Annual/Termination Reports:

[03/11/2009] [01/10/2010] [02/25/2011] [03/31/2012] [02/20/2013]

Report Information

Participants

Aggrey, Samuel - University of Georgia
Ashwell, Christopher - North Carolina State University
Bitgood, James  University of Wisconsin
Burgess, Shane  Mississippi State University
Cheng, Hans  USDA Avian Disease and Oncology Lab
Dekkers, Jack  Iowa State University
Delany, Mary  University of California, Davis
Dodgson, Jerry  Michigan State University
Emara, Marlene  University of Delaware
Foster, Douglas  University of Minnesota
Grossman, Michael  University of Illinois
Kuenzel, Wayne  University of Arkansas
Lamont, Susan  Iowa State University
McCarthy, Fiona  Mississippi State University
Miller, Marcia  City of Hope, Beckman Research institute
Muir, William  Purdue University
Petitte, James  North Carolina State University
Ponce de Leon, Abel - University of Minnesota
Porter, Tom  University of Maryland
Reed, Kent  University of Minnesota
Rhoads, Douglas  University of Arkansas
Rosa, Guilherme  University of Wisconsin
Smith, Edward  Virginia Polytechnic Institute and State University
Song, Jiuzhou  University of Maryland
Wong, Eric - Virginia Polytechnic Institute and State University

Brief Summary of Minutes

Meeting chaired by Eric Wong (NC-1170) and Huanmin Zhang (NRSP-8 Poultry).

Business meeting opened at 10:43 AM on Sunday, January 11, 2009.

Members: C. Ashwell* (NC), S. Burgess* (MS), H. Cheng* (ADOL), M. Delany* (CA), J. Dodgson* (MI), D. Foster** (MN), J. Fulton*** (Hy-Line), W. Kuenzel** (AR), S. Lamont* (IA), J. Petitte** (NC), M. Qureshi (CSREES representative), K. Reed* (MN), D. Rhoads* (AR), G. Rosa* (WI), Y M. Saif (Administrative Advisor), E. Wong** (VI), H. Zhang*** (ADOL) H. Zhou* (TX)
Guests: C. Schmidt (DE)

* = NC-1170 and NRSP-8 Poultry
** = NC-1170 only
*** = NRSP-8 only

1. Remarks from the project administrators.

1.a. Muquarrab Qureshi, CSREES Representative.

The agency is aware of the genomic science in the poultry group and its excellent contributions.
The NRSP-8 project has been renewed for 5 years, thanks to Mary Delany for her leadership with that project re-write. The review committee praised the quality of the proposal. CSREES will cease to exist October 1, 2009, and become NIFA (National Institute of Food and Agriculture). It will be headed by a Director, who is a political appointee for 6 years. Six focus areas are defined, and one includes animal health, production and products. There are already directors for each of the divisions, and they are working on the roadmaps for their divisions of the Institute. Also, the NRI program is transitioning to AFRI (Agriculture and Food Research Institute). The amount to be appropriated is not yet known.

1.b. Y.M. Saif, Administrative Advisor.

Congratulations on the approval of the new project, and the excellent progress and interdependence of the research projects.

2. New business.

Wong noted that we have little new business, because the project renewal was successful, and we are finishing the first year of our two-year officers cycle, so the officers will remain as:

NC-1170: Wong, chair; Lamont, secretary.
NRSP-8 Poultry: Zhang, chair; Zhou, secretary

3. Old Business

3.a. Potential new members.

The following were identified as potential new members: Carl Schmidt, Dave Froman, Roger Coulombe, and Rami Dalloul.

3.b. S-1037 Project overlap potential.

The previous years minute said to invite that group to join us here in San Diego. Aggrey was chair of S-1037, and the invitation was extended to him by Wong, but S-1037 did not follow up the invitation to hold a joint meeting.

3.c. Next meeting venue.

Motion (Rhoads/Petitte) to meet on Saturday and Sunday (January 9 and 10, 2010) preceding the next PAG meeting in San Diego, was approved unanimously.

3.d. Chicken-specific needs from the NRSP-8 Bioinformatics Coordinators.

The group had thoughtful discussion of the best ways to articulate, and then direct, input to the Bioinformatics coordinators for the needs of the poultry genome community. Topics included the following. High-throughput sequence is now standard, and more and more people may find that data processing is the research bottle-neck. Students (and other researchers) need to train for effective use of a variety of browser sites. It is hard to keep up on what is available and best for chicken data. There is concern regarding the splitting of data and resources over many non-linked sites, making it difficult to locate. Parker Anton is working towards a MOD for chickens, however, NIH does not want to fund this now. This may, however, be an opportune time to implement some parts of the NIH proposal. We need a species federation to represent the community. It is trivial to set up a front page for the species, such as: BirdBase. The process for individuals to give input to Bioinformatics Coordinators is by any communication medium they wish (phone, personally, email, etc.) to Jim Reecy (Coordinator) or to Shane Burgess or Sue Lamont (poultry-researcher members of the Bioinformatics team). We need a bio-informatics database that combines genomic data with all other data types are needed. A subcommittee of Burgess, Schmidt and Lamont was formed (NRSP-8 poultry bioinformatics liaison subcommittee), and intends to circulate a brief proposal in February for review and comment by the NC-1170 members and NRSP-8 Poultry members. A request to describe the computational capabilities of the Bioinformatics coordinators was requested, and will be included in a future distribution of information from the Bioinformatics Coordinators office. A question arose about what educational needs exist. Short courses could be delivered at no cost to the NRSP-8 membership. This could be done in real-time webinar, or as a tutorial to be done at leisure, or on-site (for sufficient people). Some universities might give 1-credit for participation. Topics identified included Perl programming and How to use GBrowse. Other topics might also be useful. It is important for the instructions to be very clear to the novice, without extreme technical language, and intuitive to use.

