functional and phylogenetic analyses of a melanocortin-4 receptor mutation in domestic pigs. Domestic Animal Endocrinology (In Press). Krum, S.A., Womack, J.E., and Lane, T.F.: Bovine BRCA1 shows classic responses to genotoxic stress but low in vitro transcriptional activation activity. Oncogene, 22:6032-6044, 2003. Kurar, E., J.E. Womack and B.W. Kirkpatrick. 2003. A radiation hybrid map of bovine chromosome 24 and comparative mapping with human chromosome 18. Animal Genetics 34:198-204. Larkin, D. M., A. Everts-van der Wind, M. Rebeiz, P. A. Schweitzer, S. Bachman, C. Green, C. L. , Wright, E. J. Campos, L. D. Benson, J. Edwards, L. Liu, K. Osoegawa, J. E. Womack, P. de Jong, and H. A. Lewin. 2003. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Research 13: 1966-1972. Larkin, D.M., der Wind, A.E., Rebeiz, M., Schweitzer, P.A., Bachman, S., Green, C., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., Liu, L., Osoegawa, K., Womack, J.E., de Jong, P., and Harris, A.L.: A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Research 13:1966-1973, 2003. Lewin, H. A. 2004. The future of cattle genomics: the beef is here. Cytogenetics and Genome Research (in press) McKay, S.D., White, S.N., Kata, S.R, Loan, R., and Womack, J.E.: The bovine 5? AMPK gene family: mapping and single nucleotide polymorphism detection. Mammalian Genome, 14:853-858, 2003. Mishra, B.P. and J. M. Reecy. 2003.Mutations in the limbin gene previously associated with dwarfism in Japanese brown cattle are not responsible for dwarfism in the American Angus breed. Animal Genetics 34(4):311-2 Moody, D.E., A.J. Rosa, and J.M. Reecy. 2003. Current status of livestock DNA microarrays. AgBioTech (In Press). Morrison, C.D., J.A. Daniel, J.H. Hampton, P.R. Buff, T.M. McShane, M.G. Thomas, and D.H. Keisler. 2003. Regulation of luteinizing hormone and growth hormone in ewes treated with Neuropeptide Y. Domestic Anim. Endocrinol. 24:69-80. Narro, L.A. , M.G. Thomas, G.A. Silver, K.J. Rozeboom, and D.H. Keisler. 2003. Body composition, leptin, and the leptin receptor and their relationship to the growth hormone (GH) axis in wethers treated with zeranol. Domest. Anim. Endocrinol. 24:243-255. Potts, J.K., S.E. Echternkamp, T.P.L. Smith, and J.M. Reecy. 2003. Characterization of Gene Expression In Double-Muscled and Normal-Muscled Bovine Embryos. Animal Genetics 34, 438?444 Schwerin, M., Czernek-Schafer, D., Goldammer, T., Kata, S.R., Womack, J.E., Pareek, R., Pareek, C., Krzysztof, W., and Brunner, R.M.: Application of disease-associated differentially expressed genes - Mining for functional candidate genes for mastitis resistance in cattle. Genet. Sel. Evol., 35:S19-S34, 2003. Soller, M. and J.M. Reecy. 2003. QTL Mapping and Cloning in Beef Cattle. AgBioTech (In Press). White, S.N., Kata, S.R., and Womack, J.E.: Comparative fine maps of bovine toll-like receptor 4 and toll-like receptor 2 regions. Mammalian Genome, 14:149-155, 2003. White, S.N., Taylor, K.H., Abbey, C.A., and Gill, C.A., and Womack, J.E.: Haploytype viaration in bovine Toll-like receptor 4 and computational predication of a positively selected ligand-binding domain. Proc. Natl. Acad. Sci. USA 100:10364-10369, 2003. Horse: Ainsworth, D.M., Appleton, J.A., Eicker, S.W., Luce, R., Flaminio, J.B.F., Antczak, D.F. (2003a) The effect of strenuous exercise on mRNA concentration of interleukin-12, interferon-gamma and interleukin-4 in equine pulmonary and peripheral blood mononuclear cells. Vet Immunol. Immunopath. 91:61-71. Ainsworth, D.M., Grunig, G., Matychak, M.B., Young, J., Wagner, B., Erb, H.N., and Antczak, D.F. (2003b) Recurrent airway obstruction (RAO) in horses is characterized by IFN-g and IL-8 production in bronchoalveolar lavage cells. Vet Immunol. Immunopath. 96:83-91. Bryan, T.M., C.A. Abbey, T. Raudsepp, B.P. Chowdhary, C.A. Gill, T.L. Blanchard, N.H. Ing and T.H.Welsh, Jr. ( 2003) Characterization of equine bacterial artificial chromosomes (BACs) relevant to endocrine and immune system regulation. J. Anim. Sci. 81(Suppl.1):102-103. Chowdhary, B.P., Raudsepp, T., Kata, S.R., Goh, G., Millon, L.V., Allan, V., Piumi, F., Guérin, G., Swinburne, J., Binns, M., Mickelson, J., Murray, J., Antczak, D.F., Womack, J.E., Skow, L.C. (2003) The first generation whole genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Research 13:742-751. Chowdhary B.P. & Bailey E. (2003) Equine Genomics: Galloping to new frontiers. Cytogenetics & Genome Research, in press. Curik,I., Fraser,D., Eder,C., Achmann,R., Swinburne,J., Binns,M., Crameri,R., Brem,G., Sölkner,J. and Marti,E. (2003) Association between the MHC gene region and variation of serum IgE levels against specific mould allergens in the horse. Genetics Selection Evolution 35: S177-S190. Gallagher PC, Morrison S, Bernoco D & Bailey E. (2003) Measurement of back curvature in American Saddlebred horses: structural and genetic basis for early-onset lordosis. The Journal of Equine Veterinary Science 23: 71-76. Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Biros, I., Bowling, A.T., Brandon, R., Cholewinski, G., Colling, D., Eggleston, M., Flynn, J., Gralak, B., Hasegawa, T., Ketchum, M., Lindgren, G., Lyons, L., Millon, L.V., Mariat, D., Murray, J., Neau, A., Røed, K., Sandberg, K., Skow, L.C., Tammen, I., Van Dyk, E., Weiss, B., and Ziegle, J. (2003) The Second Iteration of the International Equine Gene Mapping Workshop: Half-Sibling Linkage Map. Animal Genetics 34:161-168. Gustafson A.L., Tallmadge R.L., Ramlachan N., Miller D., Bird H., Antczak D.F., Raudsepp T., Chowdhary B.P., and Skow L.C. (2003) An ordered BAC Contig Map of the Equine Major Histocompatibility Complex. Cytogenetics & Genome Research (in press). Hamernik DL, Adelson DL (2003) USDA stakeholder workshop on animal bioinformatics: summary and recommendations. Comparative And Functional Genomics, 4 (2): 271-274. Lee, E-J, Raudsepp T., Kata S.R., Adelson D., Womack J.E., Skow L.C., Chowdhary B.P. (2003) A 1.4 Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics (in press). Mariat D, Taourit S, Guérin G. (2003) A mutation in the MATP gene is associated to the cream coat colour in the horse. Genetics, Selection and Evolution 35:119-133. Marti, E., Horohov, D.W., Antczak D.F., Lazary S., Lunn D.P. (2003) Advances in equine immunology: Havemeyer workshop reports from Santa Fe, New Mexico, and Hortobagy, Hungary. Vet. Immunol. Immunopath. 91:233-43. Mickelson, J.R., Wu J.T., Morrison L.Y., Swinburne J.E., Binns M.M., Reed K.M., Alexander L.J. (2003) Eighty-three previously unreported equine microsatellite loci. Animal Genetics 34: 71-74. Milenkovic D, Chaffaux St, Taourit S, Guérin G. (2003) A mutation in the LAMC2 gene causes the Herlitz junctional epidermolysis bullosa (H-JEB) in two French draft horse breeds. Genetics, Selection and Evolution 35: 249-256. Mousel M.R., Harrison L., Donahue M. and E. 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Characterization and linkage map assignments for 61 new horse microsatellite loci (AHT49-109). Animal Genetics 34, 65-68. Takahashi, T., Yawata, M., Raudsepp, T., Lear, T. L., Chowdhary, B. P., Antczak, D. F., and Kasahara, M. Natural killer cell receptors in the horse: evidence for the existence of multiple transcribed LY49 genes. European Journal of Immunology, in press. Tallmadge, R.L., Lear, T.L., Johnson, A.K., Guérin, G., Millon, L.V., Carpenter, S.L. and Antczak, D.F. (2003) Characterization of the ??-2-microglobulin gene of the horse. Immunogenetics 54:725-733. Tozaki T, Takezaki N, Hasegawa T, Ishida N, Kurosawa M, Tomita M, Saitou N, and Mukoyama H. (2003) Microsatellite variation in Japanese and Asian horses and their phylogenetic relationship using a European horse outgroup. Journal of Heredity 94(5): 374-80. Wagner, B., Greiser-Wilke, I., and Antczak, D.F. (2003) Characterization of the horse (Equus caballus) IGHA gene. Immunogenetics 55:552-560. Wagner M., Goh G., Wu J.T., Raudsepp T., Morrison L.Y., Alexander L.J., Skow L.C., Chowdhary B.P., Mickelson J.R. (2003). Radiation hybrid mapping of 75 previously unreported equine microsatellite loci. Animal Genetics, in press. Wagner M, Goh G, Wu JT, Raudsepp T, Morrison LY, Alexander LJ, Skow LC, Chowdhary B.P., Mickelson J.R. (2003). Radiation hybrid mapping of 65 previously unreported equine microsatellite loci. Animal Genetics, submitted. Ward TL, Valberg SJ, Lear T, Guerin G, Milenkovic D, Swinburne J, Binns MM, Chowdhary BP, Raudsepp R, Skow S and Mickelson JR (2004) Genetic mapping of GBE1 and its association with glycogen storage disease IV in American Quarter Horses. Cytogenetics and Genome Research, in press. Ward TL, Valberg SJ, and Mickelson JR Glycogen branching enzyme (GBE1) mutation causing fatal glycogen storage disease IV in American Quarter Horse foals. Mammalian Genome, submitted. 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Iowa State University. Ciobanu, D.C., S.M. Lonergan, M. Malek, J.R. Woollard, E.J. Lonergan and M.F. Rothschild. 2002. New Alleles in the Calpastatin Gene Associated with Improved Tenderness in Pigs. Swine Research Reports. Iowa State University Dawson H., Nishi S., Beshah E., Solano-Aguilar G., Zarlenga D., Urban J.F., Lunney J.K. 2002. Functional genomic assessment of porcine disease resistance: real time assays of porcine immune gene expression. Proceedings 7th World Congress on Genetics Applied to Livestock Production. #13-41. Dawson, Harry, Sandra Nishi, Ethiopia Beshah, Gloria Solano-Aguilar, Dante Zarlenga, Joseph F. Urban, Joan Lunney. 2003. Use of real-time assays of immune gene expression to assess the genetic basis of disease resistance. http://www.intl-pag.org/11/abstracts/W52_W330_XI.html Ernst, C.W., N.E. Raney, V.D. Rilington, G.A. Rohrer, J.A. Brouillette and P.J. Venta. 2004. Mapping of the FES and FURIN genes to porcine chromosome 7. Anim. Genet. In Press. 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Impact Statements

Aquaculture: The set of genomic tools and reagents being developed is accelerating our understanding of the genomes of the species under investigation. The use of these genomic tools to investigate resistance and susceptibility to disease has identified differentially expressed genes that are relevant in disease control.
Cattle and Sheep: The new, more detailed cattle-human comparative map will provide a resource for the analysis of mammalian chromosome evolution and will facilitate the identification of candidate genes for economically important traits.
The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.
Transcriptional profiling using the newly developed bovine microarrays will allow identification of pathways and candidate genes responsible for economically important traits.
The use of a common microarray by multiple researchers will facilitate a global understanding of gene function across multiple biological models.
Horse: Advancements in developing the genetic and physical map of the horse has allowed to the identification of a genetic change associated with glycogen storage disease IV (GBE1), a fatal disease in Quarter Horses. This latter finding will help develop genetic test to facilitate breeding decisions.
Swine: The genetic regulation of multiple traits of economic importance is being defined through QTL studies. These results will impact the swine industry by providing additional information to be incorporated into selection programs, ultimately providing more economical and desirable products to consumers of pork.
Current efforts focusing on database development will impact the rate at which experimental results can be applied in industries because they will facilitate the integration of information from multiple sources, allowing genes with a significant impact on swine production to be identified.

Date of Annual Report: 03/16/2006

Report Information

Annual Meeting Dates: 01/14/2006 - 01/15/2006
Period the Report Covers: 01/01/2005 - 01/01/2006

Participants

Albert Paszer Cobb-Vantress albert.paszek@cobb-vantress.com
Anna Palmisano USDA, CSREES apalmisano@csrees.usda.gov
Archie Clutter Monsanto archie.c.clutter@monsanto.com
Bent Stromberg U of Minnesota b.srto@umn.edu
Bill Muir Purdue University bmuir@purdue.edu
Caird Rexroad USDA, ARS NCCCWA crexroad@ncccwa.ars.usda.gov
Cathy Ernst Michigan State ernstc@msu.edu
Chris Ashwell NC State University chris_ashwell@ncsu.edu
Colin Kaltenbach NRSP-8-Admin. Adv, U of AZ kitnbch@ag.arizona.edu
Dave Adelson TAMU david.adelson@tamu.edu
Deb Hamernik USDA, CSREES dhamernik@csrees.usda.gov
F. Abel Ponce De Leon U of Minnesota apl@umn.edu
Hans H. Cheng USDA, ARS hcheng@msu.edu
Hutton Oddy MLA, UNE hutton.oddy@une.edu.au
James L. Zhu TAMU jzhu@poultry.tamu.edu
James Reecy Iowa State University jreecy@iastate.edu
Jinzeng Yang U of Hawaii jinzeng@hawaii.edu
Joan Lunney ARS,BARC jlunney@anu.barc.usda.gob
Joe Cassady NC State University joe_cassady@ncsu.edu
Kefei Chen UIUC kfchen@uius.edu
Kent Reed U of Minnesota reedx054@umn.edu
Larry Schook U of Illinois schook@uiuc.edu
Len Van Zyl NCSU imvonzyl@gunity.ncsu.edu
Mary Delany UC Davis medelany@ucdavis.edu
Michael Zapata ARRATXPRESS, NCSU zapata@ncsu.edu
Muquarrab Qureshi USDA, CSREES mqureshi@csrees.usda.gov
Peter Burfening USDA, CSREES pburfening@csrees.usda.gov
Stewart Bauck Merial-Igenity stewart.bauck@merial.com
Susan J. Lamont Iowa State University sjlamont@iastate.edu
Zhihua Jiang Washington State University jiangz@wsu.edu
Zhiliang Hu Iowa State University zhu@iastate.edu

In addition to participation at the General Membership Business Meeting, individual workshops recorded the following numbers of participants: Aquaculture 102; Cattle 30; Poultry 50; Sheep 20; and Swine 70.

Brief Summary of Minutes

I. Call to order at 4:30 pm by Caird Rexroad, Chair.

Minutes taken by David Adelson (standing for Clare Gill).

Sue Lamont moved to approve minutes from January 16, 2005 meeting. Motion was unanimously affirmed.

II. Old Business
1. Species Reports:
a. Cattle/Sheep/Goat
i. Noelle Cockett, Sheep Genome Coordinator

Progress on sheep RH panel: distributed to 4 labs (see coordinators report). Significant typing efforts in Cockett lab include: 257 markers screened so far, about 50% of which are scoreable, with about 2/3 of those results duplicated. Efforts now are aimed at scaling up to type large numbers of markers. There will soon be a need for a data repository and infrastructure for the analysis of typing data.

A Tools and reagents proposal was funded for BAC end sequencing and construction of a physical map from the CHORI sheep library. Kellye Eversole negotiated a very favorable price with TIGR to end sequence the full 200,000 clones from the library. Related statistics are in the coordinators report, but a key feature is that ~6% of the ovine genome is represented. A whole genome physical map is being constructed by Brian Dalrymple (CSIRO Australia) using end sequences.

International Scientists linkage program. A large scale SNP discovery project (30,000 total sheep SNPS to create a 20,000 SNP chip) was initiated with Frank Nicholas (Sydney University).

Dr. Cockett invited scientists to attend the meeting of International Sheep Genome Consortium to be held at PAG Jan. 16.

ii. James Womack, Cattle Genome Coordinator

The Cattle genome sequencing project has consumed most of the resources and attention of the coordinator. At present there are efforts to develop a cell culture repository to immortalize DNA from the animals used in the sequencing project and first phase of SNP detection. Live cell lines will be provided to investigators upon request.

The 5000RH panel is still available and results can be mapped automatically via web site supported by Womack lab. Web site is being updated to the 3rd generation IL/TX RH map, skipping the 2nd generation map.

Water buffalo RH panel made in collaboration with Brazilian investigator.

iii. Colin Kaltenbach, Administrative Advisor

Very positive comments about progress in the Bovine Genome Sequencing Project. NRSP8 was praised for its role.

iv. No Industry Representative comments.

v. No discussion.

b. Equine
i. Ernest Bailey, Equine Genome Coordinator: not present

ii. William Trumble, Administrative Advisor

Administrative Advisor (William Trumble) spoke in lieu of Ernie Bailey. Next year Jamie MacLeod will be the equine chair, Terje Raudsepp secretary. He praised the equine research community within NRSP8.

iii. Industry Representatives not present.

iv. No discussion.

c. Poultry
i. Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators

Jerry Dodgson: A draft genome sequence is out, described in a Nature paper. Many investigators are now finding the sequence very useful. To rectify some flaws in the sequence, NHGRI has approved funds to finish the chicken genome to the quality of the mouse genome. The second build is due out imminently.

Efforts are expanding to improve the linkage map and enhance the physical map between turkey and chicken.

Biggest event: a huge expansion in SNP mapping with tremendous engagement of the poultry industry. Coordinator funds were used to add birds to the group for SNP typing. This is a work in progress which will provide insights into evolution. Animals used represent birds from 75% of commercial populations world wide (Hans Cheng).

ii. Administrative Advisor not present.

iii. Industry Representatives not present.

iv. No discussion.

d. Swine
i. Max Rothschild, Swine Genome Coordinator

$10M (USDA) granted over the next two years for sequencing the pig genome. Industry money has gone to Sanger with sequencing under way. Larry Schook was thanked for efforts.

Affymetrix chips have been made available to investigators, still have some to distribute.

