Brief Summary of Minutes of Annual Meeting

Members present: C. Ashwell, S. Burgess, H. Cheng, M. Delany, J. Dodgson, D. Foster, W. Kuenzel, S. Lamont, M. Miller, W. Muir, J. Petitte, T. Porter, M. Qureshi, K. Reed, D. Rhoads, M. Saif, J. Song, E. Wong, E. Young, H. Zhang, H. Zhou Visitors: J. Fulton, A. Paszek, Carl Schmidt The annual meeting was held in conjunction with the Plant and Animal Genome Conference and consisted of the Poultry Genome Conference followed by the Business Meeting. Meeting Schedule Poultry Genome Workshop Supported by a Grant from the USDA-CSREES (to T.E. Porter) SATURDAY 9:00 AM Welcome 9:10 AM Station report, USDA Avian Disease and Oncology Laboratory; Hans Cheng and Huanmin Zhang --"Genetic characterization of Marek's disease resistance" 9:40 AM Station report, University of Arkansas; Douglas Rhoads -- "Genetic analysis and mapping of sperm degeneration in broiler breeders" and Wayne Kuenzel -- "Potential genes involved in activation of gonadal development in male chicks" 10:30 AM Station report, University of California-Davis; Mary Delany -- "Cytogenetic analysis of telomeres in normal and transformed chicken cells" 11:00 AM Station report, City of Hope, National Medical Center; Marcia Miller -- "Potential Disease Resistance Genes in the Chicken MHC-B Extended Class II Region" 11:30 AM Station report, Mississippi State University; Shane Burgess -- "AgBase: Facilitating Analysis of Chicken Functional Genomics Datasets" 11:50 AM Station report, University of Georgia; Sammy Aggrey -- "Molecular basis for feed efficiency" 1:30 PM Station report, Purdue University; William Muir -- "Innate Genetic Differences In Birds Differing In Aggressive Behavior As Determined By Affymetrix Genechip Chicken Genome Array" 2:00 PM Station report, Texas A&M University; Huaijun Zhou -- "Development of new chicken genome array and its application" 2:30 PM Station report, Virginia Tech; Ed Smith -- "Dissection of genetic factors for immune response and round heart heart disease in birds" and Eric Wong -- "Differential expression of intestinal nutrient transporters in posthatch broilers" 3:30 PM Station report, North Carolina State University; Jim Petitte -- "Avian Primordial Germ Cells" and Chris Ashwell -- "Genomic Approaches To Identifying The Underlying Cause Of Traits Of Economic Importance In Poultry" 4:00 PM Station report, Michicgan State University; Jerry Dodgson --"Progress towards a Turkey Genome Physical Map and Antiviral RNAi in Chicken Cells" 4:30 PM Station report, Iowa State University; Susan Lamont and Jack Dekkers -- Application of high-density SNPs in chickens: linkage disequilibrium and trait-association results SUNDAY 8:30 AM Station report, University of Minnesota; Kent Reed -- "Refinement and application of genetic maps in the turkey" and Douglas Foster -- "Gene expression in a fully immortalized CEF cell line" 9:00 AM Station report, University of Maryland; Jiuzhou Song and Tom Porter -- "Characterization of genetic polymorphisms and gene expression related to body fat" 9:30 AM Roger Coulombe, Utah State University -- "Characterizing Genes Associated with Aflatoxin B1 Hypersensitivity in Turkeys" 10:30 AM Michael Romanov, Zoological Society of San Diego -- "Genomic resources and tools to investigate factors associated with chondrodystrophy in California condors" 11:15 AM Elisabeth Lebihan-Duval, Institut National de la Recherche Agronomique, France -- "Recent Results On The Genetic Variation Of Chicken Technological Meat Quality" 1:15 PM Fred Leung, University of Hong Kong -- "A Chicken Full-Length cDNA Database And Its Applications" 2:00 PM Helen Sang, Roslin Institute, Scotland -- "Applications Of Lentiviral Vector Transgenesis In The Chicken" The Business Meeting was called to order at 2:55 pm by Tom Porter, Chair of NC1008. T. Porter thanked the CSREES for funding to support the travel expenses of the invited speakers at the Workshop (Coulombe, Romanov, Lebihan-Duval, Leung, and Sang). J. Dodgson presented the NRSP8 Coordinators Report. The Second Build for the chicken genome was released May 2006. The coordinates form the First Build and the Second Build are different and some of the annotations have not been transferred to the Second Build. There are still some resources available to committee members such as BAC library filters and DNA microarryas (FHCC 13k, Agilent and Nimblegen arrays). The NRSP8 rewrite is due in 2007. Minutes from the 2005 Annual Report were approved. M. Saif, the administrative advisor reported that the NC1008 project terminates in Sept 2008 and that the rewrite for the NC1008 project is due by the end of 2007. The committee that reviews these projects will meet in January 2008. He congratulated the committee for an excellent workshop and for sending the reports electronically prior to the meeting. He reminded committee members to make sure that progress reports contain impact statements. Each subject should be accompanied by a 2-3 sentence impact statement, which can be easily extracted when needed. M. Saif also indicated that NC1008 was the only committee that held its Business Meeting at the end of the workshop. There is an advantage to conducting the Business Meeting prior to the workshop, especially during years when the rewrite is due, to allow sufficient time to discuss important issues. He is very supportive of the productivity and excellence of this committee and does not feel that there will be a problem with renewal. M. Qureshi introduced Eric Young, the new NRSP8 administrator for Poultry. He thanked T. Porter and K. Reed for organizing the workshop and conducting one of the best workshops, due to the number of invited speakers. He indicated that it was a challenge to provide the funds for the outside speakers during this year of federal budget uncertainty. He distributed a copy of his report, which provided