4. NRSP-8 Poultry Business.

4.a. Jerry Dodgson and Hans Cheng, NRSP-8 Poultry Genome Coordinators Report.

The written coordinators report was distributed in advance of this meeting, and contains the details. An excellent update on the chicken genome sequence was given yesterday by M. Groenen. Regarding use of last years Coordination funds, they supported participation in the 60K SNP chip, Affy and Agilent (44 and 244) arrays. Some support of the turkey sequencing project. Communicate requests for coordination funds requests to Dodgson and Cheng; then they will survey the NRSP-8 poultry group. Microsatellite primers kits are no longer being made, because the NRSP-8 group is not requesting them. Feel free to request support to attend the NRSP-8 meeting for an NRSP-8 member or a grad student (7 were supported this year). There is one Jorgensen award for a poultry student, and Coordinators also give some support to the poultry students. Students must submit an abstract and make an application for the Jorgensen award to be eligible. Input was encouraged input into selection of excellent speakers for the general PAG program.

4.b. New member.

It was moved (Dodgson /Reed) to invite Carl Schmidt to membership into the NRSP-8 Poultry committee. The motion was approved unanimously.

4.c. 2010 meeting format of NRSP-8 meeting.

The format of next years meeting will be the same, with a species-inclusive symposium on Sunday afternoon. It is possible to invite guest speakers to the NC-1170/NRSP-8 Poultry workshop, but they get only $100 (up to 5 per session), which basically limits the invitations to those who already plan to attend the conference (PAG or workshop). The Workshop Chair is paid for, and the two chairs (NC-1170 and NRSP-8 Poultry) alternate who gets covered each year.

4. d. CSREES Animal Program Leader

Muquarrab Qureshi reported that CSREES Animal Program Leader Pete Burfening will be retiring in 2009, so we should think of nominees to fill this important position.

4. e. Turkey genome.

Kent Reed reported a plan to apply for Tools and Reagents funding for turkey sequences, and letters of support may be requested.

Motion to adjourn (Rhoads, Delany) unanimously approved.
Meeting adjourned at 11:48 a.m.

Minutes respectfully submitted by Susan J. Lamont, Secretary, NC-1170, on 14 January 2009.