Oligonucleotide microarray efforts continue. Final clustering work is to be done by Christine Elsik, array to be ready for printing/distribution perhaps in May.

ii. Administrative Advisor Bert Stromberg

Positive endorsements of sequencing efforts.

iii. Industry Representatives not present.

iv. No discussion.

e. Aquaculture
i. Caird Rexroad (organizer) and John Liu (interim coordinator)

Caird Rexroad: Reported on aquaculture workshop. This year the workshop broke into finfish and shell fish groups in the afternoon. Named next years chair (Dennis Hedgecock) and chair elect (Geoff Waldbieser).

John Liu: Aquaculture is not a species, covers ~20 species of 200 cultured world wide, ~60 species in USA. Current report lacks shrimp and striped bass, which will be added later.

Joint Genome Institute sequencing support:
1) Catfish - 300,000 bidirectional ESTs.
2) Tilapia - 0.1x coverage of 5 species of cichlid fishes.
3) Oysters - 300,000 ESTs and 50 BACs

Tilapia, salmonids and catfish are making good progress, shell fish are lagging behind a bit most likely due to a late start. The Tilapia map has been increased by new markers and a BAC physical map. QTLs for color and sex determination are being mapped and investigators are close to identifying genes responsible. Catfish physical mapping has 6x coverage using BAC fingerprinting. An additional 57,000 BAC end sequences have been done and a microarray is now available.

ii. No comments from advisor.

iii. No discussion.

f. Database
i. James Reecy, Database Lead Coordinator

Significant progress this year. Pig QTL db to be moved into other species. Support of EST clustering in various species to support microarray efforts. NRI now has RFA targeting bioinformatics. This is welcomed.

Database use logged 2.5 million hits last year. Efforts continue to improve resources from a QTL centric view.

Next year focus on supporting and facilitating dialog between investigators to develop and use bioinformatics tools.

2. Administrators Reports
a. Colin Kaltenbach, Lead Administrative Advisor

Flat funding at 99% expected this year. Stressed the importance of getting final report in on time, 60 days from PAG. There is more and more demand for impact statements; these should be included in reports submitted to coordinators/chairs. NRSP8 is held up as the model for such multi-state projects.

b. Muquarrab Qureshi, Program Leader
Very positive about animal genome research and the contribution of NRSP8, in particular for feedback at the federal level. Joe Jens leadership is acknowledged by and appreciated for bringing NRSP8 and CSREES to this point in terms of funding and genome sequencing in chicken, cow and pig.

Thanks to Ronnie Green for his sterling efforts with the interagency working group.

To NRSP8, keep up the good work and send in those impact statements.

c. Peter Burfening, NRI Animal Genomics

Update for NRI efforts and team. Last year Peter Burfening took over Animal Genome in CSREES. The PART program (program assessment and rating tool) was used to evaluate NRI. Review of the program has stressed accountability as the key. The logic model was used to evaluate and provide new (current) priorities and goals for the program.

Funding is flat, making it difficult to fund at high levels. ~22% of proposals get funded. A recommendation from National Academy of Sciences to increase award sizes has led to a decrease in funding success rates for investigators. Now awards (when made) are not significantly cut, but fewer awards are made. Over the last 6 years 139 awards were made for $53M. This is more per project than for NRI as a whole. Peter Burfening discussed the breakdown of success rate in funding by species/group as delineated in the report.

Peter Burfening is very concerned about the low success rate.

Comments about panel composition: it is very difficult to find ~15 individuals that meet all the diversity requirements for panel composition.

Peter Burfening discussed the process and mechanics of proposal ranking. 8% ranked outstanding in the last few years. Only 95% of these outstanding proposals were funded indicating how tight the funding situation is. To fund all outstanding and high priority proposals an additional $6.6M would be needed. To fund at a 40% level would entail a doubling of the budget (additional ~$12.6M).

Taking input from NRSP8 to help prioritize funding, one example is the tools and reagents program which is now split to separate out bioinformatics. As a result of internal deliberations and not in response to species lobbying, this year only proposals from species with 5x genome sequence coverage or better will be considered. This is done to focus the program and narrow down the number of proposals. The due date is June 15; the panel manager has not yet been officially named.

d. Discussion followed.
Question from Noelle Cockett who questioned the effective limitation of species that can apply for funding by using sequencing data as the metric for funding. NC urged a re-visitation of the effective moratorium this imposes. Members of the audience endorsed this.

Peter Burfening replied to reaffirm that the door is not shut to other species, but that the significant expense on genome sequences is a priority maker.

Dissent for this view from the audience who questioned the wisdom of this approach.

Peter Burfening acknowledged this objection and said that one item that is being considered is prioritizing high risk research.

Max Rothschild commented that the current rule to consider applications only from 5x genome sequence organisms makes haves and have nots. He said that this is a very dangerous road that marginalizes other species.

Anna Palmisano commented on success rates. She is concerned that many young scientists are not submitting to NRI. But the flat budget is a limiting factor that leads to hard choices. She solicited advice and guidance from the community.

Jerry Dodgson commented that while disappointing, this (22%) funding is not worse than NIH RO1 success rate. He also endorsed the view that there should not in the future be a restriction on species restrictions as imposed by 5x rule.

Anna Palmisano said that current success rate this last year is 14% compared to NSF and NIH at ~30%.

James Reecy commented that the problem is not the success rate but rather the lack of sufficient funding. There were suggestions to lobby congress to change the situation.

John Liu commented about the ethics of urging students and young researchers to enter a field that has no funding. He thanked CSREES for their responsiveness to the community in the past and endorsed that restrictions for grant applications based on species of >5x genome coverage should not be continued.

Colin Kaltenbach suggested writing to ones congress person.

3. Suggestions for future plenary speakers for PAG

Max Rothschild asked for suggested speakers. Discussion by audience about how speakers are selected and the timing for this activity.

Frustration was expressed over crowding in the cattle session. Chairs need to make sure that expected attendance is relayed to organizers to make sure adequate sized rooms are provided.

Scheduling issue: Species groups overlap, making it difficult to cross the species barrier.

III. New Business
1. Election of Officers for 2006

Clare Gill to serve as chair next year (Dave Adelson filled in as secretary for meeting due to bereavement in Clare Gills family).

Nomination for Mary Delany as secretary seconded and approved by acclamation.

2. Selection of next meeting location and date to be discussed with Mary Delany.

IV. Adjournment. 5:45 pm

Accomplishments

Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. Aquaculture Catfish: Progress in mapping the catfish genome has focused on the addition of Type I loci to genetic maps and BAC fingerprinting and end sequencing. A total of 54 genes and 26 BACs have been added to the channel catfish intraspecific genetic map at the USDA/ARS Catfish Genetics Research Unit and 350 Type I loci to the channel catfish x blue catfish interspecific map at Auburn University. An NRI Genome Tools and Resource Program was awarded to Auburn University which has resulted in 20,366 BAC end sequences (BES). BLAST analyses has identified homology to 1130 genes revealing 23 regions of conserved synteny among the catfish, zebrafish, and tetraodon genomes. Microsatellites were identified in 17% of these sequences, which will facilitate the integration of the BAC physical map with the genetic maps. At the USDA/ARS Catfish Genetics Research Unit 6X genome coverage of the CCBL1 BAC library constructed from a gynogenetic female has been fingerprinted resulting in a preliminary assembly generating 2000 contigs. Progress has also been made in the sequencing of BAC ends with 3X coverage completed to date. Oysters: Researchers at the University of Delaware and the University of Southern California are cooperating on the development of a linkage-mapping family for the Pacific oyster (Crassostrea gigas), which will be made available to the oyster community as a resource. The current focus is on mapping Type I loci using SNPs. More than 90% of the primer sets developed for C. gigas amplify in the related oyster species C. ariakensis which is an important cultured species in Asia and is currently being considered for introduction into U.S. waters owing to its resistance to the two major diseases affecting the native eastern oyster. Researchers at Rutgers University have developed 16 SNP and 53 microsatellite markers from eastern oyster (C. virginica) ESTs for use in genetic mapping. They have also constructed a preliminary genetic map for the bay scallop (Argopecten irradians) using primarily AFLP markers. Salmonids: This year a collaboration led by Washington State University at Vancouver has integrated the cytogenetic with the Nichols et. al 2003 genetic maps. The USDA/ARS National Center for Cool and Cold Water Aquaculture and the University of Guelph have developed microsatellite markers for ESTs. A BAC physical mapping project was initiated by NCCCWA, West Virgniai University, and UC Davis. Members of NRSP8 participated in two workshops discussing sequencing a salmonid genome. The first Workshop was held in Oslo, Norway during October 24-26, 2005 to discuss sequencing the Atlantic salmon genome, while the second Workshop, a Tri-lateral Workshop (US/Canada/Norway) hosted by the Royal Norwegian Embassy in Washington DC November 2 - 3, 2006 was entitled "Marine Fish Aquaculture: Genomics. Striped Bass: Collaboration between researchers at North Carolina State University, Kent SeaTech Corporation, and the USDA National Center for Cool and Coldwater Aquaculture in Kearneysville, WV has resulted in the development of 498 microsatellites markers for use in genome mapping and selective breeding of striped bass (Morone saxatilis). The majority (90%) of these markers were successfully t amplified in the white bass (Morone chrysops), which is important to the industry in the production of the hybrid. Tilapia: A second generation genetic linkage map was produced in at University of New Hampshire containing 550 markers (Lee et al., 2005). A physical map has been constructed by BAC fingerprinting resulting in a tilapia physical map with 3,000 contigs (Katagiri et al., 2005). Cattle Texas A&M University continues to lead an international effort to build bovine radiation hybrid maps. RH panels are freely distributed to investigators world wide, data can be analyzed with the first generation RH map of the cattle genome (Band et al. 2000) at <http://bovid.cvm.tamu.edu/cgi-bin/rhmapper.cgi>. A third generation comparative map 3000 containing BAC end sequences has been published (Everts-van der Wind et al, PNAS 102:18526-18531, 2005). The BESs selected for mapping are ~1 Mbp apart on the human chromosomes as determined by BLASTn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are newly discovered, 79 are extended in length, 26 were formed by newly found breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is ~91 percent, or 97 percent of the theoretical maximum. Efforts at TAMU have been directed towards identification, validation and analysis of variation in the 3 Mb of genomic sequence that constitutes the bovine major histocompatibility complex (BoLA). The primary goal of this research was to determine the haplotype structure of BoLA to provide a more efficient platform for analysis of inherent disease resistance in cattle. More than 400 simple sequence repeats in BoLA have been identified from the genomic sequence, 22 of which useful variation in the BoLA IIb region (~400kb). An area of high recombination in the region near the proteosome locus, PSMB9 has been identified. Equine During 2005 significant numbers of new markers were added to the half sibling linkage map (766 markers spanning 3740 cM, Penedo et al, 2005), the full sibling linkage map (742 markers spanning 2772 cM, Swinburne et al., 2006, Genomics 87: 1-29) and the RH map for the horse. In addition, significant efforts were made to integrate the existing horse genome maps. Those efforts are summarized in the Horse Map Viewer (http://www.vgl.ucdavis.edu/equine/caballus/). Poultry The University of Michigan has been generating avian BAC contig maps and integrating them with the respective linkage maps. Efforts have also recently begun to develop a BAC contig map for the turkey, along with a comparative turkey-chicken map. The University of Minnesota has continued to expand turkey genetic mapping by expanding the genetic map to include 438 linked markers representing a 39% increase in marker number and increases marker density to an estimated at 5 cM. The USDA-ARS Avian Disease and Oncology Laboratory coordinated the screening of 3072 SNPs on 2580 experimental and commercial birds resulting in new genetic markers and providing a high confirmation rate of the ~3 million in silico chicken SNPs. This generated a much higher density genetic map that has enhanced the second genome sequence assembly, and demonstrated that a high density SNP map can identify tightly linked markers for simple and complex traits. North Carolina State University further characterized the MHC B locus at the sequence level in numerous layer lines to provide a reproducible means to determine B haplotypes. The microsatellite marker LEI0258 known to be physically located within the MHC, was sequenced resulting in the identification of 28 distinct haplotypes. This information will be a useful tool to identify new MHC haplotypes in outbred populations of chickens. Sheep A joint collaboration has been established between Utah State University, The Institute for Genomic Research (TIGR), Australian Wool Innovation, Meat and Livestock Australia, AgResearch (New Zealand), and Genesis-Faraday (UK), with support of the Alliance for Animal Genome Research, to obtain and characterize end-sequences from the CHORI-243 BAC library. In addition, these sequences will be ordered against the soon-to-be-completed bovine genomic sequence, providing a whole genome physical map for sheep. The sequences will also be incorporated into the emerging ovine RH map. The sequencing portion of the project is complete, with 376,493 BAC-end sequences (BES) from 193,073 BAC clones hazving average insert size of 184 kb. A total of 258,650,691 bp sequence (approximately 6% of the genome) was produced from this project. A collaborative project between Utah State University and Texas A&M University has produced an ovine whole-genome radiation hybrid (RH) 5,000-rad panel consisting of 90 clones, with retention frequencies between 15-40%. To date, Utah State University has 257 markers selected from the autosomes have been screened against the panel; 131 (51%) of these markers produce resolvable patterns and will be typed in duplicate across the panel. Swine New gene markers continue to be identified and mapped; some integration of the maps continues as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 1,588 genes and 2,493 markers in the database. The physical map is also growing quickly and there are now nearly 6,000 genes and anonymous markers; thanks to a very useful somatic cell hybrid panel from INRA and two radiation hybrid panels (IMpRH7000 from INRA and the U. of Minnesota; IMNpRH12000 from INRA, U. Nevada-Reno and the U. of Minnesota). The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. Meetings have occurred at PAG and in the UK. The meetings included individuals from a number of countries including the US, France, Britain, Denmark, China, Korea, and Japan. Representatives from the USDA, the Alliance for Animal Genome Research and several of the authors of the Pig Genome Sequencing White paper participated. Funds have been committed by the National Pork Board, Iowa Pork producers Association, University of Illinois and Iowa State University, with other groups likely to follow. USDA committed a total of 10-12 million and the Sanger Institute has also participated and will commit considerable funding. Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. Aquaculture Catfish: Researchers at the University of Mississippi Medical Center have completed the sequencing of 6 BACs covering part of the catfish immunoglobulin heavy chain locus. This group has continued characterization and functional studies of catfish immune molecules, such as, T Cell Receptors and their accessory molecules CD4 and CD8, Novel Immune Type Receptors, Leukocyte Immune Type Receptors (LITR), Immunoglobulin D, FcRs and the B cell accessory molecules CD79a and 79b. Monoclonal and polyclonal antibodies specific for various LITRs, IgD, CD79b and IpFcR have been produced and are being characterized. At Auburn University much effort was made to characterize innate immune genes and analyze their expression in the resistant blue catfish as compared to the susceptible channel catfish after infection with the bacterial pathogen causing enteric septicemia of catfish (ESC). A total of 26 CC chemokine genes, 6 CXC genes, 4 antimicrobial peptide genes, interleukin-1 beta gene, 23 selenoprotein genes, 6 toll-like receptors, and a few dozens of other genes were completely sequenced, mapped to BACs, and expression analyzed. Work at the USDA/ARS Catfish Genetics Research Unit was focused on the development of a 19,000 gene (oligonucleotide) microarray developed (via Nimblegen). The microarray was tested on Lipopolysaccharide-exposed fish and initial results demonstrated good correlation between levels of hybridization to the microarray and real-time PCR expression levels for several candidate genes. Currently tests are being conducted to observe differential expression of these potentially important immune receptors in various catfish families and strains after exposure to pathogens. Also, work characterizing catfish growth hormone and the various steroidogenic factors involved in catfish growth and reproduction continues. A patent was awarded for a real-time PCR assay detecting Edwardsiella ictaluri in channel catfish. Oysters: Researchers at the University of Southern California have mapped candidate genes for growth heterosis; more samples for expression profiling and QTL-mapping from F2 populations were obtained in summer 2005. Researchers at Rutgers University have mapped twelve disease/mortality-resistance QTL in two families of the eastern oyster; at least seven of the twelve QTL are independent of each other. These results indicate that resistance to Dermo-infection or summer mortality is affected by at least seven quantitative trait loci. Salmonids: The number of ESTs for rainbow trout and Atlantic salmon increased to 239,512 and 186,364, respectively. These sequences represent transcripts from tissues and lifecycle time points not previously included in the database. Microarrays are increasingly being used to study responses to stress and chemical contaminants as well as basic biological processes. Shrimp: As a part of the USDA funded project "Shrimp gene discovery: Enlarging the EST collection for the Pacific white shrimp, Litopenaeus vannamei" (NRI Grant #2005-35205-15459), six high quality tissue specific cDNA libraries have been constructed and analyzed for depth and redundancy, with 1000 EST being collected from each library to date. Redundancy depletion and full sequencing of a minimum of 120,000 ESTs (20,000 from each library) is expected to be complete in the coming year. A first generation microarray containing in excess of 3000 unigenes has been printed and initial validation has been completed. These microarrays and are currently in use in the first round of experimental research. It has been discovered that long dsRNA of virus-specific sequence evokes a potent and specific anti-viral immune response. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets. Striped Bass: Several collaborations were established with industry members Keo Fish Farms and Kent SeaTech Corporation to extend ongoing selective breeding efforts conducted at the North Carolina State University Pamlico Aquaculture Field Laboratory. These selective breeding studies have led to the identification of broodstock showing superior growth characteristics in both extensive pond-based and intensive production systems. Tilapia: Researchers at the University of New Hampshire have mapped the tilapia gene for red skin color leading to positional cloning of tilapia mutation to a single BAC containing 2 genes. Great progress was also made in mapping and characterization of the sex determining mechanism in several species of tilapia. Cattle Dwarfism has been a problem with American Angus cattle for decades. Dwarves are inefficient in beef production systems and are undesirable for Angus breeders. Researchers at Iowa State university have fine mapped the dwarfism locus to bovine chromosome 6 (BTA 6). On further analysis of candidate genes in the region, they have discovered a mutation in bovine PRKG2 gene that introduces a premature stop codon to the open reading frame. The mutation is in 100% concordance with dwarf, carrier and wild-type status. The detection of causal mutation or closely linked markers for dwarfism is of great use to Angus producers as this gives them the ability to detect carriers in breeding populations and the potential to eliminate dwarfism from their herds. Researchers at New Mexico State University have identified polymorphisms within the growth hormone gene that seem to be a significant source of variation in average daily gain and carcass traits in Bos Taurus or Bos TaurusX Bos indicus composit cattle. They have identified that polymorphisms in the genes of the GH axis or its transcriptional regulators differ among Angus, Brangus or Brahman cattle. A QTL on chromosome 6 affecting milk fat and protein concentration was previously localized to a 4-cM confidence interval, centered on the microsatellite BM143. In collaboration with ARO, the University of Illinois has characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL (Cohen-Zinder et al., 2005). Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. Equine ESTs were identified by laboratories at Cornell University, University of Kentucky and Texas A&M University and the data pooled with the objective of creating a microarray tools for investigating gene expression in horse tissues. Over 45,000 ESTs were evaluated and approximately 10,000 unique genes were identified for incorporation into a microarray chip. Poultry The USDA-ARS Avian Disease and Oncology Laboratory continues to work on genetic resistance to Mareks disease (MD). Reassessment of the ADOL 6 x 7 F2 MD resource population confirmed at least 5 of the 15 previously identified QTL, has revealed 2 new QTL, and identified 2-way epistatic interactions that shared a QTL on chr1. Efforts are underway to identify optimal MD virus challenge conditions to characterize the lines. Polymorphisms in avian leucosis virus (ALV) receptor genes tva and tvb that confer genetic resistance were confirmed, and Pyrosequencing assays developed. Iowa State University and Hy-Line International have cooperated to conduct candidate gene and genome scan analyses in an advanced (F6) intercross between two partially inbred commercial Leghorn lines that differed in resistance to Marek's disease to detect QTL for survival following challenge with highly virulent Marek's disease virus. A total of 11 putative QTL were identified including a polymorphism in the Rh-associated glycoprotein gene which was found to be associated with survival. The University of Delaware has further mapped the chromosome 1 QTL that affected oocyst shedding during coccidiosis infection of broiler chickens. An interesting candidate gene is lymphocyte activation gene 3 (LAG-3; CD223) which was simultaneously identified in DNA microarray studies to be reduced in expression after Eimeria infection of chickens. The lympocyte-specific expression of LAG-3 has been confirmed by RT-PCR and demonstrated a rapid down-regulation of LAG-3 with coccidial infection. The University of Arkansas has characterized the vasotocin II receptor (VT2R) that was recently cloned and sequenced in the chicken using immunocytochemistry (ICC) and was found predominantly in the cephalic region of the anterior pituitary, associated with cell membranes of specific pituitary cells. Research at the University of Arkansas has also been aimed at identifying the underlying genetic and physiological causes of sperm degeneration to better understand the origins of the defect and develop genetic tests that can be used to increase male fertility. Work to define the identity and function of genes within the major histocompatibility complex (MHC) in the chicken continues at the City of Hope Medical Center with progress made on three fronts. First, CD1 genes (one active and one likely a pseudogene), encoding MHCI molecules that present lipid-type antigens to T cells, were mapped to the MHC region. Second, Y MHCI molecules were shown to be alloimmunogenic and well-expressed on blood cells providing data supporting the likelihood for a role of Y MHCI in immunity. Lastly, BG1 has been identified as a candidate gene influencing the incidence of Mareks disease in chickens. In mammals, natural killer (NK) cell C-type lectin receptors are encoded in a gene cluster called nature killer receptor gene complex (NKC). At Texas A & M University two chicken C-type lectin-like receptors were identified in a region on Chromosome 1 that is syntenic to the mammalian NKC region. The region containing NK C-type lectin like receptors in GGA 1 has been previously identified to be associated with disease resistance in chickens. The University of Maryland has performed transcriptional profiling screens using their cDNA microarrays to identify genes that respond directly to glucocorticoids in cultures of anterior pituitary cells. Six candidate genes for mediating the effects of glucocorticoids on expression in the anterior pituitary were identified. Gene expression profiles in the anterior pituitary and hypothalamus were also compared between lines of chickens genetically selected to have high or low abdominal fat identifying the same six candidate genes. The 5'-flanking region of these candidate genes are currently being sequenced in a Fat X Lean reference population in an attempt to identify genetic markers associated with differences in body fat. Virginia Tech has been studying the transport of nutrients (amino acids, peptides and sugars) across the intestinal epithelia, which is mediated by membrane bound transporter proteins. The abundance of mRNA for these transporters was determined by real time PCR and was found to vary depending upon the intestinal segment and the time of development (embryonic day 20 to 7 days post hatch). This work has shown that nutrient transporters are differentially expressed in a temporal and spatial manner. The efficient production of germ line chimeras using PGC transfer into early embryos has been hampered by the limited availability of PGCs obtained from blood and the early germinal ridge. North Carolina State University has produced germ line chimeras by using sorted gonadal germ cells when injected into stage X, germinal crescent and stage 17. This observation taken together with the scientific literature indicates that germline chimeras can be made using any source of PGCs up to stage 27-28 as the donor cells and any stage of embryo development up to stage 17 can be used as a recipient. Iowa State University maintains many unique chicken lines (highly inbred; MHC- congenic; closed populations; advanced intercross lines) for research. These lines serve as valuable resources for identifying genes of economic importance. Semen from all of the highly inbred and partially inbred lines was collected at ISU, and the staff of the National Animal Germplasm program cryopreserved the samples on site and then transported them to Ft. Collins for long-term storage. The feasibility of detection and mapping QTL in breeding populations with a high-density marker map using population-wide linkage disequilibrium was investigated by simulation at Iowa State University. Designs that allow adequate power and mapping precision were developed. Designs and statistical models for global gene expression analysis using micro-arrays based on pools of mRNA samples from multiple individuals were also investigated. For a given total number of individuals and arrays, simulated pooling resulted in loss of power compared to arraying all samples individually but under some conditions, loss of power was small and it was possible to find a low-cost pooling design with power close to that of an individual design. North Carolina State University has continued to develop new microsatellite markers mining the genome sequence data for use in fine-mapping QTL regions. This data indicates that there is at least one usable microsatellite marker every 40,000 bp and at least one polymorphic microsatellite marker every 115,000 bp in commercial chicken populations. Sheep A collaboration including Utah State University, Purdue University, USDA/ARS, and the University of Liége has identified a core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18. Using quantitative PCR, they have shown that the inheritance of the callipyge (CLPG) SNP in cis alters the expression of genes with a paternal allele-specific expression (DLK1 and PEG11) and maternal allele-specific expression (GTL2 and MEG8) in muscles that undergo hypertrophy in a genotype and age specific manner. Also, the effects of age and genotype are also significant for expression of the CLPG1 RNA that is transcribed from the intergenic region between DLK1 and GTL2 and spans the CLPG SNP. Gastrointestinal parasites have a profound effect on sheep production. In a collaborative study between Utah State University and Louisiana State University, a genome-wide QTL scan was implemented to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites. Suggestive QTLs have been identified on ovine chromosomes 1, 6, 9 and 19. A large-scale EST sequencing project for goats has been implemented at Virginia State University. To date, sequences have been obtained from about 10,000 clones from a cDNA library constructed from goat uterine/embryonic tissues collected between days 5 and 8 pregnancy. Swine QTL have continued to be reported on all chromosomes for many traits, often identifying imprinted QTL. Candidate gene analyses have proved successful with several gene tests being used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color. Progress towards Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. Researchers at universities and other research institutions are conducting multifaceted research to develop bioinformatics programs and database resources for livestock species and this research is supported in part by the NAGRP. Continued efforts to inform scientists and lay persons about genome databases have been made and many new entries are now available at www.animalgenome.org. The NAGRP genome databases were accessed over 2.2 million times by over 140,000 users world-wide. A bioinformatics program (Expeditor) was developed to design primers for livestock species. This program takes advantage of the information from the human genome and applies it to livestock cDNA. This program can be used at http://www.animalgenome.org/~hu/expeditor. With the rapid progress in genetics and genomes, there are an increasing number of genetic analysis software programs. Each program has its own pre-defined scope, assumptions, and applicability. With the large number of available programs, it can be a challenge to identify suitable options. Thus, we have created a database and related tools to effectively archive, annotate, and manage the wealth of the software information so that researchers can easily identify, locate, and retrieve appropriate software. We have also introduced ontology concepts and tools to manage the proper classification and feature annotation of this resource. To date, there are 331 software programs listed in the category of genetic analysis. We plan to add other genomics and computational biology software in the near future. As in past years the Pig Genome Database has received considerable updating. There are over 1,254 citations in the database describing 4081 loci, over 602 clone entries and 96 library entries. This last year the US Pig Genome database had over 149,600 users making more than 3 million hits. New QTL continue to be curated into the Pig QTL Database. Up to date there are 1,263 QTLs in the database representing 236 pig traits. In addition, new functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, and pig BAC physical maps, against pig QTL. It can be seen at http://www.animalgenome.org/QTLdb/. Database activities were transferred to the Bioinformatics Coordinator. The NAGRP database has a newly developed Porcine QTL database that graphically displays QTL from over 70 experiments and can be used at http://www.animalgenome.org/QTLdb/. All information has been cross-listed at NCBI and can be viewed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&term=pig+QTL. Over the past year, links have been added to the viewer allowing researchers to visualize QTL on the human genome. Texas A&M has worked to cluster and annotate porcine and bovine EST clusters. This work supports the development of a new long-oligo arrays in collaboration with the Swine Genome Coordinator and the Bovine Oligo Microarray Consortium. The marine genomics group at the Holling Marine Laboratory and MUSC maintains www.marinegenomics.org for the archiving of shrimp EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data, which are being used to archive and analyze shrimp metagenomic and microarray data. In addition, in collaboration with IFREMER at the Universite de Montpellier, a standardized nomenclature database for Penaeidin anitmicrobial peptide has been developed. Tools for comparative mapping are available from the University of New Hampshire (www.hcgs.unh.edu/comp). They include - comparative maps among cichlids, comparative maps among fishes, mapping of cichlid ESTs onto genome sequences of Tetraodon and Fugu. Personnel at the University of California-Davis are developing a cattle genome database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery. Currently the database contains 580 QTL entries from 109 traits and 295 molecular markers (69% mapped to human. The database is in MySQL with a Common Gateway Interfaces (CGI) front end. Sequences from the ovine BAC end sequencing project are now publicly available at http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html. Matches of the ovine BAC-end sequences to the bovine and human sequences and identity of clones can be obtained through a database established by CSIRO (Australia) at http://www.livestockgenomics.csiro.au/SheepGenomics/. The Bovine QTL viewer (http://bovineqtl.tamu.edu/) developed by researchers at Texas A&M University has been updated and linked to the 6.2x build of the bovine genome to show existing SNPs and gene models.