personnel updates at CSREES and provided statistics for the USDA NRI competitive grants programs. There will be one vacant position open as National Program leader for Animal Science. All grants for 2007 must be submitted electronically via Grants.gov in pdf format. Committee members should review the instructions carefully and work with their institutional grants personnel early to ensure that they are prepared to process grants submitted electronically. M. Qureshi reported that 27% of the proposals in the Animal Genomics Program were funded with an average award size of approximately $500,000. The USDA is now tracking the number of graduate students (22) and postdocs (9) trained with CSREES grants. He encouraged members to keep including graduate students and postdocs in their grants. If Congress does not pass a budget by Feb 2007, the government will operate under continuing resolution for the rest of the year, which will likely result in some financial problems. The issue was raised from last years discussion about including Industry members. This was considered to be important for the committee and Janet Fulton and Albert Paszek were nominated and approved as members. Both agreed to be members. Site of the next meeting was not decided, but an email poll will be conducted to see if it should be held prior to PAG XV in San Diego Jan. 2008. T. Porter volunteered to write the 2006 annual report. The following volunteered to lead the rewrite of specific objectives of the Project. Objective 1: Chris Ashwell Objective 2: Jim Petitte Objective 3: Sue Lamont Chris Ashwell volunteered to assemble the rewritten project. The meeting was adjourned at 3:30 pm. Although significant concerns were raised in the ensuing email poll and the site for the next meeting, sufficient support did not exist for changing the venue at this time. Next year's meeting will be held again in conjunction with the Plant and Animal Genome conference. The meeting will be organized by Kent Reed and Tom Porter.

Objective 1. Develop High Resolution Integrated Maps to Facilitate the Identification of Poultry Genes and Other DNA Sequences of Economic Importance. ADOL continues to curate the East Lansing genetic map. In the past year, 710 SNPs were added, which brings the total number of genetic markers to 3209. The East Lansing and Wageningen maps were combined into a consensus map that contained 3850 genetic markers, which was used in the second genome sequence assembly. Of the 3072 SNPs screened in our Illumina panel generated in 2005, 233 changed chromosomal positions from the first to the second genome assemblies. At AR, the promoter regions from the chicken DAZL gene, a PGC specific promoter, has been cloned. The promoter is being fused to a reporter gene to allow us to determine time of induction and extent of expression (collaborator: NCSU). To protect scientifically valuable research genetic lines of highly inbred chickens, semen samples were collected again this year from all adult males of the 21 highly and partially inbred lines held at Iowa State University (IA). Semen samples were placed into the long-term cryopreservation bank in the National Animal Germplasm program in Ft. Collins, CO. At CA (City of Hope) work continues on construction of a gene map for the chicken MHC B and Y regions. The B map for Red Jungle Fowl now spans 242 kb and encompasses 46 genes including TRIM, C-type lectin and Ig superfamily type genes. At CA (UC Davis), research continued to explore variation for telomere length within genomes (among chromosomes) and among different genotypes. Differences among genotypes are evident as telomere profiles differ (slightly) between inbred lines, although locations for some mega-telomere loci are held in common. Work was also initiated to examine integration of MDV into the chicken genome using MDV-BACs (collaborator: H. Cheng). We are studying the hypothesis that there is targeted integration into the mega-telomeres. This work will assist in determining clonality of tumors within individuals and will establish commonalities (and/or preferences) of integration sites among individuals. A project emphasized in the lab during the prior two years developed in collaboration with the USDA-ADOL. Our objective was to study single nucleotide polymorphisms (SNPs) in seven UCD developmental mutant stocks so to map and identify potential markers for carrier-testing and begin to resolve potential candidate loci. Five of seven mutations (cm, dp-1, dp-4, po, wg-2) were mapped to a chromosome and in one case (wg-2) a defined region of several Mb. One candidate gene (Sef; similar expression to fibroblast growth factor) in the region of wg-2-associated SNPs was studied at a single developmental time point post limb outgrowth (Sef expression has previously been found to be in the right place at the right time in limb outgrowth, suggesting this is a reasonable candidate despite a location). However, the relative transcript expression of forelimbs and hindlimbs among the genotypes (+/+, +/wg, wg/wg) was similar although the ratios relative to brain (highest expressing tissue) within each genotype showed a slight genotype-effect. Efforts are underway at MI to generate a turkey BAC-contig map that is aligned with the chicken genome sequence. To date, we've completed over 40,000 turkey BAC fingerprints. Generation of ~20,000 turkey BAC end sequences nearly done. Additional shotgun sequencing of the turkey genome is planned. We've made nearly 8000 turkey BAC-marker assignments. This includes most of the existing STS genetic linkage map markers available in turkey, as well as numerous chicken markers. Over 700 genetic markers (primarily microsatellites) have been genotyped by researchers at MN on the UMN/NTBF and Nte mapping families. Combined analysis of both mapping families found 684 markers to be significantly linked