Accomplishments

Accomplishments<br /> <br /> Objective 1, Develop high resolution integrated maps to facilitate the identification of poultry genes and other DNA sequences of economic importance<br /> <br /> IA maintains a number of chicken genetic resource populations, which have been shared among a number of researchers. ADOL continues to develop the East Lansing genetic map. The chicken consensus genetic map was enlarged to 9,285 markers by combining the East Lansing, Wageningen, and Uppsala maps. Recombination rates have been found to vary between the East Lansing and Uppsala maps (RJF x WL) and the Wageningen map (broiler cross) as well as on different chromosomes.<br /> <br /> Telomeres and the MHC locus continue to be regions that are being actively investigated. CA has analyzed telomeres and telomerase function in different genotypes and cell lines. The number and location of megatelomeres was found to differ among various chicken genotypes (UCD 001 and UCD 003). COH has characterized the MHC-B and MHC-Y gene regions, in particular SNPs and indels present in the 14 MHC-B haplotypes. In collaboration with CA, the order of gene regions on chromosome 16 has been determined to be centromere-NOR-MHC-Y-MHC-B. The peptide binding preferences for two alleles at the MHC class I locus for classical antigen presentation, the BF2 locus, have been identified. COH has identified one MHC-B gene, BG1, which contributes to Mareks disease (MD) resistance. CA has used cytogenetic analysis to map the MD virus integration sites in MD tumors.<br /> <br /> Gene expression analyses of economically important genes are being studied using DNA microarrays or real time PCR. NC is developing focused 70-mer, multiple spot microarrays that allow higher sensitivity detection of changes in gene expression. These arrays can detect significant changes in gene expression of plus or minus 7%. AR has been profiling novel transcripts expressed in the chicken reproductive tract. Many of these transcripts are non coding RNAs that are developmentally regulated and either testis or ovary-specific. The effect of photostimulation and/or administration of sulfamethazine on the expression of FSH and prolactin, which regulate gonadal development have been examined. Sulfamethazine was found to act not only at the level of the brain but also at the level of the pituitary to advance gonadal development. AR has showed that arginine vasotocin and corticotrophin releasing hormone play a role in the stress response in birds. AR and TX have identified genes involved in the immune response, cell cycle regulation, metalloproteinases, and cell metabolism that are differentially expressed in chicken embryo lung cells upon infection with laryngotracheitis virus. To begin to dissect the regulatory elements of two important nutrient (di- and tri-peptides and glucose) transporter genes, VA has mapped both positive and negative-acting regulatory regions in both the chicken peptide transporter 1 (PepT1) and sodium glucose transporter (SGLT1) genes. CA is studying the molecular basis for the wingless-2 mutation. The expression of a candidate gene TSEN-2, which is involved in a complex that removes introns from pre-tRNAs has unfortunately not shown a consistent pattern of differences for tissue type or embryonic age.<br /> <br /> Sequencing, mapping, and functional genomics analysis of the turkey genome are being pursued collaboratively. A consortium has been established for the sequencing of the turkey genome. The consortium consists of researchers from the Roslin Institute, Utah State University, Virginia Tech, and Michigan State. MI continues to generate a physical and comparative map of the turkey genome. From a new library, 38,400 BACs have been fingerprinted and end sequenced to generate contigs. Cytogenetic analysis was used to integrate this map with turkey chromosomes and localize gaps, inversions and translocations between chicken and turkey genomes. CA and MI have explored micro-rearrangements between the chicken and turkey genome. MN has begun an investigation of the turkey MHC. The aims are to sequence the turkey MHC-B locus and identify haplotype markers (SNPs). MHC-B and RFP-Y BAC clones have been identified and sequenced. The RFP-Y BAC clone has been annotated. MN, OH and MI are collaborating on a project to identify differentially expressed muscle genes at different developmental stages. MN is investigating the genetics of aflatoxin sensitivity. The sequence of the CYP1A5 gene has been determined and 6 GST genes have been identified. The genetics of cardiac disease is also being investigated by MN. <br /> <br /> Objective 2, Develop methods for locating new genetic variation in poultry by gene transfer and chromosome alteration<br /> <br /> Transgenic chickens are being generated using retroviral vectors or primordial germ cells. MI is investigating the use of RNAi technology in transgenic chickens to provide protection against avian leukosis virus and Mareks Disease virus. Retroviral vectors containing the RNAi constructs were introduced into the newly laid egg. These transgenic chickens showed significantly reduced MD virus viremia, along with modest reductions in MD and increased survival. NC continues to culture chicken primordial germ cells (PGCs) and evaluate their ability to migrate to the germinal ridge of early embryos. Genes associated with primordial germ cell migration have been identified by DNA microarray. Catenin alpha 3 has been identified as a candidate gene associated with avian germ cell migration. Epidermal growth factor has been found to stimulate proliferation of chicken PGCs.<br /> <br /> Stem cell research in chickens is an active area of research. ADOL is investigating chicken stem cell antigen 2 (SCA2) as a putative MD resistance gene. The profile of tissue-specific and differential expression between susceptible and resistant chickens was determined. In addition to MHC genes that confer MD resistance, non MHC genes have also been identified, which affect MD resistance and MD vaccine efficacy. MN is attempting to develop chicken inducible pluripotent stem (iPS) cells by transfecting chicken orthologs to the mammalian iPS genes into primary chicken embryo fibroblasts or DF1 cells. Foci of cells that are refractile and loosely attached have been observed, which may be iPS cells. <br /> <br /> MN is developing an infectious avian metapneumovirus that contains biomarkers (GFP, 6XHis tag) for use as a vaccine virus for tracking in the field following a vaccination program.<br /> <br /> Objective 3, Develop, compare, and integrate emerging technologies with classical quantitative genetics for improvement of economic traits in poultry<br /> Mareks Disease remains an active area of collaborative research. ADOL is identifying genes that confer genetic resistance to MD using a genome-wide test to screen for genes that show allelic differential expression in response to MD virus challenge. Genomic and deep transcriptome sequencing of line 6 (MD resistant) and line 7 (MD susceptible) will reveal potential SNPs, copy number variations, and allelic differential expression. Furthermore, recombinant MD viruses lacking viral proteins have been generated to determine their effect on MHC class II expression and virulence. Maryland is investigating the potential influence of MD virus exposure on epigenetic regulation as it relates to MD incidences and risk.<br /> <br /> The search for QTLs associated with genes of economic importance continues. IA has used high density SNP maps to identify markers associated with egg quality and egg production phenotypes. Expression QTL analysis was performed to identify cis-and trans-acting SNPs that regulate expression of several cytokine genes from Salmonella challenged chicks. Polymorphisms near the transcription factor NFKB resulted in trans regulation of these cytokine genes. Differential expression of cytokine genes in heterophils was found in commercially selected and non-selected genetic lines. Intensity data from Illumina Infinium assays can be used to estimate allele frequencies in DNA pools, resulting in substantial savings in genotyping costs. A panel of evenly distributed low density SNPs across the genome can be used to estimate genomeassisted breeding values of selection candidates in pedigreed populations. The use of genomic selection in admixed and crossbred populations was evaluated by simulation, allowing genetic improvement of purebreds for performance of their cross bred descendents in the field.<br /> <br /> NC continues to identify QTL for immune response and disease resistance in lines differentially selected for low and high antibody production. A number of QTLs associated with antibody production were identified in F1 and F2 populations. AR has identified QTLs that affect sperm mobility and sperm degeneration and QTLs that affect ascites. GA continues to map main epistatic sex-specific and QTLs for body composition. Seventeen main effect QTLs and several sex-specific and sex-antagonistic QTLs for breast meat yield, thigh yield, and abdominal fatness have been identified. A program (miR-Explore) for predicting pre-miRNAs has been improved and has been used to identify all miRNA like structures in the chicken genome.<br /> <br /> Gene expression analyses of candidate genes are an ongoing goal. MD continues to identify gene networks expressed within the hypothalamus that control feed intake and metabolism in the broiler chicken. A network of 5 genes that regulate metabolic pathways are associated with regulating feed intake. MD is identifying and functionally characterizing genes regulated by Wnt signaling involved in the induction and migration of neural crest cells. Three putative target genes have been characterized by in situ hybridization and immunohistochemistry and are being investigated through overexpression and knockdown assays in the chick embryo. TX has investigated genome-wide host response to pathogen infection using DNA microarrays. Expression profiling of chicken spleen and bursa in response to Campylobacter infection revealed a number of differentially expressed genes in resistant and susceptible broiler lines. A similar analysis revealed differentially expressed genes in heterophils following Salmonella challenge. Differentially expressed microRNAs in chicken lung and trachea were profiled following avian influenza virus infection.<br /> <br /> Because DNA microarrays are costly and thus only a limited number are used in an experiment, WI has studied five different strategies to optimally select subsets of individuals for transcriptional profiling. The genetic dissimilarity and phenotypic extremes with genotypes methods had the smallest mean square error on QTL effects and maximum sensitivity on QTL detection and thus outperformed the other selection strategies. Two stage designs for gene expression analysis are often utilized which involve DNA microarray (1st stage) and real time PCR (2nd stage). Sixty percent of the available replicates should be used in Stage 1 to maximize sensitivity while controlling the false discovery rate. Two non-parametric approaches (kernel and RKHS regression) were found to be superior strategies for incorporating genomic information into genetic evaluations. Interactions between genome and environmental factors need to be considered in association of complex traits. <br /> <br /> IN and WI have collaborated on a project to develop a mixture model for the analysis of small microarray experiments. The Mean-Difference-Mixture-Model was found to be superior to other methods and was advantageous in experiments with few replicates, poor signal to noise ratios, or non homogeneous variances. Functional genomics was used to reveal physiological mechanisms associated with aggression and stress in two lines of birds. The KGB and DXL lines differ greatly in levels of stress response and aggression in social environments. A highly significant node classified as sensory perception to smell was identified.<br /> <br />