Publications

Aquaculture Catfish Bao B, Peatman E, Li P, He C, and Liu Z.J. 2005. Catfish hepcidin gene is expressed in a wide range of tissues and exhibits tissue-specific upregulation after bacterial infection. Developmental and Comparative Immunology 29:939-950. Bao B., Yang G, Liu ZJ, Li s, Wang Z, Ren D. 2005. Isolation of Sfrs3 gene and its differential expression during metamorphosis involving eye migration of Japanese flounder Paralichthys olivaceus. Biochimica et Biophysica Acta 1725: 64-70. Baoprasertkul P., He C., Peatman E., Zhang S., Li P., Liu Z.J. 2005. Constitutive expression of three novel catfish CXC chemokines: homeostatic chemokines in teleost fish. Molecular Immunology 42:1355-1366. Chen, L., He, C., Baoprasertkul, P., Xu, P., Li, P., Serapion, J., Waldbieser G., Wolters, W., Liu, Z.J. 2005. Analysis of a catfish gene resembling interleukin-8: cDNA cloning, gene structure, and expression after infection with Edwardsiella ictaluri. Developmental and Comparative Immunology 29, 135-142. Clay LA, Wang SY, Wolters WR, Peterson BC GC Waldbieser. 2005. Molecular characterization of the insulin-like growth factor-I (IGF-I) gene in channel catfish (Ictalurus punctatus). Biochim Biophys Acta 1731(3):139-148. Hikima, J., D.L. Middleton, M.R. Wilson, N.W. Miller, L.W. Clem and G.W. Warr. 2005. Regulation of immunoglobulin gene transcription in a teleost fish: identification, expression and functional properties of E2A in the channel catfish. Immunogenetics 57: 273-282. Hikima, J., M.L. Lennard, M.R. Wilson, N.W. Miller, L.W. Clem and G.W. Warr. 2005. Evolution of vertebrate E-protein transcription factors: comparative analysis of the E-protein gene family in Fugu rubripes and humans. Physiological Genomics 21: 144-151. Karsi A and GC Waldbieser. 2005. Linkage mapping of the channel catfish proopiomelanocortin (POMC ) gene. Anim Genet.36(2):171-173. Karsi A, Waldbieser GC, Small BC and WR Wolters. 2005. Genomic structure of the proopiomelanocortin gene and expression during acute low-water stress in channel catfish. Gen Comp Endocrinol.143(2):104-112. Karsi A, Wolters WR, and GC Waldbieser. 2005. Assignment of immune-related genes to the channel catfish, Ictalurus punctatus, genetic map. Anim Genet. 36(6):502-506. Kountikov, E., M. Wilson, S. Quiniou, N.W. Miller, L.W. Clem and E. Bengtén. 2005. Genomic organization of the channel catfish CD45 functional gene and CD45 pseudogenes. Immunogenetics 57: 364-383. Li RW, Silverstein PS and GC Waldbieser. 2005 Genomic characterization and expression analysis of the baculoviral IAP repeat-containing 2 (BIRC2) gene in channel catfish, Ictalurus punctatus. Anim Genet. 36(6):537-539. Liu, Y.G., Chen, S.L., Li, B.F., Wang, Z.J., Liu Z.J. 2005. Analysis of genetic variation in selected stocks of hatchery flounder, Paralichthys olivaceus, using AFLP markers. Biochemical Systematics and Ecology 33, 993-1005. Liu, Z.J., Peatman, E. 2006. Chemokines in fish: a rapidly expanding repertoire. In Immunology Research, (Editor, Frank Columbus), Nova Science Publishers, Inc., New York, in press. Nonneman D. and G.C. Waldbieser. 2005. Isolation and enrichment of abundant microsatelites from a channel catfish (Ictalurus punctatus) brain cDNA library. Anim. Biotechnol. 16(2): 103-116. Peatman, E., Bao, B., Baoprasertkul, P., and Liu, Z.J. 2005. In silico identification and expression analysis of 12 novel CC chemokines in catfish. Immunogenetics 57:409-419. Peterson BC, Waldbieser GC and L. Bilodeau. 2005. Effects of recombinant bovine somatotropin on growth and abundance of mRNA for IGF-I and IGF-II in channel catfish (Ictalurus punctatus). J Anim Sci. 83(4):816-824. Quiniou SM, Wolters WR and GC Waldbieser 2005. Localization of Xba repetitive elements to channel catfish (Ictalurus punctatus) centromeres via fluorescence in situ hybridization. Anim Genet. 36(4):353-354. Xu P, Bao B, He Q, Peatman E, He C, Liu Z.J. 2005. Characterization and expression analysis of bactericidal permeability-increasing protein (BPI) antimicrobial peptide gene from channel catfish Ictalurus punctatus. Developmental and Comparative Immunology 29:865-878. Oysters Curole, J. P., and D. Hedgecock. 2005. Estimation of preferential pairing rates in second-generation autotetraploid Pacific oysters (Crassostrea gigas). Genetics 171:855-859. Elfstrom, C. M., Gaffney, P. M., Smith, C. T. & Seeb, J. E. (2005). Characterization of 12 single nucleotide polymorphisms in weathervane scallop. Molecular Ecology Notes 5, 406-409. Hedgecock, D., P. M. Gaffney, P. Goulletquer, X. Guo, K. Reece, and G. W. Warr. 2005. The case for sequencing the Pacific oyster genome. Journal of Shellfish Research 24:429-441. Hoover, C. A. & Gaffney, P. M. (2005). Geographic variation in nuclear genes of the eastern oyster, Crassostrea virginica Gmelin. Journal of Shellfish Research 24, 103-112. Milbury, C. A. & Gaffney, P. M. (2005). Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Marine Biotechnology 7, 697-712. Wang, L., L. Song, Y. Chang, W. Xu, D. Ni and X. Guo. 2005. A preliminary genetic map of zhikong scallop (Chlamys farreri, Jones et Preston 1904). Aquaculture Research, 36:643-653. Wang, Y., Z. Xu and X. Guo. 2005. Chromosomal mapping of 5S ribosomal RNA genes in the eastern oyster, Crassostrea virginica Gmelin by fluorescence in situ hybridization. J. Shellfish Res., 24(4):959-964. Wang, Y., Z. Xu. J.C. Pierce and X. Guo. 2005. Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones. Marine Biotechnology, 7:207-214. Yamtich, J., M.-L. Voigt, G. Li, and D. Hedgecock. 2005. Eight microsatellite loci for the Pacific oyster Crassostrea gigas. Animal Genetics 36:524-526. Yu, Z. and X. Guo. 2005. Genetic analysis of selected strains of the eastern oyster (Crassostrea virginica Gmelin) using AFLP and microsatellite markers. Marine Biotechnology, 6:575-586. Salmonids Coulibaly I, Gharbi K, Danzmann RG, Yao J, Rexroad CE, 3rd (2005) Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags. Anim Genet, 36, 309-315. Danzmann RG, Cairney M, Davidson WS, Ferguson MM, Gharbi K, Guyomard R, Holm LE, Leder E, Okamoto N, Ozaki A, Rexroad Iii CE, Sakamoto T, Taggart JB, Woram RA (2005) A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome, 48, 1037-1051. Gahr SA, Rodriguez MF, Rexroad CE, 3rd (2005) Identification and expression profile of the ID gene family in the rainbow trout (Oncorhynchus mykiss). Biochim Biophys Acta, 1729, 64-73. Hansen JD, Landis ED, Phillips RB (2005) Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish. Proc Natl Acad Sci U S A, 102, 6919-6924. Krasnov A, Koskinen H, Pehkonen P, Rexroad CE, 3rd, Afanasyev S, Molsa H (2005) Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics, 6, 3. Krasnov A, Koskinen H, Rexroad C, Afanasyev S, Molsa H, Oikari A (2005) Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss). Aquat Toxicol, 74, 70-81. Phillips RB, Morasch MR, Park LK, Naish KA, Devlin RH (2005) Identification of the sex chromosome pair in coho salmon (Oncorhynchus kisutch): lack of conservation of the sex linkage group with chinook salmon (Oncorhynchus tshawytscha). Cytogenet Genome Res, 111, 166-170. Rexroad CE, 3rd, Rodriguez MF, Coulibaly I, Gharbi K, Danzmann RG, Dekoning J, Phillips R, Palti Y (2005) Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics, 6, 54. Salem M, Yao J, Rexroad CE, Kenney PB, Semmens K, Killefer J, Nath J (2005) Characterization of calpastatin gene in fish: its potential role in muscle growth and fillet quality. Comp Biochem Physiol B Biochem Mol Biol, 141, 488-497. von Schalburg KR, Rise ML, Brown GD, Davidson WS, Koop BF (2005) A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biol Reprod, 72, 687-699. von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson CC, Davidson WS, Koop BF (2005) Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics, 6, 126. Shrimp Almeida, J.S., D.J. McKillen, Y.A. Chen, P.S. Gross, R.W. Chapman, & G. Warr (2005). Design and calibration of microarrays as universal transcriptomic environmental biosensors. Comp. Funct. Genomics 6(3):132-137. Cuthbertson, B.J., Y. Yang, E. Bachère, E.E. Büllesbach, P.S. Gross, & A. Aumelas (2005). Solution structure of synthetic penaeidin-4 with structural and functional comparisons to penaeidin-3. J. Biol. Chem. 280(16): 16009-16018. McKillen, D.J., Y.A. Chen, C. Chen, M.J. Jenny, H.F. Trent III, J. Robalino, D.C. McLean Jr., P.S. Gross, R.W. Chapman, G.W. Warr1 & J.S. Almeida (2005). Marine Genomics: a clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics 6(1):34-39. Striped Bass Bielmeyer G.K., Gatlin D., Isley J.J., Tomasso J., Klaine S.I. (2005). Responses of hybrid striped bass to waterborne and dietary copper in freshwater and saltwater. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 140: 131-137. Brown K.M., Baltazar G.A., Hamilton M.B. (2005). Reconciling nuclear microsatellite and mitochondrial marker estimates of population structure: population structure of Chesapeake Bay striped bass (Morone saxatilis). Heredity 94: 606-615. Jackson L.F., McCormick S.D., Madsen S.S., Swanson P., Sullivan C.V. (2005). Osmoregulatory effects of hypophysectomy and homologous prolactin replacement in hybrid striped bass. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 140: 211-218. Kaattari I.M., Rhodes M.W., Kator H., Kaattari S.L. (2005). Comparative analysis of mycobacterial infections in hybrid striped bass Morone saxatilis from Chesapeake Bay. Diseases of Aquatic Organisms. 67: 125-132. Lauth X., Babon J., Stannard J.A., Singh S., Nizet V., Carlberg J.M., Ostland V.E., Pennington M.W., Norton R.S., Westerman M.E. (2005). Bass hepcidin: synthesis, solution structure, antimicrobial activities and synergism, and in vivo hepatic response to bacterial infections. JBC 280: 9272-9282. Rhodes M.W., Kator H., McNabb A., Deshayes C., Reyrat J.M., Brown-Elliot B.A., Wallace, R. Jr., Trott K.A., Parker J.M., Lifland B., Osterhout, G., Kaattari I., Reece K., Vogelbein W., Ottinger C.A. (2005). Mycobacterium pseudoshottsi sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis). Int. J. Syst. Evol. Microbiol. 55: 1139-1147. Weber , Sullivan C.V. (2005). Insulin-like growth factor I induces oocyte maturational competence but not meiotic resumption in white bass (Morone chrysops) follicles in vitro: evidence for rapid evolution of insulin-like growth factor action. Biol. Reprod. 72: 1177-1186. Tilapia Katagiri T, Kidd C. Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD. 2005. A BAC-based physical map of the Nile tilapia genome. BMC Genomics 6:89. Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, Hulata G, Slettan A, Stern JE, Terai Y, Kocher TD. 2005. A second generation genetic linkage map of tilapia (Oreochromis spp.) Genetics 170: 237-244. Cattle Ashwell, M. S., D. W. Heyen, J. I. Weller, M. Ron, T. S. Sonstegard, C. P. Van Tassell and H. A. Lewin. 2005. Detection of quantitative trait loci influencing conformation traits and calving ease in Holstein-Friesian cattle. J. Dairy Sci. 88:4111-4119. Bae, K., Mallick, B.K. and Elsik, C.G.: Prediction of protein inter-domain linker regions by a hidden Markov model. Bioinformatics 21:2264-2270, 2005. Cobanoglu, O., P.J. Berger and B.W. Kirkpatrick. 2005. Genome screen for twinning rate QTL in four North American Holstein families. Animal Genetics 36:303-8. Cohen-Zinder, M., E. Seroussi, D. M. Larkin, J. J. Loor, A. Everts-van der Wind, J. H. Lee, J. K. Drackley, M. R. Band, M. Shani, H. A. Lewin, J. I. Weller and M. Ron. 2005. Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein Cattle. Genome Research 15:936-944. Dunlap, K.A., Palmarini, M., Adelson, D.L. and Spencer, T.E.: Sheep Endogenous Betaretroviruses (enJSRVs) and the Hyaluronidase 2 (Hyal2) Receptor in the Ovine Uterus and Conceptus During Pregnancy. Biol. Reprod. 73:271-279, 2005. Everts, R. E., M. R. Band, Z. L. Liu, C. G. Kumar, L. Liu, J. J. Loor, R. Oliveira and H. A. Lewin. 2005. A 7872 cDNA microarray and its use in bovine functional genomics. Vet. Immunol. Immunopathol. 105:235-245. Everts-van der Wind A, Larkin D.M., Green C.A., Elliott J.S., Olmstead C., Chiu R., Schein J.E., Marra M.A., Womack J.E., Lewin, H.A.: A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 102:18526-18531, 2005. Everts-van der Wind, A., D. M. Larkin, C. A. Green, J. S. Elliott, C. A. Olmstead, R. Chiu, J. E. Schein, M. A. Marra, J. E. Womack and H. A. Lewin. 2005. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc. Natl. Acad. Sci. (USA) 102:18526-31. Loor, J. J., H, M. Dann, R. E. Everts, R. Oliveira, C. A. Green, N. A. Janovick-Guretzky, S. L. Rodriguez-Zas, H. A. Lewin and J. K. Drackley. 2005. Temporal gene expression profiling of liver from periparturient dairy cows reveals complex adaptive mechanisms in hepatic function. Physiological Genomics 23:217-226. Murphy, W. J., D. M. Larkin, A. Everts-van der Wind, G. Bourque, G. Tesler, L. Auvil, J. E. Beever, B. P. Chowdhary, F. Galibert, L. Gatzke, C. Hitte, S. N. Meyers, E. A. Ostrander, G. Pape, H. G. Parker, T. Raudsepp, M. B. Rogatcheva, L. B. Schook, L. C. Skow, M. Welge, J. E. Womack, S. J. OBrien, P. A. Pevzner and H. A. Lewin. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617. Murphy, W.J., Larkin D.M., Everts-van der Wind A., Gurque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers S.N., Mlan D., Ostrander E.A., Pape G., Parker G.H., Raudseep T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., OBrien S.J., Pevzner P.A., and Lewin H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309, 613-617, 2005. Ross, J. W., Smith, T. K., Krehbiel, C. R., Malayer, J. R., DeSilva, U., Morgan, J. B., White, F. J., Hersom, M. J., Horn, G. W., and Geisert, R. D. (2005). Effects of grazing program and subsequent finishing on gene expression in different adipose tissue depots in beef steers. Journal of Animal Science 83, 1914-1923. Shirley,K.L., M.G. Thomas, D.H. Keisler, D.M. Hallford, D.M. Montrose, G.A. Silver, and M.D. Garcia. Case study: A Chihuahuan Desert Brangus breeding program: feed efficiency, metabolic hormones, and puberty in developing Brangus heifers sired by bulls with differing EPD for growth and scrotal circumference. In press: Prof. Anim. Sci. Feb; 2006. Smith, S. L., R. E. Everts, X. C. Tian, F. Du, L.-Y. Sung, S. L. Rodriguez-Zas, B.-S. Jeong, J.-P. Renard, H. A. Lewin and X. Yang. 2005. Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proc. Natl. Acad. Sci. (USA) 102:17582-17587. Wang, J., Adelson, D.L., Yilmaz, A., Sze, S.H., Jin, Y. and Zhu, J.J.: Genomic Organization, Annotation, and Ligand-Receptor Inferences of Chicken Chemokines and Chemokine Receptor Genes Based on Comparative Genomics. BMG Genomics 6,:45, 2005. White, S.N., Halbert, N.D., Taylor, K.H., Derr, J.N., and Womack, J.E.: TLR4 variation in Yellowstone bison. Animal Genetics 36:511-542, 2005. Wu, R., C. Ma, W. Hou, P. Corva and J.F. Medrano 2005. Functional Mapping of Quantitative Trait Loci That Interact With the hg Mutation to Regulate Growth Trajectories in Mice. Genetics 17:239-249. Yilmaz, A., Shen, S., Adelson, D.L., Xavier, S, and Zhu, J.J.: Annotation of chicken IL-10 gene cluster and effects of lipopolysaccharide stimulation on IL-10 gene expression. Animal Genetics 36:263-5, 2005. Yilmaz, A., Shen, S., Adelson, D.L., Xavier, S, and Zhu, J.J.: Identification and sequence analyses of chicken Toll-like receptors. Immunogenetics 56:743-753, 2005. Equine Beck, J., B. P. Chowdhary And B. Brenig, 2005 Assignment of the equine colony stimulating factor 1 receptor gene (CSF1R) to equine chromosome 14q15-->q16 (ECA14q15-->q16) by in situ hybridization and radiation hybrid panel mapping. Cytogenet Genome Res 109: 533. Boneker, C., D. Muller, H. Kuiper, C. Drogemuller, B. P. Chowdhary et al., 2005 Assignment of the COL8A2 gene to equine chromosome 2p15-p16 by FISH and confirmation by RH mapping. Anim Genet 36: 444-445. Boneker, C., H. Kuiper, A. Wohlke, C. Drogemuller, B. P. Chowdhary et al., 2005 Assignment of the COL16A1 gene to equine chromosome 2p15.1-p15.3 by FISH and confirmation by RH mapping. Anim Genet 36: 262-263. Bricker, S. J., L. S. Brault, A. Delvalle, L. V. Millon, J. D. Murray et al., 2005 Radiation hybrid and linkage mapping of six new type I markers in the horse. Anim Genet 36: 182-184. Brooks, S. A., And E. Bailey, 2005 Exon skipping in the KIT gene causes a Sabino spotting pattern in horses. Mamm Genome 16: 893-902. Gustafson-Seabury, A., T. Raudsepp, G. Goh, S. R. Kata, M. L. Wagner et al., 2005 High-resolution RH map of horse chromosome 22 reveals a putative ancestral vertebrate chromosome. Genomics 85: 188-200. Hillyer, L. L., L. A. Pettitt, S. L. Debenham, J. E. Swinburne, M. M. Binns et al., 2005 Equine microsatellites associated with the COMP, LRP5 and COL1A1 genes. Anim Genet 36: 261-262. Luis, C., E. G. Cothran, M. M. Oom And E. Bailey, 2005 Major histocompatibility complex locus DRA polymorphism in the endangered Sorraia horse and related breeds. J Anim Breed Genet 122: 69-72. Milenkovic, D., D. Mariat, J. Swinburne, S. Chadi-Taourit, M. Binns et al., 2005 Characterization and localization of 17 microsatellites derived from BACs in the horse. Anim Genet 36: 164-166. Penedo, M. C., L. V. Millon, D. Bernoco, E. Bailey, M. Binns et al., 2005 International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenet Genome Res 111: 5-15. Perelygin, A. A., T. L. Lear, A. A. Zharkikh And M. A. Brinton, 2005 Structure of equine 2'-5'oligoadenylate synthetase (OAS) gene family and FISH mapping of OAS genes to ECA8p15-->p14 and BTA17q24-->q25. Cytogenet Genome Res 111: 51-56. Pielberg, G., S. Mikko, K. Sandberg and L. ANDERSSON, 2005 Comparative linkage mapping of the Grey coat colour gene in horses. Anim Genet 36: 390-395. Swinburne, J. E., M. Boursnell, G. Hill, L. Pettitt, T. Allen et al., 2006 Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families. Genomics 87: 1-29. Tallmadge, R. L., T. L. Lear And D. F. Antczak, 2005 Genomic characterization of MHC class I genes of the horse. Immunogenetics 57: 763-774. Wittwer, C., B. P. Chowdhary And O. Distl, 2005 Radiation hybrid mapping of equine CDK2, DGKA, DNAJC14, MMP19, CTSL and GAS1. Anim Genet 36: 536-537. Poultry Alghamdi, A.S., D.N. Foster, C.S. Carlson, M.H.T. Troedsson. 2005. Nitric oxide levels and nitric oxide synthase expression in uterine samples from mares susceptible and resistant to persistent breeding induced endometritis. J. Reprod. Immunol. 53:230-237. Alghamdi, A.S., D.N. Foster. 2005 Seminal DNase frees spermatozoa entangled in neutrophil extracellular traps. Biol. Reprod. 73:1174-1181. Alghamdi, A.S., S, Madill, D.N. Foster. 2005. Seminal plasma improves fertility of frozen equine semen. Animal Reprod. Sci. 89:242-245. Bliss, T.W., J. E. Dohms, M.G. Emara, C.L. Keeler, Jr. 2005. Gene expression profiling f avian macrophage activation. Vet. Immunol. Immunopathol., 105:289-99. Borwornpinyo, S., J. Brake, P.E. Mozdziak, J.N. Petitte. 2005. Culture of chicken embryos in surrogate eggshells. Poultry Sci. 84:1477-1482. Chaves, L.D., J.A. Rowe, K.M Reed. 2005. Survey of a cDNA library from the turkey (Meleagris gallopavo). Genome, 48:12-17. Chen, H., Y.X. Pan, E.A. Wong, K.E. Webb, Jr. 2005. Dietary protein level and stage of development affect expression of an intestinal peptide transporter (cPepT1) in chickens. J. Nutr. 135:193-198. Cheng, H., W. M. Muir, 2005. The effects of genetic selection for survivability and productivity on chicken physiological homeostasis. Worlds Poultry Science Journal 61: 383-397. Christman, S.A., B.-W. Kong, M.M. Landry, D.N. Foster. 2005. Chicken Embryo Extract Mitigates Growth and Morphological Changes in a Spontaneously Immortalized Chicken Embryo Fibroblast Cell Line. Poultry Sci. 84:1423-1431. Christman, S.A., B.-W. Kong, M.M. Landry, H. Kim, D.N. Foster. 2005 Modulation of p53 expression and its role in the conversion to a fully immortalized chicken embryo fibroblast line. FEBS Letters. 579:6705-6715. Festucci-buselli, R. A., A. S. Carvalho-dias, M. De Oliveira-andrade, C. Caixeta-nunes, H. M. LI et al., 2005 Expression of Cyp6g1 and Cyp12d1 in DDT resistant and susceptible strains of Drosophila melanogaster. Insect Molecular Biology 14: 69-77. Forough, R. B., Weylie, C. Patel, S. Ambrus, U.S. Singh, J. Zhu. 2005. Role of AKT/PKB signaling in fibroblast growth factor-1 (FGF-1)-induced angiogenesis in the chicken chorioallantoic membrane (CAM). J Cell Biochem 94:109-116. Hansen, C., N. Yi, Y.M. Zhang, S. Xu, J. Gavora, H.H. Cheng. 2005. Identification of QTL for production traits in chickens. Animal Biotech. 16:67-79. Hartman, S., G. Touchton, J. Wynn, T. Geng, N. Chong, E. Smith. 2005. Characterization of expressed sequence tags from a Gallus gallus pineal gland cDNA library. Comparative and Functional Genomics 6:301-306. Heifetz, E. M., J.E. Fulton, N. O'Sullivan, H. Zhao, J.C.M. Dekkers, M. Soller. 2005. Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics 171: 1173-1181. Hostetler, H.A., P. Collodi, R.H. Devlin, W.M. Muir. 2005. Improved Phytate Phosphorus Utilization by Japanese Medaka Transgenic for the Aspergillus niger Phytase Gene. Zebrafish 2:19-31. Jurkevich, A., L.R. Berghman, L.E. Cornett and W.J. Kuenzel. 2005. Characterization and immunohistochemical visualization of the vasotocin VT2 receptor in the pituitary gland of the chicken, Gallus gallus. Gen. Comp. Endocrinol. 143:82-91. Kuenzel, W.J., R.F. Wideman, M. Chapman, C. Golden and D.M. Hooge. 2005. A Practical method for induced moulting of caged layers that combines full access to feed and water, dietary thyroactive protein, and short day length. Worlds Poultry Sci. J. 61:599-624. Li, H., N. Deeb, H. Zhou, C.M. Ashwell, S.J. Lamont. 2005. Chicken quantitative trait loci for growth and body composition associated with the very low density apolipoprotein-II gene. Poultry Sci. 84 (5):697-703. McElroy, J. P., J.C.M. Dekkers, J.E. Fulton, N.P. OSullivan, M. Soller, E. Lipkin, W. Zhang, K.J. Koehler, S.J. Lamont, H.H. Cheng. 2005. Microsatellite markers associated with resistance to Mareks disease in commercial layer chickens. Poultry Sci. 84:1678-1688. McElroy, J.P., J.C.M. Dekkers, J.E. Fulton, N.P. OSullivan, M. Soller, E. Lipkin, W. Zhang, K.J. Koehler, S.J. Lamont, Cheng, H.H. 2005. Microsatellite markers associated with resistance to Mareks disease in commercial layer chickens. Poultry Science 84:1678-1688. Miller, M.M., C. Wang, E. Parisini, R.D. Coletta, R.M. Goto, S.Y. 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Genome 16:801-814.