to at least one other marker in the UMN database; 41 linkage groups have been identified. Through the use of common marker sets, in silico mapping and RH mapping, 35 of the 41 linkage groups are aligned with the chicken genome. Over 1700 turkey DNA sequences have been compared and assigned to positions with the chicken genome sequence. Two MHC-B BAC clones were identified and sequenced. Gene annotation indicates three class IIb genes in the sequenced turkey haplotype, one more than in the sequenced chicken haplotype. DNA sequence polymorphisms (SNPs) identified in the turkey MHC were used to develop genotyping assays for genetic mapping in the UMN/NTBF mapping families. Segregation analysis found two turkey MHC-B SNPs (BTN2 and C4) were genetically linked. Genetic linkage was not observed between the MHC-B and MHC-Y SNPs. Gene expression profiles of turkey skeletal muscle between and within growth-selected and control turkey lines at three developmental stages were compared using three turkey skeletal muscle cDNA libraries. To date, each non-subtracted library has been extensively sequenced (15,648 reads) with 6624, 5088 and 3936 reads from the 18-day embryo, 1-day post-hatch poult, and 16-wk post-hatch turkey, respectively. NC has been using microarray analysis to identify differential chicken gene expression in response to dietary nutrient restriction. Adaptation to P and Ca restricted diets has been previously reported in chickens. Animals respond to nutrient restriction by increasing absorption rates and utilization efficiency, which decreases excretion of the restricted nutrients. NC investigated if birds had the capacity to adapt similarly and used microarray analysis to identify genes whose expression was significantly altered in response to dietary P restriction. Previous experiments with regard to market weight have suggested that broiler chickens fed a restricted phosphorus diet from hatch to 90 hours of age were better suited to a restricted diet fed from 22 to 38 days of age than those fed a control diet in the first 90 hours post hatch. Microarray analysis was used to identify additional genes whose expression was significantly altered in response to this dietary P restriction. Interestingly the list of differentially expressed genes includes the intestinal Na/Pi cotransporter type IIb previously shown to be induced by dietary P restriction (Yan et al, 2007). Within this list there are genes that are involved in cell signaling, transport, and proliferation. The studies conducted at NC are some of the first to focus on nutritional and thus environmental impact of poultry production from a genetic point of view. This information obtained in the studies of nutrition related genes can then be used to implement marker assisted selection practices to identify and select for superior individuals in breeding programs that can reduce the environmental impact of nutrients in the excreta. The outcome of this research will provide a means to improve the innate ability of poultry to utilize environmentally important nutrients such as N and P, therefore reducing their excretion, and therefore greatly aid in reducing the cost of poultry litter disposal and in maintaining the productivity of poultry industry. At TX, a new chicken 44K Agilent whole genome array was developed. To validate this new developed chicken 44K array, 4 major tissue samples (liver (L), spleen (S), cecal tonsil (CT), and ileum (IL)) from the six two weeks old commercial broiler chickens were collected. There were four biological replicates for every two tissues comparison. The results demonstrated that this new developed chicken oligonucleotide array is very informative and tissue-specific. Objective 2. Develop Methods for Creating New Genetic Variation in Poultry by Gene Transfer and Chromosome Alteration CA completed and published research in collaboration with Origen Therapeutics (Burlingame, CA) on long term culture procedures of stem cells (embryonic stem cells, primordial germs cells) and their utilization/utility for making transgenics (Origen) and analysis of features related to genome stability and differentiation status of these cell systems (UCD). Differentiation status was examined by profiling telomerase activity, a hallmark feature of cells with high proliferative potential (toti-, multi-potent cells as well as renewable stem cells). Both the long term embryonic stem cells (cultured from Stage X embryos) pre- and post manipulation and primordial germ cells (cultured for hundreds of days) were found to be telomerase positive. Long term cultures were typically found to be normal in terms of karyotype to the level of analysis conducted, although occasionally cell lines were found with macrochromosome aberrations (in one case involving a deletion of a large portion of GGA 2) and of course these would not be suitable for use. Thus, the analysis of cells to be used for transgenic purposes as to their chromosomal status is an important parameter which needs consideration. MI generated a Gateway-compatible entry plasmid containing the micro RNA (miRNA) sequence of chicken miR-30a that allows RNAi cassettes to be inserted into an ALV subgroup(A) retroviral destination vector. RNAi targeted either against the viral envB gene or host receptor tvb gene has been shown to be an effective antiviral strategy against subgroup(B) ALV. Similar reductions in plaque number and size of Marek's disease virus (serotype III) have been achieved by constructs that target the essential gB glycoprotein gene. Work conducted at MN indicated that the phenotype of the spontaneously immortalized chicken cell line SC-2, changed dramatically at about passage 80, appearing smaller and more compact than at earlier passages. Passage 43 SC-2 cells expressed undetectable levels of p53 mRNA, but the elevated levels detected by passage 95 