Publications

Impact Statements

1. The completion of the draft sequence and the development of genetic and physical maps of the chicken genome have allowed for the identification of genes that control growth and reproduction as well as disease resistance and susceptibility. This will result in more efficient production and a safer and healthier food product for the consumer.
2. Mareks Disease is a highly contagious, viral neoplastic disease in chickens. New insights into the genes and molecular mechanisms that lead to the onset and propagation of this disease have been identified. This knowledge can be used to develop novel strategies to reduce the incidence and severity of the disease.
3. Turkey is the fourth economically most important species in the U.S. Sequencing and mapping of the turkey genome will facilitate the identification of genes that control economically important traits, enhance disease resistance, and facilitate the completion of the chicken genome.

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Report Information

Participants

Aggrey, Samuel, University of Georgia
Ashwell, Christopher, North Carolina State University
Burgess, Shane, Mississippi State University
Cheng, Hans, USDA Avian Disease and Oncology Lab
Dekkers, Jack, Iowa State University
Delany, Mary, University of California, Davis
Dodgson, Jerry, Michigan State University
Foster, Douglas, University of Minnesota
Kong, Byung-Whi, University of Arkansas
Kuenzel, Wayne, University of Arkansas
Lamont, Susan, Iowa State University
Miller, Marcia, City of Hope, Beckman Research institute
Muir, William, Purdue University
Petitte, James, North Carolina State University
Ponce de Leon, Abel, University of Minnesota
Porter, Tom, University of Maryland
Reed, Kent, University of Minnesota
Rhoads, Douglas, University of Arkansas
Rosa, Guilherme, University of Wisconsin
Song, Jiuzhou, University of Maryland
Taneyhill, Lisa, University of Maryland
Wong, Eric, Virginia Polytechnic Institute and State University
Zhang, Huanmin, USDA Avian Disease and Oncology Lab
Zhou, Huaijun, Texas A&M

Brief Summary of Minutes

Minutes of NC-1170/NRSP-8 Poultry Business Meeting
January 10, 2010

Meeting chaired by Huanmin Zhang (NRSP-8 Poultry) and Eric Wong (NC-1170).

Business meeting opened at 10:23 AM on Sunday, January 10, 2010.

Members present: S. Burgess* (MS), H. Cheng* (ADOL), M. Delany* (CA), J. Dodgson* (MI), D. Foster** (MN), J. Fulton*** (Hy-Line), B.-W. Kong** (AR), S. Lamont* (IA), K. Reed* (MN), D. Rhoads* (AR), Y M. Saif (Administrative Advisor), C. Schmidt (DE)***, J. Song** (MD), E. Wong** (VI), H. Zhang* (ADOL), H. Zhou* (TX)

Guests: D. Burt (Roslin/U Edinburgh), M. Hughes (USC), S. Redmond (IA), H.-C. Liu (NCSU), Peter DEustachio (NYU)

* = NC-1170 and NRSP-8 Poultry
** = NC-1170 only
*** = NRSP-8 only
(classification per NIMMS participant list)

1. Comments from Project Administrators

1.a. Dr. M. Saif, Administrative Advisor

The projects midterm review will take place this year. Progress reports and minutes must be submitted in timely fashion. The NC advisory committees look for evidence of IMPACT in their evaluation, as well as productivity and cooperation between states, evidence of leveraging of funds from other sources, and strong publication record. Dr. Saif commented that our project performance appears very good to date.

1.b. Dr. M. Qureshi, NIFA Representative

Sent his regrets in advance to the membership that he was unable to attend.

2. Old business

2.a. Minutes of 2009 meeting

Minutes were approved when the draft was circulated in January, 2009, and were posted in the NIMSS site as submitted.

3. New business

3.a. Next meeting venue.

Motion (Delany/Schmidt) to meet on Saturday and Sunday (January 15-16, 2011) preceding the next PAG meeting in San Diego, was approved unanimously. Hans Cheng requested that comments of the program and whole PAG meeting (all aspects) be relayed to him, to pass to the PAG organizers for program and meeting improvement.

3.b. Election of officers

NC-1170 Chair. Motion (Dodgson/Delany) that secretary Lamont move to the position of chair for two years was approved.

NC-1170 Secretary. Motion (Dodgson/Reed) to elect Rhoads to position of secretary for two years was approved.

NRSP-8 Chair. Motion (Rhoads/Delany) that secretary Zhou move to the position of chair for two years was approved.