Impact Statements

The USDA-ARS Avian Disease and Oncology Laboratory coordinated the screening of 3072 SNPs on 2580 experimental and commercial birds resulting in new genetic markers. This generated a much higher density genetic map that has enhanced the second genome sequence assembly, and demonstrated that a high density SNP map can identify tightly linked markers for simple and complex traits.
It has been discovered that long dsRNA of virus-specific sequence evokes a potent and specific anti-viral immune response. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets.
Collaborations with industry members Keo Fish Farms and Kent SeaTech Corporation to extend ongoing selective breeding efforts conducted at the North Carolina State University Pamlico Aquaculture Field Laboratory have led to the identification of broodstock showing superior growth characteristics in both extensive pond-based and intensive production systems.
Dwarves are inefficient in beef production systems and are undesirable for Angus breeders. Researchers at Iowa State university have fine mapped the dwarfism locus to bovine chromosome 6 (BTA 6) revealing a mutation in the PRKG2 gene. The detection of causal mutation or closely linked markers for dwarfism is of great use to Angus producers as this gives them the ability to detect carriers in breeding populations and the potential to eliminate dwarfism from their herds.
Iowa State University and Aviagen studied 12 immune-related genes for associations with general mortality and other performance traits in three elite commercial broiler chicken lines raised in high and low hygiene environments. Ten of the 12 immune-related genes had associations with at least one trait; most detected effects were on mortality and growth. These results indicate that variation in candidate genes associated with important broiler traits can be identified in multiple environments.
Iowa State University maintains many unique chicken lines (highly inbred; MHC- congenic; closed populations; advanced intercross lines) for research. These lines serve as valuable resources for identifying genes of economic importance. Semen from all of the highly inbred and partially inbred lines was collected at ISU and cryopreserved by the staff of the National Animal Germplasm program in Ft. Collins, CO.
Gastrointestinal parasites have a profound effect on sheep production. In a collaborative study between Utah State University and Louisiana State University, a genome scan was implemented to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites. Suggestive QTLs have been identified on ovine chromosomes 1, 6, 9 and 19.
A bioinformatics program, Expeditor, was developed to design primers for livestock species. This program takes advantage of the information from the human genome and applies it to livestock cDNA. This program can be used at http://www.animalgenome.org/~hu/expeditor
Virginia Tech has been studying the transport of nutrients (amino acids, peptides and sugars) across the intestinal epithelia, which is mediated by membrane bound transporter proteins. The levels of mRNA for these transporters was determined by real time PCR and was found to vary depending upon the intestinal segment and the time of development (embryonic day 20 to 7 days post hatch). This work has shown that nutrient transporters are differentially expressed in a temporal and spatial manner.
Researchers at Rutgers University mapped twelve disease/mortality-resistance QTL in two families of the eastern oyster; at least seven of the twelve QTL are independent of each other. These results indicate that resistance to Dermo-infection or summer mortality is affected by at least seven quantitative trait loci.
UC Davis is utilizing mouse congenic strains to understand the biological mechanisms underlying growth traits in animals. A unique mouse model has been characterized that produces a 30-50% increase in post-weaning growth rate and mature body size, as well as a substantial increase in feed conversion efficiency during growth. Understanding the processes controlling growth in this model organism will aid in identifying genes for investigation in livestock species.
UC Davis has developed ArrayGene, a software package that allows researchers to create custom databases on genes from sequenced organisms. This tool can be implemented for any sequenced organism, and it can be very valuable in choosing microarray platforms for fine mapping and genomic dissection of chromosomes.
Researchers at New Mexico State University have identified polymorphisms within the growth hormone gene that seem to be a significant source of variation in average daily gain and carcass traits in Bos Taurus or Bos TaurusX Bos indicus composit cattle. They have identified that polymorphisms in the genes of the GH axis or its transcriptional regulators differ among Angus, Brangus or Brahman cattle.

Date of Annual Report: 03/18/2005

Report Information

Annual Meeting Dates: 01/16/2005 - 01/16/2005
Period the Report Covers: 01/01/2004 - 12/01/2004

Participants

Participants Attachment:

Attachment

Brief Summary of Minutes

I. Call to order at 4:30 pm by Dr. Bhanu Chowdhary, NRSP8 Technical Committee Chair

a. Dr. Max Rothschild made a motion to approve the last meetings minutes, second by Dr. Joe Cassidy and approved by a voice vote

II. Old Business

a. Summary of the Executive Committee Meeting

i. In 2006 the committee meeting must return to an early Sunday morning breakfast meeting at 7:00am

ii. All species workshops must finish by 4:00 pm Sunday so participants may attend the General Membership Business Meeting from 4:30 to 6:00 pm

b. Species Reports

i. Equine-Dr. Ernest Bailey
1. NRSP8 Objective 1. Most efforts have focused on adding to linkage and radiation hybrid maps
2. NRSP8 Objective 2. Limited activity in this area, four institutions are working on a plan
3. NRSP8 Objective 3. Genome Viewer at UC Davis integrates linkage information
4. Workshop participants will meet in Dublin in July 2006 to discuss mapping, functional genomics, and their applications.

ii. Poultry-Dr. Jerry Dodgson
1. This year the chicken genome sequence was published in Nature
2. This was the first post sequence workshop, topics included:
a. Draft sequence has some miss-assemblies and places that require further annotation
b. Use of sequence to improve genetic analyses
c. Application of chicken sequence to other poultry

iii. Cattle -Dr. James Womack
1. Draft sequence of 3.3X coverage was completed this fall
2. Now focus is on adding animals other than the original Hereford
3. Will keep fibroblast cell lines for these animals and others
4. The ArkDB server is no longer maintained at TAMU, moved to ISU
5. Online radiation hybrid mapping at TAMU using first generation RH map, will soon update to a more recent version
6. Somatic Cell hybrid panel still available
7. IBRP usage has dropped off significantly

iv. Sheep-Dr. Noelle Cockett
1. An NRI Tools and Reagents Grant was awarded to Dr. Cockett and Dr. Womack to construct an ovine radiation hybrid panel, now using coordinators funds to distribute
2. this will strengthen comparative maps between species, Dr. Harris Lewin will map markers
3. CHORI 243 BAC library constructed by Pieter DeJong available since last year, also gridded filters, Dr. Cockett purchased some with Coordinators funds for distribution
4. BAC end sequencing project is a collaborative effort, USDA has also funded through NRI Tools and Reagents. Dr. Cockett can do .5X of the library, she leveraged funding for the rest through other international sources which will result in full library, work to be done at TIGR
5. collaboration with national animal germplasm group has been set up to collect/conserve germplasm in US. Attended meeting in Cheyenne, great info for genetic diversity study, will supply this group with primers to study their collections and use this germplasm for SNP validation

v. Swine-Dr. Max Rothschild
1. design oligos for a 13K oligo array, sent to 35 labs, primarily in US, also Europe and Asia
2. Discussed a second generation oligo microarray
3. PigQTLdb on angenmap website
4. Expeditor primer design tools, other database tools
5. Swine Genome Sequencing Consortium, worked with industry to raise funds, big news is that USDA/CSREES will issue an RFA in the ball park of $10 million, possibly $1 million more from ARS, matching funds from Sanger, puts them much closer to goal of $30 million, hope to start sequencing in summer 2005
6. Industry was well represented at the workshop by Sygen and Monsanto, who are actively using molecular genetic tools from this effort

vi. Aquaculture-Dr. John Liu
1. The Aquaculture group is very complex, with 6 primary species and additional sub species, includes an executive committee.
2. This year 3 species coordinators Program Chair and Chair Elect changed
3. Four proposals for sequencing project were submitted to the JGI Community Sequencing Program (trout, catfish, oyster, tilapia) oyster and tilapia scored well.
4. Aquaculture species need to set priorities
5. Two white papers were developed, one to addressed to save the NRI Tools and Reagents Program, a second distributed to other funding agencies concerning the genomic enablement of these species
6. The Aquaculture Genome website was developed and moved to ISU this year.
7. Dr. Caird Rexroad summarized the workshop report including plenary speakers, student presentations, and evening poster session

vii. Database-Dr. James Reecy
1. work on objective to centralize resources for all species with bioinformatic expertise to ISU
2. team involves Dr. Chris Tuggle, Dr. Max Rothschild, Dr. Sue Lamont, and Dr. Zhiliang Hu
3. The species coordinators serve as a consulting board
4. The ISU database is a place to put programs used by all, also resources like maps, etc&
5. PigQTLdb-a database for pig QTL information, can do other species
6. Expeditor-primer design software for SNP discovery
7. in-house blast server
8. The website and Angenmap both continue to increase in number of hits and usage
9. This year the group will assist in pig oligo microarray construction, would like to make pipeline for other species

c. Administrators Reports

i. Margaret Dentine, Lead Administrative Advisor
1. NRSP8 is a model of how support program should work
a. Democratic process, funding spread around, successful workshops
2. New review for NRSPs in experiment station system, NRSP8 received a good review and did get the budget requested. This is significant as funding comes from directors budgets
3. We all bear responsibilities to work with coordinators
4. Project will be up for review again, it is important to do a good job

ii. Dr. Dr. Muquarrab Qureshi, USDA/CSREES National Program Leader
1. Thank species coordinators and executive committee for good job, help to accomplish mission, of advancing knowledge
2. Strategic goals-enhance efficiency of agricultural production systems, including genetics, under programs 303 and 304, genetics and genomics
3. Help meet performance based budget progress
4. High priority area for USDA
5. $15 million per year
6. pleased with updates in meeting including sequencing efforts
7. NRSP8 received excellent reviews, complemented for adding aquaculture
8. funded Shrimp Genome Consortium
9. hosted Animal Bioinformatics Workshop
10. NRI RFP 2006 planning is underway
11. 2005 budget is flat compared to previous year

III. New Business

a. NRSP8 Business Meeting schedule-see above

b. USDA/CSREES workshop on Animal Genomics held in September 2004, summary by Dr. Ronnie Green

i. Summary report given in swine meeting, copies available
ii. Workshop came about by charge by Dr. Joseph Jen, USDA Undersecretary for Research, Education and Extension.
iii. Once we are passed sequencing genomes of major species, what next?
iv. Dr. Green and Dr. Qureshi were asked to put workshop together to ask scientist and administrators what to do
v. Asked subset to stay and brief the Interagency Working Group on the workshop, the working group was pleased to see scientists priorities of long term needs for animal genomics.
vi. A summary of the workshop will be made public and published in Animal Genetics in March
vii. Also charged to take out strategic planning exercise in this effort in 2005, involving all agencies in animal genomics, will do in 2nd and 3rd quarters of this year
viii. Interagency report on NSTC website , have 2003 report now, 2004 soon

c. Animal Genome Tools and Reagents Program-future prospects

i. Discussion initiated by Dr. Anna Palmisano, USDA/CSREES Deputy Administrator
1. NRI is the largest competetive program in USDA
2. Now starting 2006 planning
3. Need help setting priorities-How can we make the greatest impact?
4. Need to develop linkages with other agencies, but limit overlaps
5. In FY06 planning we need to think long term approaches
6. Think big, think about more comprehensive approaches to animal genomics portfolio at CSREES
7. Question-Dr. Bob Chapman-We have an opportunity to think big, how about incorportative ecogenomics, as all of our species have environmental impacts. Answer-CSREES is working on a program for FY06 concerned with ecogenomics, mostly at the microbial level. Also, the Natural Resources group is thinking about ecogenomics.
8. Comment-Dr. Jerry Dodgson-on the importance of Tools and Reagents. Response-CSREES needs to know the priorities for Tools and Reagents for this group.
9. Comment-Dr. Max Rothschild-for swine SNPs are a high priority not funded in pigs, have for chicken and cattle. So we must prioritize not between species, but within. Response-to increase success rate may require a better, more focused RFP.
10. Comment-Dr. John Liu-Tools and Reagents has generated tools and science, still need tools for Aquaculture species, need to apply different criteria to different species. Response-group needs to articulate needs.
11. Comment-Dr. Bhanu Chowdhary-Species coordinators need to conduct prioritization. Response-Asked to provide input to Dr. Qureshi and Dr. Brayton.
12. Summary-to impact the planning process submit comment in next 2-3 months, remember to think long term.

d. Motion by Dr. Noelle Cockett to include goats on the Cattle/Sheep committee.

i. Not a request to re-allocate funds, goats would be a subcommittee of sheep
ii. Second by Dr. Max Rothschild
iii. Discussion-Virginia State, Valley State, and Prairie A&M, 1890s schools, want to move towards genomics to study traits
iv. Passed voice vote

e. Election of officers for 2005

i. Cattle/Sheep committees turn to nominate-nominate Dr. Clair Gill
ii. Second by Dr. Max Rothschild
iii. Passed voice vote

f. Other

i. suggestions for future plenary speakers for PAG on animal genome side, send to Dr. Hans Cheng or Dr. Max Rothschild

IV. Adjournment 5:53 pm

Respectfully submitted,

Caird E. Rexroad III for Thomas Kocher, Co-Chair

Overall attendance to the NRSP-8 species workshops: 65 (Aquaculture), 56(Cattle & sheep), 51 (Horse), (Poultry), 97 (Swine).