did not correlated to functional protein activity. The altered expression of genes involved in the p53 and Rb pathways, specifically, p53 and p21WAF1, may have contributed to the immortalization of the SC-2 CEF cell line. The regulation of chicken p15INK4b was shown to increase substantially at senescence and was transcriptionally silenced in two immortalized chicken cell lines. Short-hairpin RNA (shRNA)-mediated knockdown of chicken INK4b provided only modest lifespan extension, suggesting that other factors contribute to senescence in CEFs. The transgenic chicken line developed in NC, now designated NCSU-Blue1, is a useful tool for several areas of research, and they have been used for studies of early embryonic development (Stem Cells Dev. (2006) 15:17-28). Functional beta-galactosidase was expressed in all tissues of the digestive tract, particularly in the small intestine. This should give the birds the ability to hydrolyze lactose, which normally cannot be utilized as a source of energy in birds. NC examined this possibility through a feeding trial in which isocaloric diets containing 0, 5, 7.5 and 10% dietary lactose were fed to wild type and transgenic birds from 10-24 days of age. Transgenic birds were observed to have a greater ability to digest lactose through the hydrolysis of lactose to galactose and glucose than those of nontransgenic wild-type chicks at least by 10%. The greater lactose digestibility of the transgenic birds does not result in better growth performance. These studies point to the fact that the nutritional requirements of transgenic poultry can be significantly altered and the nutritional requirements may need to be re-evaluated in birds with high expressing transgenes. The culture of PGCs from male and female embryos at the NC station will have significant applications in reproductive biology, developmental biology and transgenics. Work with the NCSU-Blue1 line of transgenic chickens suggests that the nutritional requirements of transgenic poultry may need to be evaluated, particularly in high expressing lines Objective 3. Develop, Compare and Integrate Emerging Technologies with Classical Quantitative Genetics for Improvement of Economic Traits in Poultry. ADOL continues to work on genetic resistance to Mareks disease. Evaluation of the line 6 x 7 F2 resource population for two-epistatic interactions identified a large number (239) of highly significant interactions involving loci located throughout the genome that account for MDV viremia titers in infected birds. Recombinant congenic strains (RCS) developed from lines 6 (background) and 7 (donor) were evaluated and shown that the 19 RCS generated are both genetically and phenotypically variable from one another, thus, serve as unique genetic resources for identifying and characterizing QTLs or candidate genes conferring genetic resistance to Mareks disease as well as other traits of interest. Based on prior two-hybrid results, the MDV protein R-LORF10 may be the responsible protein in the novel up-regulation of MHC class II cell surface expression based upon defined MDV recombinants via MDV-BAC clones. In addition, a worldwide and genome-wide assessment was made for commercial poultry by genotyping 2551 informative SNPs spaced throughout the chicken genome on 2580 unique individuals including 1440 commercial birds. Results from several analytical methods combined with theory indicate that individual commercial breeding stocks have lost 70% or more genetic diversity of which no more than 10% can be recovered by combining all breeds from commercial poultry. These results emphasize a need for concerted national and international efforts to preserve chicken biodiversity. AR initiated a SNPlotype mapping project for Sperm Degeneration and Sperm Mobility, with partial support from Director funds. A detailed full-length cDNA sequencing project to characterize over 450 novel transcripts expressed in the chicken reproductive tract was begun. In work conducted at IA, Fatness QTL were mapped in two F2 resource populations that were established by crossing one broiler sire with dams from two unrelated highly inbred lines (Fayoumi and Leghorn). Thirty-three markers in 8 regions on chromosomes 1 to 4 showed significant association (1% FDR) with AF. We evaluated the efficiency of the pQTL transcriptome mapping approach, which combines the mRNA pooling with eQTL transcriptome mapping. Through simulation studies, we found that pQTL transcriptome mapping using the standard regression method achieved statistical power comparable to the power that can be achieved by eQTL transcriptome mapping. We evaluated the influence of heritability used in analysis of SNP data on the significance and magnitude of SNP effects and their standard errors (SE) and developed an approximation that would allow results for alternate levels of heritability to be obtained without reanalysis, using actual data from a broiler breeder population. Use of SNP-trait associations detected in one population for use in other populations requires LD between loci to be consistent across populations. We used genotype data for over 100 SNPs on two chromosomes from 10 broiler breeder lines to evaluate similarities in LD across the lines and compared this to phylogenetic relationships among lines estimated using differences in SNP allele frequencies. The correlation between LD measured by r2 between lines for SNP at short distances is a good predictor of line relationships, although somewhat less so than the typical allele frequency-based distance. At MD, analysis of global gene expression in the neuroendocrine system of chickens genetically selected for high and low body weight or body fat was accomplished using custom cDNA microarrays produced in collaboration with DE. Hundreds of genes were identified that are expressed at different levels in the pituitary