NRSP-8 Secretary. Motion (Reed/Delany) to elect Schmidt to position of secretary for two years was approved.

3.c. Status of potential new members

Dr. Saif reported that several new members were added to the project recently and are included in the NIMSS database.

4. NRSP-8 Poultry Business.

4.a. NRSP-8 Poultry Genome Coordinators Report (Dodgson and Cheng).

The written coordinators report was distributed in advance of this meeting, and contains the details of 2009 activities. In the past year, the NRSP8 poultry genome coordinators funds have been primarily used to provide seed money for the turkey genome sequence and SNP chips (60K) for the good of the NRSP-8 poultry research community, and about $5,000-7,000 on travel. Dodgson requested that, if not already done, each member send him an estimate of additional funds that were obtained or leveraged by NRSP-8 support, for reporting purposes. The coordinators can provide a little seed funding, but not support a whole project. Input for next years funding usage was requested. The annual budget is anticipated to be about $65,000.
Within the objectives of this 5-year term is to improve populations. Discussion on research priorities continued.

Do we need more poultry species sequenced? The duck sequence is already done by BGI, with manuscript to be submitted soon by Li Ning. Data are already loaded in ENSEMBL. Burt has sequenced Japanese quail.

What about a new chicken genome build? Within the year, UMD will release a new build of the chicken genome (not Wash U, where priorities have changed). Although some additional regions are available now (Z and MHC), it is important to have one official assembly. Schmidt indicated willingness to post Z chromosome data (or other information) on GBrowse. It is currently in GenBank with delay pending publication.

Is there any thought in Europe about how to get the missing chromosomes? No, this is not grant-fundable as a stand-alone project. The data are probably already available as a by-product of other work, but this does not cover the assembly and annotation. An activity deleted from a prior proposal was to have FHCRC flow-sort for the small chromosomes to get the sequence.
Reed indicated there is money to sequence the turkey, and perhaps they should flow-sort to get good microchromosome sequence. A motion (Burgess/Schmidt) to form a subcommittee to examine the technical aspects of getting the sequence of the small chromosomes and report back to group via NIMSS email was approved. The committee members from NRSP-8 are: Delany, Reed, Cheng, Schmidt, and the following will be invited to advise (ex officio): Burt, Groenen, Warren.

5. Poultry Bioinformatics Subcommittee Report

The BirdBase site has been designed and is up for a period of two months for community feedback. The NRSP-8 group will be reminded via NIMSS. Suggestions of additional links are encouraged.

6. Other new business: potential approaches to new AFRI grants program structure

Schmidt suggested developing a megaproposal to maintain stocks of chicken and turkey, collect phenotypes, and characterize targeted populations, including informatics. This could address the feeding the world priority, climate change and energy usage (feed efficiency).
Poultry is a winner in global feeding the world (more so than swine and cattle). For industry to use the information for genetic improvement, it needs to be out in the public and accessible for use. Saif suggests considering a CAP-like project in the area, for example, of genomics of disease resistance

Motion to adjourn (Lamont/Dodgson) unanimously approved. Meeting adjourned at 11:35 a.m.

Minutes respectfully submitted by Susan J. Lamont, Secretary, NC-1170, on 12 January 2010.