Accomplishments

For a complete report, please see: http://www.wisc.edu/ncra/NRSP8-2004-SAES422Link.doc Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. Aquaculture. Good progress has been made toward reaching objective 1 among aquaculture species in 2004. The current state of aquaculture genomics include availability of relatively high-density genetic linkage maps from Atlantic salmon and rainbow trout (with over 1000 markers), moderate density linkage maps for tilapia and catfish (with several hundreds of markers), and framework linkage maps of for oysters and shrimps. BAC-based contigs have been established for Atlantic salmon and tilapia, but are lacking for catfish, rainbow trout, striped bass, shrimps, and oysters. In spite of the lack of one or the other maps, efforts were devoted to enhance and integrate these maps as detailed below: Cattle. Jim Womack from Texas A&M University gave a detailed presentation titled "Highlights of the bovine sequencing project. He reviewed that discussion to sequence a bovine genome occurred as early as 1993 by NRSP-8. Much of the initial sequencing effort is occurring at the Human Genome Sequencing Center at Baylor College of Medicine in Houston, TX. Richard Gibbs and George Weinstock are directing these efforts and a ~3X working draft was published in October of 2004 and is available at Genbank. The animal resources from this project were derived from the historic linebreeding Hereford project at the Fort Keogh United States Department of Agriculture Agriculture Research Service (USDA-ARS) station in Miles City, Montana. A Bacterial Artificial Chromosome (BAC) DNA library was originally created from tissues of the bull L1 Domino 99375 and the whole genome shotgun sequences were derived from DNA extracted from the white blood cells of his daughter, L1 Dominette 01449. Dominette was selected since her sire was used to create the BAC library and because of the concept that sequence assembly could be made easier working with sequences from animals with similarities in their genetic background. Other contributions to this project now include sequencing within other breeds such as Holstein, Angus, Brahman, Jersey, Limousine and Norway Red. Some of these other efforts include SNP mapping as well as ~10,000 full-length mRNA sequences to be provided by Genome Canada. A 7 to 8X coverage map is expected by late summer of 2005. Other mapping efforts were presented by H. Lewin of the University of Illinois. In brief, a second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map as well as to sparsely populated map intervals. Discussion also occurred regarding an international consortium formed to create a sequence-ready comparatively anchored bacterial artificial chromosome (BAC) map of the cattle genome. Horse. The resources now used most frequently for equine genome mapping include a 5000 rad horse x hamster whole genome radiation hybrid panel, a collection of stallion-based half-sib families comprising 500 offspring, and a pedigree in which a single stallion sired over 60 conceptuses from two sets of identical twin mares. Two new genetic linkage maps are in the publication process. The first contains 766 markers on the half-sib families (combined with previous maps from other families) with a single linkage group on all autosomes, and the second contains 745 markers on the 3 generation full-sibling family and reports a single linkage group on all autosomes plus the X. Microsatellite markers continue to be developed and mapped on both resource populations. Gene markers from individual human chromosomes, as well as markers from across the genome, are being mapped on the RH panel, frequently accompanied by FISH localization. Many microsatellites are also being mapped on the RH panel. More than 2,500 markers have been typed on this panel and the goal is to soon have a greater than 3,000 marker RH and comparative map. Dense (greater than 1 marker/Mb) maps are now in process for many of the autosomes as well as the X and the Y. The two genetic linkage maps, as well as the RH map are becoming increasingly integrated through the mapping of common markers on all three resources. In addition to the mapping efforts, over 2,000 BAC end sequences comprising 1.8 Mb of sequence have been collected and being used for prediction of gene content and comparative sequence alignment with human and other species, as well as for selected inclusion on the RH map. Poultry. High resolution poultry genome maps. The Reference Linkage Map(s). Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples from the same two international reference crosses, the Compton population (Bumstead and Palyga, Genomics 13, 690-697, 1992), and the East Lansing population (Crittenden et al., Poultry Science 72, 334-348, 1993). This map has been enhanced by genotyping of a third cross, the Wageningen population, by Martien Groenen and colleagues (Groenen et al., Genomics 49, 265-274, 1998). A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Updates bring the number of markers on the consensus map to 2204, placed into 51 linkage groups, covering nearly 4000 cM (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). The East Lansing map has expanded to 1276 markers on 42 linkage groups (other evidence places E46 on GGA2 and E66 on GGA5, but there is not enough statistical support in our map alone to establish these linkages). This map includes 326 mapped genes. In connection with the genome sequence, the Beijing Genomics Institute randomly sequenced 0.25X, each, of a broiler, layer and Silkie genome, generating 2.8 million potential SNPs for future high resolution linkage mapping experiments (International Chicken Polymorphism Map Consortium, Nature 432:717-722, 2004). Sheep. (Develop high resolution comparative genome maps): NRSP-8 Sheep Coordinator funds have contributed to the development of an ovine radiation hybrid (RH) panel in a collaborative project between Utah State University and Texas A&M University. Ninety clones with retention frequencies between 15-40% have been selected for inclusion in the 5,000 rad RH panel. Large DNA preparations have been made for the 90 clones and the panel has been distributed to Dr. Tom Goldhammer, Research Institute for Biology of Farm Animals, Dummerstorf, Germany, and Dr. John Williams, Roslin Institute, Edinburgh, UK. An on-line, real-time comparative database being developed at Texas A&M University will be used for web-based transmission of mapping data on the distributed ovine RH panels. Database displays will include ovine RH maps of each chromosome that are cross-referenced to homologous human and bovine chromosome segments, with lines between orthologous markers indicating internal rearrangements. The goal is to type the ovine panel with 500 microsatellite markers that have been mapped on the ovine and bovine linkage maps, as well as 500 ESTs developed from ovine and bovine cDNA sequences with known locations on the human genome map. These data will be used to develop a framework/comprehensive RH map for sheep. Swine BARC and Baylor Univ researchers, with the ISAG SLA committee, established an internationally recognized nomenclature to identify and classify SLA class I gene polymorphisms. This will serve as a basis for determining critical genetic effects on infectious disease and vaccine responses. They have made data fully accessible at an international website, the IPD-MHC Sequence Database website: www.ebi.ac.uk/ipd/mhc/sla/nomenclature.html. A large number of genes continue to be identified and mapped by ISU researchers. An emphasis has been made (and will continue to be made) on genes that improve the comparative map as well as in connecting the genetic and physical pig genome maps. Several new genes that may be important QTL are being mapped by ISU researchers. These include genes associated with cured meat quality and sow longevity. QTL for several meat quality traits have been discovered. Additional fine mapping is underway and positional candidate genes are being considered. Mapping of over 400 comparative loci to pig chromosomes SSC1, 4, 7, 8 and X adds additional information to comparative maps. Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. Aquaculture. In 2004, great progress has been made in the area of transcriptome analysis using ESTs. A summary of current available ESTs in various aquaculture species is listed below. These ESTs has allowed the development of microarrays in various species as detailed below. Species Current ESTs Approximate unique sequences Rainbow trout 160,816 50,773 Atlantic salmon 120,000 40,000 Catfish 45,000 30,000 Oyster Crassostrea gigas 3,300 Crassostrea virginica 9,200 5,900 Shrimps 9,400 3,300 Tilapia 1,700 Striped bass <500 The largest progress in this area was made with salmonids. A 16,000 gene array has been developed by GRASP using salmon and trout EST data sets. This array has been tested for use in various salmonid fishes. The array has been used to study developmentally regulated genes and genes induced under various environmental conditions. Cattle. Several universities reported progress in this area. In brief, these reports included advancements in understanding of genes regulating milk production traits, muscle development (i.e, callipyge), marbling, growth hormone, disposition, gastrointestinal nematode infection, and tolerance to endophyte toxicity in cattle grazing fescue grass. Invited speakers for the cattle and sheep symposium presented that a new SNP marker in CAPN-1 associated with tenderness in cattle of indicine, taurine, and admixed decent. There is tremendous interest in the trait of tenderness in the basic scientific community and in the commercial genotyping industry. A challenge in the application of some of the initially discovered polymorphisms related to tenderness was that the markers inferred variability in prediction of tenderness traits and had diversity among genotypes in Bos taurus cattle, but not in Bos indicus cattle. These studies revealed that chromosome 29 contained an important gene defined as µ-calpain (CAPN-1) which has a large role in postmortem tenderization. There are a series of SNPs within or closely linked to this gene. Two of these SNPs appear to be informative in Bos indicus and Bos taurus cattle (316 and 4753), but a SNP at 530 only appears to be informative in Bos taurus cattle. Moreover, it appears that these markers maybe more useful in predictions using analytical procedures involving haplotypes. Stephen Moore from the University Alberta-Edmonton delivered a talk on Candidate genes of feed efficiency. The trait of residual feed intake was introduced and efforts to find genetic tools to select for this trait were discussed. Data of other measure of animal efficiency were also presented which involved evaluating oxygen consumption and methane production using a respiratory calorimetry hood. The rationale for these measures were from the concept that measures of gas consumption or production could be used to estimate metabolic rate/efficiency in cattle. Efforts to use these measures to identify candidate genes were also presented, particularly their associations with hormones such as leptin. Jeremy Taylor (University of Missouri) reported results in fine quantitative trait loci (QTL) mapping in dairy cattle (in collaboration with scientists at USDA-ARS and University of Arizona) as well as results in positional cloning in beef cattle. To fine-map QTL affecting milk production traits in dairy cattle on BTA6, 3317 bulls comprising 45 half-sib families were genotyped for 38 markers. The data were analyzed using least squares regression (QTL Express), linkage disequilibrium (LDVCM) and full pedigree MCMC (LOKI) methods. A total of 19 sires were segregating for at least one QTL under a half-sib model at chromosome-wide P < 0.05. LD results across families indicated the presence of up to 7 QTL (3 within a 6 cM region) whereas LOKI revealed only 3 QTL. Positional/functional candidate genes have been identified for five of the QTL. Osteopontin (OPN or SPP1) is a strong candidate for the QTL near marker BM143. The entire OPN gene and 5kb upstream was sequenced from four segregating sires and four non-segregating sires (12.3kb per animal). A total of 15 SNPs were identified but only one SNP resulted in sire genotypes that were concordant with the segregation status of all eight sires. For position cloning in beef cattle, the strategy outlined in Taylor and Schnabel was applied and built upon the previous projects involving Bos taurus x Bos indicus crosses and study of Bos taurus autosomal (BTA) chromosome 2 and 14. A DNA Repository from semen on 1,660 registered bulls representing 14 generations of the American Angus Association was assembled. Expected progeny differences (EPD)s and reliabilities for 20 traits are available for this population. In addition, 5,300 DNA samples were collected on commercial Angus steers (36 halfsib families have at least 30 progeny) with growth and slaughter phenotypes. A total of 113,637 genotypes for 56 microsatellite loci and SNPs for thyroglobulin in exon 5 (TG5) and diacyl glycerol acyltranferase in exon 1 (DGAT1) on BTA2 and BTA14 in 1,361 Angus sires and 559 steers were scored. Results suggested TG5 had no effect on sire Marbling EPDs or steer marbling phenotypes. Three previously published marbling QTL, 1 birth weight QTL and 1 carcass weight QTL are segregating within Angus and map to identical locations to the published reports. Horse. ESTs have been collected from unstimulated and stimulated equine leukocytes, from articular cartilage, from brain, and from skeletal muscle. 1,000 element microarray has been printed from the leukocyte EST collection and is being used to study genes involved in pathogenesis of experimentally-induced laminitis. A 9,410 element microarray is under development from the cartilage ESTs. Discussions of combining sequences from all sources and developing a larger oligo-based microarray have been initiated. It is anticipated that this resource would assist the group in defining the processes associated with many disease and economically important traits, such as laminitis, joint disease, colic, etc. A contig of 23 overlapping BAC clones comprising the equine MHC (ELA) has been assembled and subclones scheduled for an estimated 7X sequencing of the region. Description of the gene loci in this region will help to define genetic influences on disease susceptibility and resistance. In addition, studies to characterize the T-cell receptor B gene family in horses are ongoing. Recently the molecular genetic basis of glycogen storage disease type IV (GBED) in Quarter Horses and junctional epitheliosis bullosa (JEB) in Belgian horses have been described through the use of genome mapping tools. Studies to define the molecular basis polysaccharide storage myopathy (PSSM) and hyperelastosis cutis (HERDA) in Quarter Horses, and exertional rhabdomyolysis (RER) in Thoroughbreds are ongoing as are studies to identify the gene responsible for Degenerative Suspensory Ligment Disease and the grey, sabino overo, and appaloosa coat color patterns. Poultry. Physical maps and map integration. A library of over 115,000 BACs (~15X; Lee et al., Animal Genetics 34:151-152, 2003) was generated and 65,000 of these were fingerprinted at Texas A&M, leading to a first generation physical map (Ren et al., Genome Research 13:2754-2758, 2003). P. de Jong (Childrens Hospital of Oakland Research Institute, CHORI) generated a ~10X BAC library (CHORI-261) with extra large inserts using DNA we provided from the same bird used for the Texas A&M BACs and for sequence analysis. CHORI also prepared a large insert turkey BAC library (CHORI-260). The Washington U. Genome Sequencing Center (WUGSC) was provided copies of the Texas A&M and CHORI-261 chicken BAC libraries and fingerprinted over 150,000, generating over 130,000 useable BAC fingerprints. These were employed to generate a second generation BAC contig map comprised of 260 contigs, 226 of which have been anchored to the genetic linkage/chromosome map (Wallis et al., Nature 432:761-764, 2004). Several labs participated in integrating the BAC contigs and sequence with the linkage map, primarily using overgo hybridization (Romanov et al., Cytogenetics and Genome Res., 102:277-281, 2003). This research generated over 7800 BAC assignments to over 900 distinct markers or genes. Recently, similar efforts applied to the turkey CHORI-260 library have generated over 2400 BAC assignments for 176 markers/genes. Boardman et al. (Current Biology 12:1965-19-69, 2002) announced the sequencing of over 300,000 chicken ESTs from a wide variety of tissues and developmental stages. A joint project between the U. of Manchester and the Sanger Institute (Jane Rogers) sequenced full length chicken cDNA clones using both UMIST and other libraries. A world-wide consortium of investigators report 19,626 finished cDNAs and 485,337 ESTs (Hubbard et al., Genome Research advance Epub, Dec. 8, 2004). NCBIs dbEST (http://www.ncbi.nlm.nih.gov/dbEST/) presently lists 531,351 chicken ESTs. Array development will be reported below. Masabanda et al. (Genetics 166:1367-1373, 2004) generated a molecular cytogenetic analysis of the chicken, including identification of all microchromosomes, either by chromosome paints or BAC FISH probes. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA (Morisson et al., Genet. Sel. Evol. 34:521-533, 2002), and a framework RH map is being constructed (e.g., Morisson et al., Mamm. Genome 15:732-739, 2004). The Washington U. Genome Sequencing Center (WUGSC) has completed 6.6X sequencing of the chicken genome (primarily whole genome shotgun) and the first assembly of the draft chicken sequence was released on March 1, 2004. The initial analysis and annotation of the sequence was recently published (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). In addition to the companion physical map and SNP papers mentioned above, the January, 2005 issue of Genome Research will be devoted to companion chicken sequence analysis papers (Genome Research advance Epub, Dec. 8, 2004). Sheep. (Increase marker density of existing linkage and physical maps): The ovine linkage map is continuously updated, primarily through the efforts of Dr. Jill Maddox, University of Melbourne, Australia. The linkage map now includes over 1,250 loci [http://rubens.its.unimelb.edu.au/~jillm/jill.htm ]. A collaborative project including the US, Australia, New Zealand, and the UK will soon commence with the objective of developing a whole genome physical map (see below). Swine. BARC researchers have provided means to study expression and function of additional immune genes in normal breeding populations to identify early responders which might be more disease resistant/susceptible. New work in porcine reproductive and respiratory syndrome virus (PRRSV) resistance with UNE researchers may help identify pigs which are more disease resistant and the protective mechanisms they employ to induce resistance. ISU researchers have used two molecular techniques to identify some of the genes which increase or decrease expression levels in the early response to Salmonella choleraesuis or S. typhimurium infection. These are subtractive suppression hybridization (SSH) and microarray. Genes include signal transduction and steroid biosynthesis which are involved in the embryo elongation process. ISU and NADC researchers have begun to analyze the lungs of pigs infected with S. choleraesuis by using the NRSP8 funded long oligonucleotide microarray, and find 57 genes with some statistical evidence (P <0.001) for differential expression; of the 40 genes from this group with human functional annotation, 40% are related to the immune system. The transcriptional profiling results were verified by quantitative techniques with BARC researchers. Transcriptional profiling of skeletal muscle tissue at Michigan State Univ. reveals important genes in the pathways regulating skeletal muscle growth and development. Their development of a unique pig resource population provides a novel resource for identifying QTL associated with growth and carcass merit in pigs. NCSU researchers are characterizing changes in allelic frequencies for two RFLPs associated with the follistatin gene in a line of pigs selected for increased litter size (LS). In a separate project they are working to identify genes associated with adipose metabolism. For this they are analyzing gene expression during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. In an effort to identify genes responsible for anti-microbial responses in the gut, UMN researchers isolated expressed sequence tags (EST) from an activated porcine Peyers patch cDNA library. 3687 ESTs, representing 2414 unique nucleotide sequences were analyzed and spotted onto a microarray for gene expression profiling. Approximately 30% of these ESTs BLAST to genes of unknown function and 20% appear to be novel, i.e., have no known homology in the public databases. To determine chromosomal location, PCR-based mapping was performed across a swine radiation hybrid panel; 125 ESTs were mapped with a lod score > 6.0. These ESTs therefore should provide insight into early immune mechanisms and processes activated in Peyers patches. Islet gene expression profiles were assessed at UMN using the NRSP8 funded porcine 70-mer oligonucleotide microarray and real-time PCR. Microarray data were analyzed by direct pairwise comparison between culture conditions and by loop design using GeneSpring and R/maanova, respectively. Cytokine treatment resulted in increased expression of genes involved in stress, immune response, apoptosis, and cellular defense. Islets cultured under conditions of elevated glucose showed increased expression of genes involved in intracellular protein transport, glucose and lipid metabolism, and stress response. Transcriptional profiling of the response of porcine islet beta cells to inflammatory and hyperglycemic conditions will help identify molecular targets that are likely to protect porcine islets during islet isolation and engraftment. Progress Toward Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. Aquaculture: Overall, bioinformatic tool development is a very weak area in aquaculture genomics. Thomas Kochers group continues to build informatic tools to integrate the genetic and physical maps of the tilapia genome with with the genome sequences now available for Fugu, Tetraodon, medaka and zebrafish. The comparative genome databases and browsers are available at http://hcgs.unh.edu/. Greg Warrs group continue to maintain the website www.marinegenomics.org for the archiving of EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data. They have developed tools for the design of microarrays from species with limited genomic information (see Chen et al., 2004). In collaboration with Dr. Lei Liu at the Keck Bioinformatics Center, an ESTIMA system has been developed that provides searchable databases for the catfish ESTs at Auburn University. As soon as it is tested, the website will be available to the research community. Cattle: Jim Reecy of Iowa State University presented information regarding database activities of NRSP-8. During the symposium, Trey Ideker of the University of California, San Diego, gave a presentation titled Modeling cells with molecular interaction networks. Molecular interaction networks are experimentally derived connections of metabolites and proteins within pathways. While these molecules may not directly interact, they likely are related through the enzymes that process them. Dr. Ideker presented evidence that overlays, the alignment of pathways according to protein sequence or other data where similarity scores are available, may be of great use. Specifically, overlays of known networks from well studied species may elucidate the function or role of unknown metabolites and proteins in less well understood organisms. The implications of this research involve an increase in the speed of which function can be ascribed to unknown compounds in bovine using information gathered in human, mouse, and rat. Christine Elsik of Texas A&M University (TAMU) spoke on the current state of the bovine long oligo array developed among a consortium of researchers at TAMU, University of Missouri, Iowa State University, and The University of Minnesota. Sequences mined from GenBank are currently undergoing a screening process to remove duplicated sequences, vector sequences, and other artifacts of the cloning process. It is expected that a first draft of the sequences to be spotted on the array will be available by Summer of 2005. Horse: This objective is not currently a major focus of the equine group. Bioinformatic tools available include a Web interface for RH panel typing data submission and mapping, a publicly available and searchable database that houses the leukocyte ESTs at the University of Georgia, and DNA marker databases maintained at INRA and Roslin. Poultry: Database and other map resources. Sequence and Map: The sequence, along with a variety of options and tools, can be accessed at three different browsers: the UCSC Chicken Genome BrowserGateway, (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0&hgsid=30948908); the NCBI Chicken Genome Resources, (http://www.ncbi.nlm.nih.gov/genome/guide/chicken/); and the EBI's Ensembl Chicken Genome Browser, (http://www.ensembl.org/Gallus_gallus/). See also the WUGSC chicken site at http://genome.wustl.edu/projects/chicken/. SNP data can be accessed at http://chicken.genomics.org.cn/index.jsp or the UCSC or Ensembl browsers. The ChickFPC browser at http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC allows for various searches of the BAC contig map. Similarly, BAC locations denoted by BAC end sequences can be found on other sequence browsers noted above. The BAC map can also be obtained by ftp at http://genome.wustl.edu/projects/chicken/. The SNP data generated by the Beijing Genomics Institute (described above) can be accessed on the UCSC or Ensembl browsers, but more extensive descriptions (including QTL information) are available at the BGI site at http://chicken.genomics.org.cn/index.jsp. ChickGBASE: The latest version of ChickGBASE is constructed in the comparative mapping Arkdb format. Arkdb was primarily developed at the Roslin Institute. ChickGBASE is available in the Arkdb format at http://www.thearkdb.org/browser?species=chicken . A mirror site for the poultry database has been mounted at the Iowa State database site, http://www.genome.iastate.edu/. James Reecy at Iowa State has taken over direction of all bioinformatics efforts for the NAGRP, including chicken. WWW Homepage: We maintain a WWW homepage (http://poultry.mph.msu.edu) for the Poultry Genome that provides a variety of genome mapping resources, including the latest EL maps and mapping data, an updated list of published microsatellites, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps. Sheep: (Expand species genome databases and provide other genome mapping resources): An informational database for the ovine genome map continues to be enhanced. SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects, along with physical and linkage maps of the sheep genome, and information on individual loci and associated references. The information is presented using the WWW interface and can be accessed through a number of nodes including Roslin Institute (UK) and the University of Melbourne (Australia). Currently, there are 2832 map assignments in SheepBase, with 1988 derived through linkage analysis and 844 via physical mapping. Dr. Jill Maddox, University of Melbourne, Australia, has been updating the database using NRSP-8 coordinator funds to serve as the curator of SheepBase. A memorandum of understanding was established among AgResearch (New Zealand), Meat and Livestock Australia, the USDA/ARS Meat Animal Research Center (Nebraska), and the NRSP-8 Sheep Coordinator in order to fund the construction of a 10-fold redundant BAC library by BACPAC Resources. A copy of the library has been received by Utah State University. In addition, arrayed filters have been purchased and are distributed upon request. Swine: Database development is continuing at ISU. An EST database has been developed and is quite useful. ISU researchers developed a relational pig quantitative trait loci (QTL) database (PigQTLDB) to integrate all available pig QTL data in the public domain and thus facilitate the use of QTL data in further studies. PigQTLdb has been well used since its release last December (http://www.animalgenome.org/QTLdb/). They developed a trait ontology to standardize names of traits and to simplify organization of the data making it possible to compare primary data from diverse sources and methods. The database contains all pig QTL data published during the past 10+ years. The database and its peripheral tools were made to compare, confirm, and locate on pig chromosomes the most feasible location for a candidate gene responsible for quantitative trait(s) important to pig production. To date, 791 QTL from 73 publications have been curated into the database. Those QTLs cover more than 300 different traits. Contact Zhiliang Hu (zhu@iastate.edu) with any suggested improvements or additional data to add to the database. These data have been submitted to the Gene and Map Viewer resources at NCBI, where the information about markers has been matched to marker records in NCBI's UniSTS database. This allows automatic matching of markers to public sequence data by e-PCRand data retrieval from NCBI resources. Efforts at ISU and UMN have been aimed at developing better annotation of the NRSP8 funded porcine 70-mer oligonucleotides for microarray data analyses. WSU researchers have take 3 steps to collect and generate full-length cDNA sequences of orthologous genes in livestock species, i.e., puzzle sorting, puzzle retrieving and puzzle making for a final puzzle solving. They have developed a bioinformatics tool, ELF-Walking (electronic flanking walking) to facilitate large-scale in silico cloning of full-length cDNA sequences by mining the sequence databases. All sequence data and annotation information can be downloaded from our Bioinformatics website at http://www.ansci.wsu.edu/programs/bioinformatics/.