gland or hypothalamus in either fat versus lean chickens or high growth versus low growth chickens. These are excellent candidate genes for controlling body fat and body growth in chickens. Single nucleotide polymorphisms (SNPs) have been identified in many of these genes and a study has been initiated at MD to assess these SNPs for their utility as genetic markers in marker assisted selection programs. mRNA splicing variants have been identified in BDNF, which is known to control body fat accumulation. In collaboration with ADOL, it was determined that these BDNF splice variants are associated with chicken lines which accumulate different amounts of body fat. In other work at MD, novel computer algorithms are being developed for analysis of microarray results from time-series experiments. This work has the potential to identify numerous genetic markers for use in marker assisted selection programs aimed at improving growth performance and reducing body fat in broiler chickens. MS has developed and demonstrated computational tools, as well as proteomics techniques, to improve the structural annotation of the chicken genome. This is especially important for identifying those genes unique to birds for which obvious mammalian homologs do not exist. Resistance to MD is the result of complex interactions between chicken and MDV genes and current research is aimed at defining one molecular genetic mechanism that may be a critical determinant of this host-pathogen relationship. Results demonstrate the applicability of high throughput proteomics followed by computational modeling to understand biological function in the chicken. Databases are being maintained and computational tools developed that facilitate chicken researchers ability to derive biological meaning from their functional genomics datasets. This is broadly applicable throughout the chicken research community regardless of the field of study. NC has focused on the identification of QTL for immune response and disease resistance in lines differentially selected for antibody production. NC has developed a new resource population which consists of reciprocal crosses of lines divergently selected for antibody response to sheep red blood cells. Selection for immune response parameters may lead to improved general disease resistance in part due to they are difficult to measure and have low to moderate heritability. To determine if SNP allele frequencies were altered as a result of selection for SRBC response in the HAS and LAS lines a representative sample of unrelated individuals were genotyped using the Illumina GoldenGate Assay system. Illumina evaluated 3072 SNP loci dispersed across the genome. No loci were fixed within either line. 30 genome regions consisting of one or more SNPs showed significant differences in allele frequency between the HAS and LAS lines. These loci are located on 19 chromosomes with specific regions of Gga1, Gga2, Gga5, Gga6, Gga18, and Gga28 that correspond to regions previously associated with disease resistance or antibody response QTL. The nature of selection appears to favor the contribution of a large number of loci with relatively small effects as opposed to single loci with large effects. Further characterization of these selected lines and their intercross population will provide additional information on the complexity of antibody response in the chicken as well as the genetic basis of selection in general. A second round of SNP genotyping by Illumina also supported in part by the NRSP-8 species coordinator with cooperation from 5 institutions is currently underway and includes samples to selectively genotype the F2 generation of this population. In work at TX, the chicken 44K Agilent array was used to analyze RNA of heterophils from SE-resistant (line A) and SEsusceptible chickens (line B) with SE (I) or without SE infection (N). The results indicated that: for the comparisons of SE infection with non-infection, 3096 genes in line A and 3312 genes in line B were differentially expressed (P<0.05). In the comparison of linage (line A and line B) difference, 4377 genes in the non-infected and 4333 genes in the infected groups have shown differential expression (P<0.05). The results discovered in the present study have laid a solid foundation to elucidate cellular and molecular mechanisms of SE infection in chickens. RNA interference was used to specifically inhibit expression of NF- B and to elucidate the role of NF- B in the signal transduction pathway of Salmonella infection in chicken HD11 cell line. After a 24-hour transfection, the treated cells were followed by Salmonella enteritidis infection (MOI=100) or non-infected for 1 and 4 hours. Four candidate genes (interleukin (IL)-1², IL-6, Toll like receptor (TLR)-4 and TLR-15) were selected to examine the effect of NF-kB inhibition on gene expressions with SE infection by the real-time quantitative PCR. The results showed that, with 1.6-fold of inhibition of NF- B gene expression, the gene expression of IL-6 was consistently and significantly increased at both 1 hour and 4 hours with Salmonella challenge; whereas the gene expression of IL-1² and TLR-15 were increased at 4 hours only. The results of the current study have laid foundation for uncovering the gene networks of innate immune system in chickens. VA has examined the spatial and temporal expression of nutrient (amino acid, peptide, and monosaccharide) transporters in the small intestine of late embryonic and early posthatch chicks. Expression of these transporters showed different developmental profiles and different levels in the intestinal segments. The peptide transporter PepT1 is expressed highest in the duodenum, the monosaccharide transporters are expressed highest in the jejunum and the amino acid transporters are expressed predominantly in the ileum. Because early nutrition plays an important role in overall growth performance, optimizing diets to match the absorptive capacity of the posthatch chick may result in increased growth performance.