Accomplishments

Objective 1, Create and share data and technology to enhance the development and application of genomics and systems biology in poultry<br /> Sequencing, mapping, and functional genomics analysis of the turkey genome are being completed by the consortium (MN). Approximately 93% of the turkey genome has been sequenced with 17x coverage. Annotation identified nearly 16,000 genes and 15,093 recognized as protein coding genes and 611 RNA genes. A BAC-contig based physical and comparative map of the turkey genome has been generated (MI, TX, CA). The turkey autosomal genome is covered by 150 contigs. The BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled for the first draft of the turkey genome. About 30 rearrangements between the chicken and turkey genomes have been identified.<br /> A high density 60K chicken SNP array was developed to evaluate genome-wide marker assisted selection using the Illumina platform. The final array contained 56,702 SNPs and is available to the public (ADOL).<br /> <br /> The chicken and turkey MHC gene clusters continue to be analyzed. To further the study of the MHC-Y gene cluster, a complex of YF1*7.1 heavy chain and beta2 microglobulin was crystallized and examined at 1.32 angstrom resolution (COH). MN has completed sequencing of BACs that contain portions of the turkey MHC. A survey of sequence variation in the B-locus of commercial turkeys has been completed and found to be highly recombinant. A wider range of sequence variation and haplotype number at the MHC-B locus was observed in wild turkeys compared to commercial turkeys.<br /> <br /> Objective 2, Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer<br /> IA maintains many unique chicken research lines that serve as resources for identifying genes and QTLs of economic importance. Financial constraints resulted in the termination of 4 of the 24 lines in 2009. All lines are currently vulnerable to economic extinction. A number of the lines are being used in active collaborations with researchers from Cornell, MSU, U DE, and USDA-ARS.<br /> <br /> NC continues to characterize chicken primordial germ cells (PGCs). Epidermal growth factor stimulated the proliferation of cPGCs via activation of Ca2+ PKC through the NFKB1 signaling pathway . Retinoic acid was found to induce cPGCs of both sexes to enter meiosis.<br /> <br /> Studies using retroviral delivery of RNA interference against viral receptor and env proteins of MDV to generate viral resistance in vivo have been completed (MI).<br /> <br /> Objective 3, Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices<br /> A number of genome wide SNP-trait association analyses have been conducted. SNPs associated with dermal hyperpigmentation, polydactyly, and other morphological traits such as silkie feathering or hookless, feathered legs, vulture hock, and duplex comb were identified in Silkie chickens (NC). Whole genome SNP analyses were also used to identify genes affecting sperm mobility and ascites susceptibility (AR, NC, ADOL). SNP association analysis for growth in two advanced intercross lines has revealed SNPs within the anti-Mullerian hormone, insulin-like growth factor 1 receptor and neurotensin receptor 1 genes (IA). MD examined an association between SNP and multiple production traits such as abdominal fat and body weight in fat and lean chicken lines. Four candidate genes (superoxide dismutase, aldo-keto reductase, glypican, and syndecan) located in chromosomes with known QTL for abdominal fat were selected. SNPs within the promoter region of these genes were found to be associated with fat yield, fat weight, and breast yield. Genomic selection (GS) studies in egg layer chickens have been conducted at IA. The GS program could obtain substantially greater responses per year than the traditional program by halving generation intervals through early selection using breeding values from dense marker data. A genome wide polymorphism association study has been conducted between broiler lines that differ in their Campylobacter jejuni colonization. A number of SNPs were detected between the resistant and susceptible lines (TX). A phenotypic database using the AR randombred population has been established (GA). These traits are grouped into 7 categories: growth, feed intake/feed efficiency, nutrient digestibility and retention, body composition, meat quality, physiological traits or hormones such as IGF1, IGF2, insulin, T3, T4, glucagon, ghrelin, and GH, and skeletal traits (GA). Association of SNPs with IGF1 and IGF2 was also conducted. The IGF-1 SNP was associated with residual feed consumption, whereas the IGF2 SNP was associated with body weight gain and feed intake.<br /> <br /> IA completed a comparison of Chi-Square, ANOVA, and MANOVA for analysis of high density SNP data from case-control pools. ANOVA was found to be an effective substitute for the Chi-square test to identify significant SNPs and MANOVA can be used to identify the joint effect of region in case-control studies across lines. Genomic selection using breeding values (GS-EBV) estimated from dense marker data is a promising approach for genetic improvement (IA). <br /> <br /> Expression analyses of economically important genes are being studied using DNA microarrays or real time PCR. NC examined the expression of genes in the duodenum of turkey embryos using a focused array. At hatch, there was an increase in enzymes to digest disaccharides and transporters to absorb monosaccharides and small peptides (i.e., PepT1). VA continues to study the regulation of expression of the peptide transporter, PepT1. The nuclear receptor peroxisome proliferator activated receptor alpha gene may play a role in the regulation of PepT1 gene expression, during fasting. NC continues to investigate the molecular basis for the sex-linked barring gene. A region of the Z chromosome was found to be significantly associated with a defect in PGGT1B, a member of the gene family involved in prenylation, a post-translational modification essential for normal melanocyte function. Genes involved in the photoneuroendocrine system were investigated in male chicks following transfer from a short to long photoperiod or treatment with sulfamethazine (SMZ), a compound that affects early sexual maturation.. Long day length in combination with SMZ significantly elevated FSH beta mRNA transcripts and increased plasma levels of FSH (protein). Long day length alone significantly increased FSH beta mRNA transcripts but not plasma FSH. Therefore SMZ was shown under the experimental conditions to release protein (FSH) into the vasculature. In contrast, prolactin mRNA transcripts and plasma prolactin concentration were stimulated solely by long day length (AR). AR investigated genes involved in the stress response. A synergistic release of the stress hormone corticosterone following peripheral administration of corticotrophin releasing hormone and arginine vasotocin appears to involve both peptides binding to their respective receptors juxtapositioned on the same pituitary corticotropes forming heterodimers. Differential expression of muscle genes in turkeys at different developmental stages has been identified (MN, OSU, MSU). MN continues to investigate the underlying genetic predisposition of turkeys to ascites and round heart disease. MN is also investigating the molecular mechanisms and genetic variation underlying aflatoxin resistance in turkeys. The role that GST genes play in this resistance is being studied. Proteomic profiling of chicken splenocytes exhibiting natural killing activity has been initiated (COH).<br /> <br /> The problem of optimizing two stage transcriptional profiling experiments involving microarrays (Stage 1) and qRT-PCR (Stage 2) in order to maximize sensitivity while controlling false discovery rate was investigated. A novel method for the analysis of relative quantification of qRT-PCR data was examined using a general linear mixed model methodology. This new method is especially useful for studies involving multiple experimental factors and complex designs. (WI) Other studies included a dynamic linear model for quantitative genetic analysis of longitudinal traits. The accuracy of prediction of phenotypes for complex traits in poultry was studied in a genome assisted context.<br /> <br /> Research continues on Mareks Disease (MD). ADOL continues to identify genes that confer resistance to MD. Utilizing QTL analysis, DNA microarrays, and 2-hybrid screens, three MD resistance genes (GH1, SCA2, and BLB) have been identified. An alternative approach using allele specific screens, has revealed many genes that respond to Mareks Disease Virus (MDV) infection, such as genes involved in T cell activation, vesicle mediated transport and cell cycling pathways. The role that the transcription factor, Meq plays in MDV continues to be investigated. Proteins that bind to Meq have been identified. The cell cycle regulatory protein CWF19L2 interacts with Meq and may be one mechanism for MDV induced transformation. The role that stem cell antigen 2 (SCA2) plays in MD resistance was further investigated. SCA2 was found to influence MDV replication and spread and is dependent on the presence of MDV US10, which expresses an enhanced EGFP fusion protein. Genetic resistance to MD consists of both MHC and non-MHC genes. Using unique genetic lines at ADOL, statistical analyses showed that both vaccination and genetic line were important main effects that affected MD incidence and survival post infection. Epigenetic alterations induced by MDV exposure is being examined by MD. Methylation patterns and array based comparative genomic hybridization data have been analyzed. A 225 bp insert in the 3 untranslated region of the MHC-B haplotypes has a large effect on the occurrence of MD. The incidence of MD was 47% in congenic birds bearing the BG1*R4 allele and only 19% in congenic birds bearing the BG1*R2 allele (COH). Analysis of telomeres-telomerase regulation and function in MDV is ongoing (CA). The timing of MDV integration into the host chromosome has been investigated. At 7 days post infection, the MDV integrates into the genome. The integration profile is not uniform within or among tissues.<br /> <br /> Studies of the molecular mechanism of infection or resistance/susceptibility for other avian diseases caused by avian metapneumovirus (AMPV), avian influenza virus (AIV), infectious laryngotracheitis virus (ILTV), Salmonella and Eimeria have been conducted. An infectious AMPV that contains biomarkers was developed using reverse genetics to use as a vaccine virus. Individual AMPV genes were cloned and cotransfected into cells in order to produce infectious virions that contain the biomarkers (GFP and 6xHis tag). This allows the biomarker AMPV vaccines to be readily detected from wild type AMPV. TX has examined associations between polymorphisms in the chicken Mx gene with antiviral responses in avian influenza infected embryos and broilers. A non synonymous substitution (S631N) in the chicken Mx gene has been reported to be associated with resistance to AIV. There was a tendency for NN genotypes to have lower virus titer than SS gentoypes. An integrated analysis of micro RNA expression and mRNA transcription in AIV infected chicken lungs was examined. There were 91 miRNAs and 146 genes that were differentially expressed between infected and non infected chicken lungs (TX). AR has identified and characterized the expression of seven ILTV encoding microRNAs. Immunogens that protect against cellulitis in turkeys are being developed at MN. Recombinant fusion proteins of the alpha subunit of Clostridium septicum will be used as a vaccine in poults to reduce C. septicum exotoxin and thus reduce cellulitis. A comparison of differentially expressed genes in bursa between chickens infected with wild type Campylobacter jejuni and non-infected chickens was conducted (TX). There were 2591 and 2936 genes significantly changed between 1 and 4 hours post innoculation in infected and non-infected chickens. Genome wide transcriptome profiles of chicken macrophages have been completed using DNA microarrays following exposure to Salmonella derived endotoxin (IA). 10% of the differentially expressed genes were involved in the inflammatory response. NFKBIA, IL-1B, IL8, and CCL4 genes were consistently induced following endotoxin treatment (IA). Differential expression of intestinal genes following an Eimeria maxima challenge has been investigated (VA). Downregulation of the liver expressed antimicrobial peptide-2 (LEAP-2) gene, which is part of the innate immune system, was found to be correlated with high lesion scores in chicks. <br /> <br /> IN continues to investigate physiological mechanisms associated with aggression and stress in poultry using a functional genomics approach. Two lines of chickens, KGB and Dekalb, have been subjected to environmental stressors and the transcriptome response in the hypothalamus has been measured by microarray. Involvement of dopamine and serotonin pathways was revealed. Genomic selection has been used to select for animal well being concerns, such as livability in layers and leg angle in broilers. IN is also mapping QTL for growth using Paul Siegels high and low weight selected lines. Four interacting QTLs have been identified and are predicted to cause nearly half of the 9-fold difference in body weight. These 4 QTL alleles from the low line are being introgressed into the high line using marker assisted back-crossing to the high line.<br /> <br /> Telomere length variation of different genotypes and cell lines is an ongoing project (CA). Significant variation exists within and among chicken genotypes for chromosome-specific telomeric array organization and total genome telomeric sequence content. The molecular basis for the wingless-2 mutation continues to be investigated with attention focused on the TSEN-2 gene, which plays a role in the removal of introns from specific pre tRNAs.<br /> <br />