Publications

Aquaculture: Baoprasertkul, P., Peatman, E., He, C., Kucuktas, H., Li, P., Chen, L., Simmons, M., and Liu, Z.J. 2004. Sequence analysis and expression of a CXC chemokine in resistant and susceptible catfish after infection of Edwardsiella ictaluri. Developmental and Comparative Immunology 28, 769-780. Bilodeau, A.L. and G.C. Waldbieser. 2005. Activation of TLR 3 and TLR5 in channel catfish exposed to virulent Edwardsiella ictaluri. Developmental and Comparative Immunology, accepted for publication 12/4/2004. Boutet, I., A. Tanguy, and D. Moraga. 2004. Characterization and expression of four mRNA sequences encoding glutathione S-transferases pi, mu, omega, and sigma classes in the Pacific oyster Crassostrea gigas exposed to hydrocarbons and pesticides. Marine Biology 146:53-64. Chen YA, Mckillen DJ, Wu S, Jenny MJ, Chapman R, Gross PS, Warr GW, Almeida JS, (2004) Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 2004, 5:191 Chen, L., C. He, P. Baoprasertkul, P. Xu, P. Li, J. Serapion, G. Waldbieser, W. Wolters, and Z. Liu. 2004. Analysis of a catfish gene resembling interleukin-8: cDNA cloning, gene structure, and expression after infection with Edwardsiella ictaluri. Developmental and Comparative Immunology 29:135-142. Chen, L., Jiang, H., Zhou, Z., Li, K., Li, K., Deng, G.Y. and Liu, Z.J. 2004. Purification of vitellin from the ovary of Chinese mitten-handed crab, Eriocheir sinensis, and development of an anti-vitellin ELISA. Comparative Biochemistry and Physiology B Biochemistry and Molecular Biology 138, 305-311. Cnaani, A., Lee, B.-Y., Ron, M., Hulata, G., Kocher, T.D., Seroussi, E. 2003. Linkage mapping of major histocompatibilty complex class I loci in tilapia (Oreochromis spp.). Animal Genetics 34(5): 390-391. Elfstrom, C. M., P. M. Gaffney, C. T. Smith, and J. E. Seeb. Characterization of 13 single nucleotide polymorphisms in the weathervane scallop. 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Mammalian Genome 15, 570-577. Poultry: Sheep: Refereed manuscripts published or accepted: 12 Agca, C., C.A. Bidwell, and S.S. Donkin (2004) Cloning of bovine pyruvate carboxylase and 5' untranslated region variants. Animal Biotechnology15:47-66. Bidwell, C. A., L. N. Kramer, A. C. Perkins, T. S. Hadfield, D. E. Moody and N. E. Cockett (2004) Expression of PEG11 and PEG11AS transcripts in normal and callipyge sheep. BMC Biology 2:17. DOI:10.1186/1741-7007-2-17. Cockett, N. E. (2004) Summary of the 2004 International Conferences for Animal Genetics, held in Tokyo, Japan. Japanese Journal of Animal Breeding (in press). Cockett, N. E., M. Smit, C. A. Bidwell, K. Sergers, T. L. Hadfield, G. D. Snowder, M. Georges and C. Charlier (2004) The callipyge mutation and other genes that affect muscle hypertrophy in sheep. Genetics Selection Evolution 37(Suppl. 1):S65-S81. The Complex Trait Consortium (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. 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Cockett (2004) Opportunities for detection and use of QTL influencing seasonal reproduction. Genetics Selection Evolution (in press). Rodriguez, S. M., C. A. Bidwell and S. S. Donkin (2004) Cloning the genomic sequence and proximal promoter of bovine pyruvate carboxylase. Journal of Animal Sciences 82:365. Warden, C. H., S. Stone, S. Chiu, A. L. Diament, D. Shattuck, R. Riley, P. Corva, J. Easlick, J. S. Fisler and J. F. Medrano (2004) Identification of a congenic mouse line with obesity and body length phenotypes. Mammalian Genome 15:460-71. Book chapters: 2 Cockett, N. E. And F. Galibert (2004) Genome Mapping at the Molecular Level. In: Mammalian Genomics. Editor: A. Ruvinsky. CAB International, UK (in press). Brenig, B., T. E. Broad, N. E. Cockett and A. Eggen (2004) Achievements of Research in the Field of Molecular Genetics. In: The World Association for Animal Production, Book of the Year for 2003. Wageningen Academic Publishers, The Netherlands (in press). Published abstracts and proceedings: 6 Bidwell, C.A., L.N. Kramer, T.S. Hadfield, D.E. Moody C. Charlier, M. Georges and N.E. Cockett (2004) Expression of PEG11 and AntiPEG11 transcripts in normal and callipyge sheep. Keystone Symposia: Emerging Mechanisms of Epigenetic Regulation. Tahoe City CA. Cockett, N. E. (2004) Advances in Livestock Genomics. Conference on Agricultural Genomics: Who, What and Why. AAAS, Pacific Division. Eng, S. L., E. Owens, J. E. Womack and N. E. Cockett (2004) Development of an ovine-whole genome radiation hybrid panel. Proc., Plant and Animal Genome XII, poster P650, p. 233. Liu, W-S., C. W. Beattie, N. E. Cockett and F. A. Ponce de Leon (2004) Comparative analysis of 38 bovine Y-chromosome microsatellites in cattle, sheep and goats. Proc., Plant and Animal Genome XII, poster P632, p. 229. Perkins, A. C., L. N. Kramer, D. E. Moody, T. S. Hadfiled, S. Eng, N. E. Cockett and C. A. Bidwell (2004) Developmental expression of paternally expressed genes from the callipyge locus of sheep chromosome 18. Proc., 29th International Conference on Animal Genetics, p. 73. Smit, M., F. Baraldi, E. Davis, X. Tordoir, T. Hadfield, G. Gyapay, N. Cockett, M. Georges and C. Charlier (2004) Extending the boundaries of the callipyge imprinted gene cluster on ovine chromosome 18. Proc., Plant and Animal Genome XII, poster P649, p. 233. Takeda, H., X. Tordoir, M. Smit, N. Cockett, M. Georges and C. Charlier (2004) Dnase I hypersensitive sites around the ovine callipyge mutation. Proc., 29th International Conference on Animal Genetics, p. 73. Dissertations: 1 Maria Smit. PhD in Animal Science with Molecular Genetics specialization, Utah State University. Dissertation Title: Long Range Transcriptional Regulation at the Ovine Callipyge Imprinted Gene Cluster. Swine: http://www.genome.iastate.edu/community/NRSP8/2004/index.html Bertani G, Gladney C, Johnson RK, Pomp D 2004. Evaluation of gene expression in pigs selected for enhanced reproduction. II: Anterior Pituitary. J Anim Sci 82:32-40. Blowe, C. D., E. J. Eisen, O. W. Robison, and J. P. Cassady. 2004. Characterization of a line of pigs selected for increased litter size for two RFLPs identified in follistatin. Abstract. J. Anim. Sci Supplement 1. Caetano AC, JB Edeal, K Burns, RK Johnson, C Tuggle, D Pomp 2005. Physical mapping of the differentially expressed porcine ovarian transcriptome. Animal Genetics (Accepted). Caetano A, J Ford, RK Johnson, D Pomp 2004. Microarray profiling for differential gene expression in ovaries and ovarian follicles of pigs selected for increased ovulation rate. Genetics 168: 1529-37. Cao H, Robinson JA, Jiang Z, Melville JS, Golovan SP, Jones MW and Verrinder Gibbins AM. 2004. A high-resolution radiation hybrid map of porcine chromosome 6. Anim. Genet. 35:367-378. Churchill GA and 101 others including D Pomp 2004. The Collaborative Cross: A community resource for the genetic analysis of complex traits. Nature Genetics 36:1133-1137. Ciobanu, D.C., J.W.M. Bastiaansen, S.M. Lonergan, H. Thomsen, J.C.M. Dekkers, G.S. Plastow and M.F. Rothschild. 2004. New alleles in calpastatin gene are associated with meat quality traits in pigs. J. Animal Sci. 82:2829-2839. Ciobanu, D.C., Lonergan, S.M., Bastiaansen, J.W.M., Mileham A, Miculinich, Schultz-Kaster, C., Sosnicki, A.A., Plastow , G.S. and M.F. Rothschild. 2004. Association of new Calpastatin alleles with meat quality traits in commercial pigs. 50th Int. Congress of Meat Science and Technology, Helsinki, Finland. Dawson HD, Royaee AR, Nishi S, Kuhar D, Schnitzlein WM, Zuckermann F, Urban JF, Lunney JK. 2004. Identification of Key Immune Mediators Regulating T helper 1 Responses in Swine. Vet. Immunol. Immunopathol. 100: 105-111. Dawson HD, Beshah E, Nishii S, Solano-Aguilar G, Morimoto M, Zhao A, Madden KB, Ledbetter TK, Dubey JP, Shea-Donohue T, Lunney JK, Urban, JF Jr. 2005. Localized multi-gene expression patterns support an evolving Th1/Th2-like paradigm in response to infections with Toxoplasma gondii and Ascaris suum in pigs. Infection and Immunity. 73: 1116-1128. Dvorak, C.M.T., K.A. Hyland, J.G. Machado, Y. Zhang, S.C. Fahrenkrug, and M.P. Murtaugh. 2004. Gene discovery and expression profiling in porcine Peyers patch. Vet. Immunol. Immunopathol. In press. Ernst, C.W., N.E. Raney, V.D. Rilington, G.A. Rohrer, J.A. Brouillette and P.J. Venta. 2004. Mapping of the FES and FURIN genes to porcine chromosome 7. Anim. Genet. 35:142-143. Farber, C.R., N.E. Raney, V.D. Rilington, P.J. Venta and C.W. Ernst. 2003. Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig. Cytogenet. Genome Res. 102:139-144. Flickinger, G.H., C.M.T. Dvorak, J.A. Hendrickson, M.P.Murtaugh, and M.S. Rutherford, 2004. Radiation hybrid mapping of porcine ESTs from porcine Peyers Patch. Plant and Animal Genome XII, San Diego, CA, January 11-14. Gaboreanu, A.M., L. Grapes, A. M. Ramos, J.-J. Kim and M. F. Rothschild. 2004. Characterization of an X-chromosome PCR-RFLP marker associated with fat deposition and growth in the pig. Animal Genetics 35: 401-403. Galina-Pantoja L, Solano-Aguilar GI, Mellencamp MA, Bastiaansen J, Lunney JK. 2004. Relationship between immune cells and pig growth on a commercial farm. Proc. 18th IPVS Congress, Hamburg, Germany, 2004, Vol. I. p.381. Gladney C, G Bertani, MK Nielsen, D Pomp 2004. Evaluation of gene expression in pigs selected for enhanced reproduction. I: Ovarian Follicles. J Anim Sci 82:17-31. Grapes, L., J.C.M. Dekkers, M.F. Rothschild, and R.L. Fernando. 2004. Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Genetics 166: 1561-1570. Grapes, L., M. Z. Firat, J. C. M. Dekkers, M. F. Rothschild, R. L. Fernando. 2004. Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci. American Association of Animal Science Midwest Region, Mar 15-17, Des Moines, IA Grapes, L., S. Rudd, R. L. Fernando, M. F. Rothschild. 2004. In silico SNP identification from porcine EST sequences and comparative analysis with human SNP density. Plant and Animal Genome XII, Jan 10-14, San Diego, CA Grindflek, E, N Hoen, H Sundvold, MF Rothschild, G Plastow and S Lien. 2004. Investigation of a Peroxisome Proliferator Activated Receptor gamma (PPARG) haplotype effect on meat quality and carcass traits in pigs. Anim. Genet 35:238-241. Holl JW, JP Cassady, D Pomp, RK Johnson 2004. A genome scan for QTL and imprinted regions affecting reproduction in pigs. J Anim Sci 82:3421-3429. Hu, Z-L, K. Glenn, A. M. Ramos, C. J. Otieno, and M. F. Rothschild. 2004. Expeditor: A Pipeline for Designing Pig Primers Using Human Gene Structure and Pig EST Information. Plant and Animal Genome XII, Jan 10-14, San Diego, CA Hu Z, Dracheva S , Jang W , Maglott D , Bastiaansen H , Reecy JM , Rothschild MF. 2005. PigQTLDB - A Pig QTL Database. Plant and Animal Genome XIII, Jan 15-19, San Diego, CA (Abstract) P839. Jiang Z, Wu X-L, Garcia MD, Griffin KB, Michal JJ, Ott TL, Charley T. Gaskins CT, Raymond W. Wright Jr. 2004. Comparative Gene-based In Silico Transcriptome Analysis of Different Tissues/Organs in Cattle. Genome 47:1164-1172. Kim, J.-J. and J. C. M. Dekkers. 2004. A combined line-cross and halfsib model to detect and characterize QTL in an F2 outbred cross population. American Society of Animal Science Annual meeting (Abstract). http://www.fass.org/2004/abstracts/414.PDF Kim, K.S., J. J. Kim, J. C. M. Dekkers, and M. F. Rothschild. 2004. Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mammalian Genome 15:552-559. Kim, K.S., J.J. Kim, J.C.M. Dekkers, and M.F. Rothschild. 2004. Polar overdominance imprinting is associated with growth and fat deposition in pigs. PAG XII p240 Kim, K.S., J.M. Reecy, W.H. Hsu, L.L. Anderson. 2004. Functional and phylogenetic analyses of a melanocortin-4 receptor mutation in domestic pigs. Domestic Animal Endocrinology 26: 75-86. Klee EW, Carlson DF, Fahrenkrug SC, Ekker SC, Ellis LB. 2004. Identifying secretomes in people, pufferfish and pigs. Nucleic Acids Res. 32:1414-21. Kunej T, Wu X-L, Milosevic Berlic T, Michal JJ, Jiang Z, Dovc P. 2005. Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferator-activated receptor-gamma coactivator-1 (PPARGC1) gene between Chinese and Western pig breeds. J. Anim. Breed. Genet. (in press). Liu G, Geurts AM, Yae K, Srinivasan AR, Fahrenkrug SC, Largaespada DA, Takeda J, Horie K, Olson WK, Hackett PB. 2005. Target-site Preferences of Sleeping Beauty Transposons. J Mol Biol. 346:161-73. Lunney, J.K. 2003. Are there immune gene alleles that determine whether a pig will be healthy? Genetics of Pig Health Symposium, Des Moines, IA. M. Boggess, Ed.; National Pork Board Press, DesMoines, IA. p.63-72. Martínez, M.M., G.M. Hill, J.E. Link, N.E. Raney, R.J. Tempelman and C.W. Ernst. 2004. Impact of pharmacological zinc and phytase on liver metallothionein concentration and mRNA abundance in the young pig. J. Nutr. 134:538-544. Moller M, Berg F, Riquet J, Pomp D, Archibald A, Anderson S, Feve K, Zhang Y, Rothschild MF, Milan D, Andersson L, Tuggle C 2004. High-resolution comparative mapping across pig chromocome 4 (SSC4), emphasizing the FAT1 region. Mammalian Genome 15:771-31. Mote, B. E., J. D. Loy, M. F. Rothschild. 2004. Identification of SNPs in the insulin-like growth factor gene family and subsequent mapping of IGF2R and IGFBP1 in pigs. Plant and Animal Genome XII, Jan 10-14, San Diego, CA Nadershahi A, Fahrenkrug SC, Ellis LB. 2004. Comparison of computational methods for identifying translation initiation sites in EST data. BMC Bioinformatics. 5:14. Rothschild, M.F. 2004. Porcine genomics delivers new tools and results: This little piggy did more than just go to market. Genetical Research 83:1-6. Rothschild, M.F. 2004. DNA advances offer big payoffs. Pig Progress Magazine. 20:1-3. Rothschild, M.F. J. P. Bidanel and D.C. Ciobanu. 2004. Genome Analysis of QTL for Muscle Tissue Development and Meat Quality. In: Muscle Development of Livestock Animals. Physiology, Genetics and Muscle Quality. Eds: M.F. W. te Pas, H.P. Haagsman and M.E. Everts. CABI Publishing pgs 247-266. Rothschild, M.F., G.S. Plastow and S. Newman. 2004. Patenting in animal breeding and genetics. In: WAAP Book of the Year 2003, Eds: A. Rosati, A. Tewolde and C. Mosconi. Pgs 269-280 Royaee AR, Husmann R, Dawson HD, Calzada-Nova G, Schnitzlein WM, Zuckermann F, Lunney JK. 2004. Deciphering the involvement of innate immune factors in the development of the host responses to PRRSV vaccination. Vet. Immunol. Immunopathol. 102: 199-216. Smith DM, Martens GW, Lunney JK, Ando A, Lee J-H, Ho C-S, Schook L, Renard C, Chardon P. 2005. Nomenclature for Factors of the SLA Class I System, 2004. Tissue Antigens. 65: 136-149. Stalder, K. J., M. Knauer, T. J. Baas, M. F. Rothschild, and J. W. Mabry. 2004. Sow Longevity. Pig News and Information. 25:53N-74N. Thomsen, H., J. C. M. Dekkers, H. K. Lee, and M. F. Rothschild. 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine J. Anim. Sci. 82:2213-2228. Tuggle, C.K., and Midwest Consortium. 2004. Finding the genes expressed in female reproductive tissues in pigs. Bulletin AS 650, January, 2004, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1950. Tuggle, C.K., X.W. Shi, L. Marklund, A. Stumbaugh, T.J. Stabel, M.A Mellencamp, L. Galina-Pantoja, and J. Bastiaansen 2004. Association of bacterial infection traits with genetic variation at candidate genes for porcine disease resistance. Bulletin AS 650, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1952. Tuggle, C.K., Y. Zhang, M.F. Rothschild, M.Moller, F. Berg, L. Anderson, J. Riquet, D. Milan, D. Pomp, A. Archibald, S. Anderson. 2004. A detailed gene map of pig chromosome 4, where the first quantitative trait locus in livestock was mapped. Bulletin AS 650, Animal Industry Report 2004, Iowa State University, Ames, IA ASL-R1951. Walker, S. E., O.W. Robison, C.S. Whisnant, and J.P. Cassady. 2004. Effect of divergent selection for testosterone production on testicular morphology and daily sperm production in boars. Journal of Animal Science. 82: 2259-63. Wang, C., C. Reilly, and M.S. Rutherford, 2005. A method for the comparison of cluster analyses. Statistica Sinica, in press. Wesolowski, S.R., N.E. Raney and C.W. Ernst. 2004. Developmental changes in the fetal pig transcriptome. Physiol. Genomics. 16:268-274. Wu X-L, Griffin KB, Garcia MD, Michal JJ, Xiao Q-J, Wright Jr. RW, Jiang Z. 2004. Census of orthologous genes and self-organizing maps (SOM) of biologically relevant transcriptional patterns in chickens (Gallus gallus). Gene 240:213-225. Zhang, X., N. Reilly, and M.S. Rutherford, 2005. An RNA interfering system for primary porcine alveolar macrophages. Anim. Biotechnol, in press. Zhang, X., N. Schreiber, M.P. Murtaugh, and M.S. Rutherford, 2004. Suppression of porcine reproductive and respiratory syndrome virus (PRRSV) infection by RNA-mediated gene silencing. Amer. Soc. Virol. 23rd Annual Meeting, Montreal, Canada, July 10-14. Zhao, S.-H. A. Erickson, and C.K. Tuggle. 2004. Physical and Linkage mapping of lymphocyte antigen 86 (Ly86) gene to porcine chromosome 7. Anim. Genet. 35:164. Zhao, S.-H. and C.K. Tuggle. 2004. Linkage mapping and expression analyses during early gestation in the pig of a novel gene, PLacentally Expressed Transcript 1 (PLET1). Anim. Genet. 35:72-74. Zhao, S.-H., D. G. Simmons, J.C. Cross, T.E. Scheetz, T.L. Casavant, M. B. Soares, and C.K. Tuggle. 2004. PLET1, a highly expressed and processed novel gene in pig and mouse placenta is transcribed but poorly spliced in human. Genomics 84:114-125.