ARKANSAS, UNIVERSITY OF ARKANSAS, Fayetteville, AR D.P. Froman, J.D. Kirby, and D.D. Rhoads. (2006) An Expressed Sequence Tag Analysis of the Chicken Reproductive Tract Transcriptome. Poultry Science 85:1438-1441. Klein S., Jurkevich A., Grossmann R. (2006). Sexually dimorphic immunoreactivity of galanin and colocalization with arginine vasotocin in the chicken brain (Gallus gallus domesticus). J Comp Neurol 499:828-839. Kuenzel, W.J. and C.D. Golden. 2006. Distribution and change in number of Gonadotropinreleasing hormone-1 neurons following activation of the photoneuroendocrine the chick, Gallus gallus. Cell Tissue Res. 325(3):501-512. Kuenzel, W.J., A.M. Rowland, P.B. Pillai, T.I. OConnor-Dennie, J.L. Emmert and Wideman. 2006. The use of vitamin A-deficient diets and jugular vein ligation intracranial pressure in chickens, Gallus gallus. Poultry Sci. 85:537-545. CALIFORNIA, CITY OF HOPE, Duarte, CA Miller, MM. 2006. Why do we need to conserve what we have? A post-genome sequencing perspective on existing chicken strains. Poult Sci. 85:243-245 Hunt, H.D., Goto, R.M., Foster, D.N., Bacon, L.D., and Miller, M.M. 2006. At least one YMHCI molecule in the chicken is alloimmunogenic and dynamically expressed on spleen cells during development. Immunogenetics, 58:297-307. CALIFORNIA, UNIVERSITY OF CALIFORNIA, DAVIS, Davis, CA Chang, H., and M.E. Delany. 2006. Complicated RNA splicing of chicken telomerase reverse transcriptase revealed by profiling cells both positive and negative for telomerase activity. Gene 379:33-39. van de Lavoir M.-C., Diamond, J.H., Leighton, P.A., Mather-Love, C., Heyer, B.S., Bradshaw, R., Kerchner, A., Hooi, L.T., Gessaro, T., Swanberg, S.E., Delany, M.E., and Etches, R.J. 2006. Germline transmission of genetically modified primordial germ cells. Nature 441: 766-769. van de Lavoir, M.-C., Mather-Love, C., Leighton, P., Diamond, J.H., Heyer, B.S., Roberts, R., Zhu, L., Winters-Digiacinto, P., Kerchner, A., Gessaro, T., Swanberg, S., Delany, M.E., and R.J. Etches. 2006. High-grade transgenic somatic chimeras from chicken embryonic stem cells. Mechanisms of Development 123:31-41. Delany, M.E. 2006.Avian genetic stocks: the high and low points from an academia researcher. Poultry Science 85:223-226. OHare, T.H., and M.E. Delany. 2005. Telomerase gene expression in the chicken: telomerase RNA (TR) and reverse transcriptase (TERT) transcript profiles are tissue-specific and correlated with telomerase activity. AGE 27:257-266. Swanberg, S.E. and M.E. Delany. 2006. Telomeres in aging: Birds. In Handbook of Models for Human Aging (editor: M. Conn), Chapter 29, p. 339-349. Academic Press (Elsevier, Inc.). Burlington MA (USA). GEORGIA, UNIVERSITY OF GEORGIA, Athens, GA Lagarrigue S., Pitel F., Carré, W, Abasht B., Le Roy P., Neau A., Amigues Y. Sourdioux M., Simon, J., Cogburn L., Aggrey S., Leclercq B., Vignal A., and Douaire M., 2006. Mapping quantitative trait loci affecting fatness and breast muscle weight in experimental meat type chicken lines divergently selected on fatness. Genetics Selection Evolution. 38:8597. Nahashon, S.N., S.E. Aggrey, N.A. Adefope, A. Amenyenu, and D. Wright, 2006. Growth characteristics of pearl gray Guinea Fowl as predicted by the Richards, Gompertz, and Logistic models. Poultry Science 85:359363. Abasht B. Pitel F., Lagarrigue, S.,BihanDuval, E., Pascal, P., Olivier, D., Simon J., Cogburn L., Aggrey S., Vignal A., and Douaire M., 2006. Fatness QTL on chicken chromosome 5 and interaction with sex. Genetics Selection Evolution 38: 297311. Nahashon, S.N., S.E. Aggrey, N.A. Adefope, A. Amenyenu, and D. Wright, 2006. Modeling growth characteristics of meat type Guinea Fowl. Poultry Science 85: 943946. Carre, W., X. Wang, T. E. Porter, Y Nys, J. Tang, E. Bernberg, R. Morgan, J. Burnside, S. E. Aggrey, J. Simon and L. A. Cogburn, 2006. Chicken genomic resources: sequencing and annotation of 37,557 ESTs from single and multiple Tissue cDNA libraries and CAP3 assembly of a chicken gene index. Physiological Genomics 25:514524. INDIANA, PURDUE UNIVERSITY, West Lafayette, IN Devlin, RH Sundström, LF and WM Muir. 2006. Interface of biotechnology and ecology for environmental risk assessments of transgenic fish. Trends in Biotechnology 24:89-97. Sun,W., V. M. Margam, L. Sun, G. Buczkowski, G. W. Bennett, B. Schemerhorn, W. M. Muir and B. R. Pittendrigh 2006. Genome-wide analysis of henobarbitalinducible genes in Drosophila melanogaster Insect Molecular Biology. Insect Molecular Biology 15: 455464 W.M. Muir, J. Romero-Severson, S.D. Rider Jr., A. Simons, and J. Ogas. 2006. Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis. J. Data Science 4, 323-341. Muir, W.M. and P. Bijma. 2006. Incorporation of competitive effects in breeding programs for improved performance and animal well-being. WCGALP 17:806-812 Bijma, P. and W. M. Muir 2006. Genetic analysis and improvement of traits affected by interaction among individuals WCGALP 17:974-980 IOWA, IOWA STATE UNIVERSITY, Ames, IA Abasht, B. Dekkers, J.C.M, and Lamont, S.J. 2006. Review of quantitative trait loci Identified in the chicken. Poultry Sci. 85:2079-2096. Cheeseman, J.H., Kaiser, M.G., Ciraci, C., Kaiser, P. and Lamont, S.J. 2006. Breed effect on early cytokine mRNA expression in spleen and cecum of chickens with and without Salmonella enteritidis infection. Devel. Comp. Immunol. 31: 52-60. Grapes, L., M. Z. Firat, J.C.M. Dekkers, M.F. Rothschild, and R.L. Fernando. 2006. Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci using identity-by-descent. Genetics 172: 1955-1965. Hangalapura, B. N., Kaiser, M. G., van der Poel, J.J., Parmentier, H. K., and Lamont, S. J. 2006. Cold stress equally enhances in vivo pro-inflammatory cytokine gene expression in chicken lines divergently selected for antibody responses. Develop. Comp. Immunol. 