Publications

Impact Statements

1. The continued development and sharing of genomics resources such as the 60K SNP array provides valuable tools for genome-wide association analyses and candidate gene studies.
2. The molecular basis of infection and disease resistance have been examined for a variety of poultry diseases, such as Mareks Disease, avian influenza, coccidiosis, cellulitis, avian metapneumovirus, and infectious laryngotracheitis. New insights into the genes and molecular mechanisms that lead to the onset and propagation of this disease have been identified. This knowledge can be used to develop novel strategies to reduce the incidence and severity of the disease.
3. Turkey is the fourth economically most important animal species in the U.S. Completion of the sequence (17x coverage) and comparative map of the turkey genome will facilitate the identification of genes that control economically important traits and enhance disease resistance.
4. Gene expression studies using DNA microarrays or qRT-PCR continue to reveal genes that play important roles in economically important traits.

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Participants

Members presenting in scientific session:; Kong, Kuenzel, Rhoads (AR); Delany (CA); Miller (COH); Aggrey (GA); Dekkers, Lamont (IA); Muir (IN); Porter, Song (MD); Dodgson (MI); Foster (MN); Burgess (MS); Ashwell, Petitte (NC); Zhou (TX); Cheng, Zhang (USDA-ARS-ADOL); Rosa (WI)

Brief Summary of Minutes

NC1170/NRSP8 Poultry Technical group
San Diego, CA, January 15 and 16, 2011

Co-Chairs were: Sue Lamont (NC1170), and Huaijun Zhou (NRSP8).

The scientific meeting was held Saturday, January 15, 8:15 AM to 5:50 PM, and Sunday January 16, 8:00 AM to 11:30 AM. The business meeting was Sunday, January 16, 11:30 AM to 12:30 PM.