Impact Statements

NRSP8 Objective 3. Genome Viewer at UC Davis integrates linkage information
This year the chicken genome sequence was published in Nature
Draft sequence of 3.3X coverage was completed this fall
An NRI Tools and Reagents Grant was awarded to Dr. Cockett and Dr. Womack to construct an ovine radiation hybrid panel, now using coordinators funds to distribute
Design oligos for a 13K oligo array, sent to 35 labs, primarily in US, also Europe and Asia
The Aquaculture Genome website was developed and moved to ISU this year.
PigQTLdb-a database for pig QTL information, can do other species

Date of Annual Report: 05/27/2008

Report Information

Annual Meeting Dates: 01/12/2008 - 01/15/2008
Period the Report Covers: 10/01/2006 - 09/01/2007

Participants

Aquaculture, Bioinformatics, Cattle, Equine, Pig, Poultry, Sheep/Goat Species Groups

Brief Summary of Minutes

Brief Summary of Minutes of the Annual Meeting:

OLD BUSINESS
A. Call to Order 3:40 pm - Mary Delany, NRSP-8 2007 Chair.
Motion to approve minutes from January 14, 2007 meeting by C Ashwell, NCSU; 2nd J Reecy, ISU; approval by acclimation.

B. Species Coordinator Reports
1. Sheep/Goat Report - Noelle Cockett, Sheep Genome Coordinator. NRSP8 funds have been used to leverage other funding for the International Sheep Genome Consortium. BAC end sequencing of the CHORI-243 ovine BAC library was completed under a USDA-NRICGP project, and the BAC end sequences were used to develop a sheep whole genome physical map. Combined data was compared to reference genomes, including human, cattle and horse, to give the final product, the virtual sheep genome map. A 1536 SNP array has been used for typing multiple populations, including the sheep reference population used for linkage map and the USU RH panel. New sets of primers have been generated for 1800 genes and are being typed across the RH panel. The RH and linkage maps are used to confirm the virtual sheep genome map. These primers may be useful for the planned goat RH panel. The push for a whole genome sequence for sheep will be discussed at the ISGC meeting on Monday, 1/14/08 at PAG. Several new members have been added to the NRSP8 sheep and goat committee. NRSP-8 coordinator funds are an important incentive for travel to the meeting.
2. Cattle - James Womack, Cattle Genome Coordinator. NRSP8 funds were used for travel for workshop speakers and students. Primers originally developed for RH panel are now being used successfully for RH map in other bovids. Bovine sequencing assembly is still continuing, much more effort will be required for full sequence assembly.
3. Equine - Ernest Bailey, Equine Genome Coordinator. Whole genome sequencing has already been completed for horse in 2007 at Broad Institute, MIT, MA. Plans are underway for development of new Illumina 60K SNP chip with support by Morris Animal Foundation. A major update of the horse genome webpage has been completed. It includes added information for scientists as well as for members of the horse industry. Ernie urged all species to evaluate their websites for utility by the general public and stakeholders.
4. Poultry - Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators. Chicken genome sequencing has been accomplished, two iterations, 2004 and 2006, even though not representative of a truly completed assembly nor fully annotated. However, the sequence availability has opened up major areas for future work including SNP efforts, comparative studies in turkeys, copy number variant investigations. There are currently no funds, but clear need and hope, for developing more comprehensive SNP chips for chickens. It is now much more evident that breeding companies have invested in genomics and are actively using tools developed by NRSP-8 scientists for their chicken work.
5. Swine - Max Rothschild, Swine Genome Coordinator. NRSP-8 funds have been used to support development and use of new expression arrays using long oligos. Slides printed at Univ. AZ are being validated at MSU, UMN and BARC in 2008 with NRSP-8 support. Swine genome sequencing is continuing at Sanger; it is coming together but not expected to be finished until mid-2009. It is currently at 2x coverage with 4-6x final coverage expected. A new swine SNP chip with 40-60K SNPs is being developed. Purchase of 700-1000 chips is planned for US labs using specifically stockpiled funds from the NRSP8 Swine Coordinator.
6. Aquaculture - John Liu, Aquaculture Genomes Coordinator. Currently 6 aquaculture species are covered under NRSP-8; at PAG 30 aquaculture species reported their research results. WGS of tilapia is scheduled by the Broad Institute. Genome BC is planning WGS for Atlantic salmon; the community is working on funding for that. New Co-Coordinator for Aquaculture is Caird Rexroad, ARS, Leetown, WV.
7. Database - James Reecy, Database Lead Coordinator. There has been recent funding for animal bioinformatics projects, e.g., Shane Burgess for GO annotation, Carl Schmidt for GallusGBrowse; Chris Elsik for bovine annotation, and Jim Reecy for expanding the web viewer to be used for many species. Jim Reecy is working with rat and mouse genome groups to develop comparative applications. Expertise and computer structure is available for developing needed relational databases; if want to pursue could take advantage of ISU supercomputers for different applications. There was a general email message with 2 surveys for NRSP-8 web tools. Please respond to provide input.

C. Administrator Reports
1. Lead Administrative Advisor - Colin Kaltenbach. There has been good progress by all the species Coordinators with improvements at both basic plus applied levels. The most important current issue is the NRSP-8 renewal. Note that the annual report must be submitted within 60 days. The writing for the new project has progressed very well, thanks to the leadership of NRSP-8 Chair, Mary Delany. Reviews to date have been very good. New species Coordinators are expected to be selected before Oct.1 2008, the start date for a new project. All scientists should remember to sign up for the new NRSP-8 project. Participation does not role over. Please contact your Experiment Station Director to add members for the new project (Appendix E form). All levels of participants are welcome, PIs, postdocs, and students.
2. Other Administrative Advisors - Eric Young and Bert Stromberg. Each affirmed the impact of the current NRSP-8 project and the importance of the efforts to renew it. It was noted that industry partners are allowed; contact Colin Kaltenbach for further information. Scientists from other countries are also welcome to participate in NRSP-8.
3. USDA-CSREES National Program Leader - Muquarrab Qureshi. NRSP-8 is a high impact project. It is impressive how many species sequencing have been completed since 2003. In 2008 numerous species sequencing are underway or being completed. These efforts are viewed as very important to the US government and its PMA and OSTP. This is viewed nationally as one of the best NRSP programs. The revised project has paid attention to USDA Animal Genome Blueprint www.csrees.usda.gov/nea/animals/pdfs/animal_genomics_blueprint.pdf
Animal genomics are valued at CSREES as evidenced by NRI grant rfps. Thanks to the bioinformatics efforts, to the QTL group, for its impact for industry. Approval of the NRS-P8 rewrite is underway. Once completed CSREES will expedite Coordinators selection. The aim is for a mid-June deadline. Remember to email species leadership changes to NRSP-8 Secretary, Joan Lunney so she can send the updates to Muquarrab Qureshi.

D. NRSP-8 Project Re-write Mary Delany
The new NRSP8 project objectives were each reviewed and approved.

NEW BUSINESS
1. Election of officers for 2008. Jerry Dodgson nominated Joan Lunney, USDA BARC, for chair and Ernie Bailey nominated Cecilia Penedo, UC Davis, for secretary. Both nominations were approved by acclamation.
2. Selection of next meeting location and date. Jerry Dodgson suggested the meeting be held next year at PAG on Sunday; approved by acclamation.
3. Meeting format. Jerry Dodgson noted that the Poultry group suggested a modification of the format of the NRSP-8 PAG meeting stating a need for joint species sessions at PAG for common animal genome related topics. Its difficult to move between the separate species meetings. The suggestion is for the species meetings to end by lunch on Sunday. This would open up time for a common scientific meeting for general topics for all species, e.g., SNPs would have been good this year. Motion: Jerry Dodgson moved that NRSP-8 scientists consider a Sunday afternoon joint animal session; 2nd by Sue Lamont. Discussion: Qureshi noted that this would improve cross-species communication. Liu said many scientists only stay the weekend so a larger session on Sunday is a good idea. Reecy asked why not go for earlier Sunday for this NRSP-8 plenary session? Cassady noted that now it is difficult to go to other species sessions; it is important particularly for people working on multiple species. There had been a previous agreement for swine meeting on Saturday and cattle on Sunday. This year cattle had a 2 day meeting Saturday and Sunday. Change in meeting schedule will depend on room availability; Cheng will check possibilities and ask Scherago for options. Species chairs will plan this session with the NRSP8 leadership and with Coordinators. All present approved the motion that NRSP-8 scientists consider a Sunday afternoon joint animal session. Motion was made by Qureshi to thank Mary Delany and Joan Lunney (2007 Secretary) for a good job with this NRSP8 meeting. Meeting adjourned at 5:30 pm.

Accomplishments

Progress toward Objective 1. Aquaculture. Catfish. Over 300 microsatellite markers derived from ESTs were mapped. To integrate the linkage and physical maps hundreds of microsatellites derived from BAC-end sequence were genotyped. Two BAC contig-based physical maps of the channel catfish were generated using fingerprints; combined contig size was about 931 and 961 Mb. Some 48,275 BAC end sequences were generated with 12,586 microsatellites identified. Salmonids. Eighty percent of the NCCCWA Swanson 10x BAC library clones were fingerprinted and BAC end-sequencing of 100,000 clones was completed by a collaborative partnership (Genoscope and INRA). Assignments of 27 Atlantic salmon linkages groups were made to the 29 chromosomes pairs. BACs were assigned to 46 of the 50 rainbow trout chromosome arms using FISH. Centromere assignments were made to the trout genetic maps. Tilapia. About 20,000 BAC clones were sequenced (Genoscope). The sequencing project was assigned by NIH-NHGRI to the Broad Institute. Oysters. A JGI/Standford project to sequence 58 BAC clones progressed. A BAC-based physical map was constructed of the Pacific oyster genome from a single inbred male. The library was fingerprinted (Genome Sciences Ctr). A project that progressed was the deep-sequencing of Pacific oysters ESTs from tissue and age-specific libraries. Work also continued for the eastern oyster in marker development. Shrimps. First order genetic maps have been published, marker development continues. Striped bass. New microsatellite markers were developed (~500) and creation of the first genetic linkage map is underway. Bioinformatics. Work focused on linking QTL data to the human and livestock genome sequences for researchers to transfer information between maps; in addition minor allele frequencies and microarray features have been included as available. Cattle. Contributions were made to the NIHGR bovine genome sequencing project technical committee. Equine. A first assembly of the horse genome was accomplished (Broad Institute) and the sequence was analyzed by the horse genome group; this involved sharing amongst numerous national and international lab from previously completed RH maps, linkage maps, and FISH markers. Comparative genomic questions can now be addressed between equine, other sequenced animal genomes and human. Pig New gene markers were identified, mapped and map integration continued with expansion of QTL map and physical maps. The sequencing consortium continued its fund raising efforts and a review of progress was published; sequencing continues to advance with significant coverage of all chromosomes. Poultry The chicken linkage map provides a framework for QTL and other mapping research and the platform on which the sequences have been assembled and linked to chromosomes. Prior SNP research was built upon by USDA NRI support of an US and EU consortium to genotype thousands of birds and utilizing the EL and W linkage families further enhancing the linkage map. A second SNP study was supported by coordination funds re-using SNP genotyping information and reagents combined this SNP data improve the linkage map and contributes to numerous on-going research to find causative genes involved in many chicken QTL. Sheep/Goats An ovine whole-genome RH 5,000-rad panel consisting of 88 clones was generated and used to construct map with 1306 markers. The result was 95 RH linkage groups over26 autosome. Progress continued with NRSP-8 collaboration in the International Sheep Genome Consortium to create new resources which includes a high coverage BAC library, end-sequencing, integrated ovine map, BAC physical map, development of the virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep ) and a 1,536 SNP chip. Progress toward Objective 2. Aquaculture. Catfish. About 300,000 EST clone sequences (200K from catfish, 100K from blue catfish) have been generated (project with Joint Genome Institute and NRSP-8 members). Salmonids. The community continues to identify ESTs from tissues and physiological conditions from a number of salmonids. Functional genomics involving global gene expression with respect to proteolysis and toxicological responses are producing candidate genes for further analysis. Two QTL were found in a study using clonal lines (WSU) and stress analysis with opposing effects. A growth QTL analysis found 22 QTL across 11 linkage groups with effects on numerous growth parameters. Tilapia. A major EST study was approved by the USDA-NRICGP to sequence 100,00 ESTs from a variety of tilapia libraries. Oysters. Deep sequencing of 16,000 Pacific oyster clones derived from multiple tissues and age-specific libraries has been completed and working is continuing. Shrimps. About 130,000 white shrimp EST clone sequences (from both ends) are being checked (Joint Genome Institute) against the physical library; these will be used to create a microarray. Striped bass. A new inter-disciplinary program of graduate education in aquaculture genomics was developed at NCSU with funding from the USDA CSREES Food and Agricultural Sciences National Needs Grants Program. This group has been very active in collaborative efforts for improved breeding and development of specialized stocks, with an emphasis on enhancing genetic diversity and commercially important traits. Bioinformatics. Focus was on curation of cattle, chicken and swine QTL information generated from hundred of manuscripts describing QTL or association tests for these species. The database was expanded to include sheep QTL information. Equine Numerous studies were conducted and published related to QTL analyses and also diseases involving bone, muscle, skin as well as coat color variants and aspects of performance and infectious disease. The work involved use of the genetic marker maps previously developed by NRSP-8. Pig QTL are reports in all chromosomes for numerous traits; imprinted QTLs continue to be discovered. Candidate gene analysis was successful with several gene tests used by the industry for traits including fat, feed intake, growth, meat quality, litter size and coat color. Poultry BAC libraries were extensively fingerprinted and integrated with linkage and gene maps and used to generate a second generation contig map updated in parallel with the second build of the chicken genome sequence. Similar efforts were undertaken for the turkey CHORI-260 library to generate a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. Over 21,000 BAC end sequences and 15,200 BAC overgo hybridization assignments were made to 1248 markers or genes. More tha 40,000 turkey BAC fingerprints were generated allowing a first generation physical map for turkey of about 5.6x coverage. Sheep/Goats A resource population was created by crossing Dorset ewes with East Friesian rams, with an F1 backcross to both parental populations. Phenotyping was initiated. Microsatellites will be used for genotyping. Research on the callipyge trait continued by analysis of gene expression (using bovine arrays). A QTL scan was initiated of a sheep population segregating parasite burden. A large scale EST sequencing project of 10,000 clones from a cDNA library from goat uterine/embryonic tissues was initiated. Progress toward Objective 3: Aquaculture. Catfish. Work progressed on creating chromosome-anchored ESTs with large sale informatic mining of microsatellites and SNPs Salmonids. Atlantic salmon and rainbow trout gene indices can be found at http://compbio.dfci.harvard.edu/tgi/tgipage.html Tilapia. The Gbrowse software has migrated to the University of Maryland, www.cichlidgenome.org . Shrimps. Archiving of EST and microarray can be found at www.marinegenomics.org . Bioinformatics. Extensive communication was held with curators of other relevant livestock-genomics databases, along with compilation of database information and assessment of content and function, to allow for US coordination efforts to focus on development in areas of high priority and utility. In addition alignment and display of microarray data was successful. On line tools were developed to generate PCR primers across species, a GO term counter and also graphing tools are accessible. An Animal Trait Ontology was developed. A bovine genome annotation meeting was co-hosted. Cattle Web site was maintained for on-line radiation hybrid mapping for investigators using the 5000 rad bovine RH panel available from the coordinator. Distribution of bovine reference family panel DNA (IBRP) was continued. Microsatellite primers were purchased and were distributed by the coordinator (quality tested by coordinator lab). Other tools are also available: RH panels of (5,000 and 12,000 rad)), BAC libaries, panel of 31 hybrid somatic cells. Equine Sharing of resources continued including reference families DNAs, primers, RH mapping resources, BAC clones (CHORI). Contributions were made to database develop for genetic data, BAC map data, SNP data. Pig The PigQTLdb serves as a repository for QTL related studies. There are 1,675 QTL in the database representing 246 pig trais. New functions have been added including tools to align pig RH map-human comparative maps, BAC physical maps, new microsatellite markers, pig SNPs from various sources and micro array elements against pig QTL. News and updates are communicated to membership routinely. A second generation novel 7-mer oligo microarray for profiling expression was developed. The informational materials are available to the community (no cost); the array can be purchased via the coordination unit. Validation is ongoing through a collaborative venture. Poultry The sequence is available on three browsers (UCSC, NCBI, Ensembl). Numerous unique and resource-packed databases and browsers are available and maintained by researchers supported by USDA-NRI funds along with the NRSP-8 Bioinformatics coordination site(s), all can be accessed by the NRSP-8 poultry genome website (http://poultry.mph.msu.edu ). Sheep/Goats Sequences from the CHORI-243 BES project are available via NCBI. Matches of the ovine to bovine and human sequences and clone identity are available through CSIRO (http://www.livestockgenomics.csiro.au/SheepGenomics ). Virtual sheep genome information and mammalian comparisons are available through the site.

Publications

Impact Statements

Cutting-edge genomic tools continue to be generated for the community in the form of reagents, high throughput assay systems, bioinformatic resources, and sequence data for all species designated which serves national and international researchers at very economical terms.
Sequence analysis is contributing to our understanding of comparative vertebrate biology, making it possible to understand genome organization and evolution in the context of production animal systems, model organisms and human.
Analysis of expression data is creating new information of molecular pathways and networks previously unexplored and highly relevant to commercial productivity and success with a continued focus on growth, reproduction and disease.