30:503-511. Hasenstein, J.R., Zhang, G., and Lamont, S.J. 2006. Analyses of five gallinacin genes and the Salmonella enterica serovar enteritidis response in poultry. Infect. Immun. 74:3375-3380. Kaiser, M.G., J.H. Cheeseman, Kaiser, P., and Lamont, S.J. 2006. Cytokine expression in chicken peripheral blood mononuclear cells after in vitro exposure to Salmonella enterica serovar Enteritidis. Poultry Sci 85:1907-1911. Lamont, S.J. 2006. Perspectives in chicken genetics and genomics. Poultry Sci. 85:2048-2049. McElroy, J.P., Kim, J.J., Harry, D.E., Brown, S.R., Dekkers, J.C., and Lamont, S.J. 2006. Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens. Poultry Sci. 85:593-605. McElroy, J.P., Zhang, W., Koehler, K.J., Lamont, S.J., and Dekkers, J.C.M. 2006. Comparison of methods for analysis of selective genotyping survival data. Genet. Selec. Evol. 38:637-655. Soller, M., Weigend, S., Romanov, M.N., Dekkers, J.C.M., and Lamont, S.J. 2006. Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance. Poultry Sci. 85:2061-2078. Tuggle, C.K., J.C.M. Dekkers, and J.M. Reecy. 2006. Integration of structural and functional genomics. Anim. Genet. 37 S1:1-6. Ye, X., Avendano, S., Dekkers, J.C.M. and Lamont, S.J. 2006. Association of twelve immune-telated genes with performance of three broiler lines in two different hygiene environments. Poultry Sci. 85:1555-1568. Ye, X., McLeod, S., Elfick, D., Dekkers, J.C.M., and Lamont, S.J. 2006. Rapid identification of single nucleotide polymorphisms and estimation of allele frequencies using sequence traces from DNA pools. Poultry Sci. 85: 1165-1168. Zhou, J., Deeb, N., Ashwell, C.M., and Lamont, S.J. 2006a. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain. Poultry Sci. 85:1700-1711. Zhou, J., Deeb, N., Ashwell, C.M., and Lamont, S.J. 2006b. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. II. Body composition. Poultry Sci. 85: 1712-1721. MARYLAND, UNIVERSITY OF MARYLAND, College Park, MD Porter TE, Lopez ME, Mike R, Huberty AF (2006) The increase in prolactin-secreting cells in incubating chicken hens can be mimicked by extended treatment of pituitary cells in vitro with vasoactive intestinal polypeptide (VIP). Domest Anim Endocrin 30:126134 Porter TE, Ellestad LE, Fay A, Stewart JL, Bossis I (2006) Identification of the chicken growth hormone-releasing hormone receptor (GHRH-R) mRNA and gene: regulation of anterior pituitary GHRH-R mRNA levels by homologous and heterologous hormones. Endocrinology 147:2535-2543 Ellestad LE, Carre W, Muchow M, Jenkins SA, Wang X, Cogburn LA, Porter TE (2006) Gene expression profiling during cellular differentiation in the embryonic pituitary gland using cDNA microarrays. Physiol Genomics 25(3):414-25 Carre W, Wang X, Porter TE, Nys Y, Tang J, Bernberg E, Morgan R, Burnside J, Aggrey SE, Simon J, Cogburn LA (2006) Chicken Genomics Resource: Sequencing and Annotation of 37,557 ESTs from Single and Multiple Tissue cDNA Libraries and CAP3 Assembly of a Chicken Gene Index. Physiol Genomics 25:514-24 MICHIGAN, MICHIGAN STATE UNIVERSITY, East Lansing, MI Sazanov, A.A., A.L. Sazanova, V.A. Stekolnikova, A.V. Trukhina, A.A. Kozyreva, A.F. Smirnov, M.N. Romanov, L.-J. Lawson-Handley, T. Malewski and J.B. Dodgson. 2006. Chromosomal localization of the UBAP2Z and UBAP2W genes in chicken. Animal Genetics 37:72-73. Niikura, M., J.B. Dodgson and H.H. Cheng. 2006. Direct evidence of host genome acquisition by the alphaherpesvirus Marek's disease virus. Archives of Virology 151:537-549. Niikura, M., J.B. Dodgson and H.H. Cheng. 2006. Stability of Mareks disease virus 132 bp repeats during serial in vitro passages. Archives of Virology 151:1431-1438. Romanov, M.N. and J.B. Dodgson. 2006. Cross-species overgo hybridization and comparative physical mapping within avian genomes. Animal Genetics 37:397-399. Siegel, P.B., J.B. Dodgson and L. Andersson. 2006. Progress from chicken genetics to the chicken genome. Poultry Science 85:2050-2060. MINNESOTA, UNIVERSITY OF MINNESOTA, St. Paul, MN Chaves, L.D., T.P. Knutson, S.B. Kreuth, and K.M. Reed. 2006. Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo). Animal Genet, 37:130-138. Christman, S.A., B.-W. Kong, M.M. Landry, H. Kim, and D.N. Foster. 2006 Contributions of differential p53 expression in the spontaneous immortalization of a chicken embryo fibroblast cell line. BMC Cell Biology, 7:27. Hunt, H.D., R.M. Goto, D.N. Foster, L.D. Bacon, and M.M. Miller. 2006. At least one YMHCI molecule in the chicken is alloimmunogenic and dynamically expressed on spleen cells during development. Immunogenetics 58:297-307. Kim, S-H., J. Rowe, H. Fujii. R. Jones, B. Schmierer, B-W Kong, K. Kuchler, D. Foster, D. Ish-Horowicz, and G. Peters. 2006. Upregulation of chicken p15INK4b at senescence and in the developing brain. J. Cell Sci. 119:2435-2443. Kong B.-W., L.K. Foster, and D.N. Foster. 2006. Comparison of Avian Cell Substrates for Propagating Subtype C Avian Metapneumovirus Virus Res. 116:58-68. Reed, K.M., M.K. Hall, L.D. Chaves, and T.P.Knutson. 2006. Single nucleotide polymorphisms for integrative mapping in the turkey (Meleagris gallopavo). Animal Biotech., 17:73-80. Reed, K.M., L.R. Sullivan, L.K. Foster, L.D. Chaves, and F.A. Ponce de Leon. 2006. Assignment of linkage groups to turkey chromosome 1 (Mga1). Cytogenet Genome Res, 115: 176-178. MISSISSIPPI STATE UNIVERSITY, Starkville, MS McCarthy, F. M., S. M. Bridges, N. Wang, G. B. Magee, W. P. Williams, D. S. Luthe, and S. C. Burgess. 2006. AgBase: a unified resource for functional genomics analysis in agriculture. Nucleic Acids Research. Fiona M McCarthy, Nan Wang, G. Bryce Magee, Bindu Nanduri, Mark L. Lawrence, Evelyn Camon, David Hill, Mary E Dolan, W. Paul Williams, Dawn Luthe, Susan M Bridges and Shane C Burgess. 2006. AgBase: A Functional Genomics Resource for Agriculturally Important Species. BMC Genomics. 7(1):229 Corzo, A., M. T. Kidd, W. A. Dozier, 3rd, L. A. Shack, and S. C. Burgess. 2006. Protein expression of pectoralis major muscle in chickens in response to dietary methionine status. Br J Nutr 95:703-8. McCarthy, F. M., A. M. Cooksey, N. Wang, S. M. Bridges, G. T. Pharr, and Burgess. S. C. 2006. Whole Organ Proteomics and Proteogenomics Using the Model Avian Genome. Proteomics. Proteomics 6:2759-71. NORTH CAROLINA, NORTH CAROLINA STATE UNIVERSITY, Raleigh, NC Yan F, Angel R, Ashwell CM. 2007. Characterization of the chicken small intestine type IIb sodium phosphate cotransporter. Poult Sci. 86(1):67-76. Zhou H, Deeb N, Evock-Clover CM, Ashwell CM, Lamont SJ. 2006. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. II. Body composition. Poult Sci. 85(10):1712-21. Zhou H, Deeb N, Evock-Clover CM, Ashwell CM, Lamont SJ. 2006. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain. Poult Sci. 85(10):1700-11. Sun JM, Richards MP, Rosebrough RW, Ashwell CM, McMurtry JP, Coon CN. 2006. The relationship of body composition, feed intake, and metabolic hormones for broiler breeder females. Poult Sci. 85(7):1173-84. Fulton JE, Juul-Madsen HR, Ashwell CM, McCarron AM, Arthur JA, O'Sullivan NP, Taylor RL Jr. 2006. Molecular genotype identification of the Gallus gallus major histocompatibility complex. Immunogenetics. 58(5-6):407-21. Cho, J., K. Choi, T. Darden, P.R. Reynolds, J.N. Petitte, and S.B. Shears. 2006. Avian multiple inositol polyphosphate phosphatase is an active phytase that can be engineered to help ameliorate the planet's "phosphate crisis" Journal of Biotechnology, 126(2): 248-59. Mozdziak P.E., R. Wysocki, J. Angerman-Stewart, S.L. Pardue, and J.N. Petitte. 2006. Production of chick germline chimeras from fluorescence-activated cell-sorted gonocytes. Poultry Science, 85:1764-1768. Petitte, J.N. 2006. Avian germplasm preservation: Embryonic stem cells or primordial germ cells? Poultry Science, 85(2):237-242. Mozdziak, P.E., Q. Wu, J.M. Bradford, S. L. Pardue, C. Giamario, S. Borwornpinyo, and J. N. Petitte. 2006. Identification of lacZ insertion site and beta-galactosidase expression in transgenic chickens. Cell and Tissue Research, 324 (1): 41-53. TEXAS, TEXAS A & M UNIVERSITY, College Station, TX Haghighi HR, Gong J, Gyles CL, Hayes MA, H. Zhou, Sanei B, T. Hayes, Chambers JR, Sharif S. 2006. Probiotics stimulate production of natural antibodies in chickens 2006. Clinical and Vaccine Immunology 13:975-980. Aimie J. Sarson, Abdul Careem M.F., H. Zhou, S. Sharif. 2006. Transcriptional analysis of host responses to Mareks disease virus infection Viral Immunology 19:747-758. Zhou, H. N. Deeb, C.M. C. M. Ashwell, and S. J. Lamont. 2006. Genome-wide linkage analysis to identify chromosome regions affecting phenotypic traits in the chicken. II. Body composition. Poultry Sci. 85:1712-1721. Zhou, H. N. Deeb, C.M. C. M. Ashwell, and S. J. Lamont. 2006. Genome-wide linkage analysis to identify chromosome regions affecting phenotypic traits in the chicken. I. Growth and Average daily gain. Poultry Sci. 85:1700-1711. Abdul Careem M.F., B.D. Hunter, A. J. Sarson, A. Mayameei, H. Zhou, S. Sharif. 2006. Mareks Disease Virus-induced transient paralysis is associated with cytokine gene expression in the nervous system. Viral Immunology 19:167-176. USDA, USDA-ARS; AVIAN DISEASE ONCOLOGY LABORATORY, East Lansing, MI Niikura, M., Dodgson, J, and Cheng, H.H. 2006. Direct evidence of host genome acquisition by the alphaherpesvirus Mareks disease virus. Arch. Virol. 151:537-549. MacLea, K.S., and Cheng, H.H. 2006. Cloning and expression of deoxyribonuclease II from chicken. Gene 373:44-51. Niikura, M., Dodgson, J, and Cheng, H.H. 2006. Stability of Mareks disease virus 132 bp repeats during serial in vitro passages. Arch. Virol. 151:1431-1438. Ben-Avraham, D., Blum, S., Granevitze, Z., Weigend, S., Cheng, H, and Hillel, J. 2006. W-specific microsatellite loci detected by in silico analysis map to chromosome Z of the chicken genome. Anim. Genet. 37:180-181. Backström, N., Brandström, M., Gustafsson, L., Qvarnström, A., Cheng, H., and Ellegren, H. 2006. Genetic mapping in wild bird population. Genetics 174:377-386. Atzmon, G., Ronin, Y.I., Korol, A., Yonash, N., Cheng, H., and Hillel. J. 2006. QTLs associated with growth traits and abdominal fat weight and their interactions with gender and hatch in commercial meat-type chickens. Anim. Genet. 37:352-358. Zhang, H.M., Hunt, H.D., Kulkarni, G.B., Palmquist, D.E., and Bacon, L.D. 2006. Lymphoid organ size varies among inbred lines 63, 72 and their thirteen recombinant congenic strains of chickens with the same major histocompatibility complex. Poult. Sci. 85:844-853. Liang, L., Yan, R., Ma, W., Zhang, H.M., and Wang, S. 2006. Exploring RPE as a source of photoreceptors: differentiation and integration of transdifferentiating cells into embryonic chick eyes. IOVS. 47:5066-5074. Dennis, R., Zhang, H.M., and Cheng, H.W. 2006. Effect of selection for resistance and susceptibility to viral diseases on concentrations of dopamine and immunological parameters in six-week-old chickens. Poult. Sci. 85:2135-2140. VIRGINIA, VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY, Blacksburg, VA Hartman S, Taleb SA, Geng T, Gyenai K, Guan X, Smith E. 2006. Comparison of plasma uric acid levels in five varieties of the domestic turkey, Meleagris gallopavo. Poultry Sci. 85(10):1791-4. Lin KC, Gyenai K, Pyle RL, Geng T, Xu J, Smith EJ. 2006. Candidate gene expression analysis of toxin-induced dilated cardiomyopathy in the turkey (Meleagris gallopavo). Poultry Sci. 85(12):2216-21. Ray , S.A. , Drummond, P.B., Shi, L., McDaniel, G.R., and Smith, E.J., 2006. Mutation Analysis of the Aggrecan gene in chickens with tibial dyschondroplasia. Poultry Science 85:1169-1172.