For the Scientific meeting, there were 21 NC1170 members and over 48 guests and students participating, based on Saturday sign-in sheets. There were 32 research presentations by Technical Committee members, guests and invited speakers.

Business Meeting:

Minutes recorded by Douglas Rhoads (NC1170 secretary).

NC1170 Members in Attendance at Business Meeting: Kong, Kuenzel, Rhoads (AR); Delaney (CA), Miller (COH); Lamont (IA); Porter (MD); Dodgson (MI); Foster (MN); Burgess (MS); Ashwell, Petitte (NC); Zhou (TX); Cheng, Zhang (USDA-ADOL)

Other Attendees: Qureshi (NIFA), Saif (AA, OH); Fulton (Industry); Schmidt (DE-NRSP8)

NC1170 Members Absent from Business Meeting: Aggrey, de Leon, Dekkers, Edelmann, Reed, Rosa, Song, Taneyhill, Wong.

Presentation from Mo Saif:

1. Good job on including leveraged funds in station reports.

2. NCRA wants emphasis on cooperation and nature of cooperation between stations.

3. Mid-term review looks positive.

Presentation from Muquarrab Qureshi:

1. Congratulations to Lamont and Zhou for a very good meeting grant.

2. NIFA reorganization still underway.

3. Search for new National Program Leader for Animal Genetics and Genomics is underway to replace Peter Burfening. Candidates welcome. Need strong person.

4. Foundational RFP is out.

5. Q&A with members about priority areas, foundational, and funding balance between Animal & Plant.

Old Business:

1. 2010 meeting minutes approved.

2. Officers remain the same, moving into second year of two-year terms.

New Business:

1 Approved motion to hold next meeting weekend (Saturday all day, half day Sunday, joint NRSP8 meeting Sunday PM) preceding PAG in January 2012.

2. Need to explore invitation to NE1034 to joint meeting in January 2013.

3. Lamont is assembling mid-term report based on station reports submitted.

Poultry coordinator report from Jerry Dodgson:

1. Has about $65k per year. Spends about $5k on travel. Requests input for coming year. Consider sequencing other genomes (cell lines or inbred lines). Wants suggestions for priority list. Any data would have to be in public domain. BGI indicates app $5k for 6x coverage and assembly.

2. New genome assembly from U Maryland expected soon that will incorporate NGS and GgaZ data.

NRSP8 poultry bioinformatics subcommittee report from Shane Burgess:

1. Requests input on what is right and wrong for Birdbase. What does community want? Attendees agreed to request that NRSP8 support expansion to include all aves species and provide funding.

NRSP8 New Business

1. Tom Porter nominated and elected by Poultry group to fulfill role as Secretary then leader for NRSP8.

Move to adjourn by general acclamation.

Accomplishments

NC-1170<br /> Accomplishments 2010<br /> <br /> Overall summary. Now midway through the 5-year cycle, the NC-1170 project is very effectively achieving the milestones described in the proposal. Outputs have included the generation and improvement of comprehensive genetic and physical maps for chicken and turkey; development and testing of novel techniques for gene transfer in chickens; greater insight into how genomic sequence variation affects phenotypic variation in poultry; and identification of QTL, specific genes and pathways associated with important biological traits in poultry. Research resources, such as genetic lines and high-density SNP chips, have been developed and widely used across the stations in a coordinated manner. The project has jointly (with NRSP-8) annually organized a very well-attended scientific session at the Plant and Animal Genomic meeting, which attracts many national and international scientists from outside of NC-1170, and including industry scientists. Impacts of the work of NC-1170 include increased scientific knowledge of the chicken and turkey genomes and their organization, more effective research utilizing newly developed bioinformatic tools, enhanced understanding of gene function and expression, identification of genes affecting economically important traits in poultry, and technology transfer to the poultry breeding industry of enhanced tools to apply genomic selection in commercial lines. <br /> <br /> Examples of specific accomplishments in 2010 are listed below by project objective.<br /> <br /> Objective 1. Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. <br /> <br /> The core turkey MHC sequence was expanded, and studies completed to measure MHC haplotypes diversity in commercial and wild turkeys. Expression of loci in both classical MHC-B and MHC-Y regions of the turkey was demonstrated. The chicken YF1*7.1 MHC class I molecule was shown to be classical, but binds non-classical ligands.Sequences were assembled for the chicken MHC and extending the MHC map on Chr16. A BAC contig-based physical and comparative map of the turkey genome was generated. Cytogenetic analyses integrated the map with turkey chromosomes and localize gaps and inversions/translocations between chicken and turkey genomes. To enhance sequence coverage of the unassigned portion of the turkey genome, pools of BACs from the CHORI and Texas A&M turkey BAC libraries are currently being sequenced using next-gen sequencing. Global gene expression in the cecae of neonatal chicks following Salmonella challenge and probiotic treatment was used to determine gene expression and potential gene networks involved in reduction of Salmonella by probiotic treatment. RNA-Seq was used to characterize the transcriptome level changes in the liver of birds exposed to AFB1 with and without probiotics (Lactobacilli). Using computational epigenetic analysis of CpG sites and temporal gene expression analysis, we are identifying the methylated genes. Now we are building the genetic regulatory network of gene involved in the etiology of Mareks disease by analyses of the temporal microarray data. We computationally screened over 230 restriction enzymes to maximize CpG coverage while attempting to minimize sequencing requirements for application to RRBS. We also found that significantly decreased CpG methylation content of CD4 was accompanied by significantly up-regulated mRNA expression level of CD4in MDV-infected line 7.2 birds. The role of miRNA in the expression of BG1, a locus with a significant influence in the incidence of Mareks disesase tumors was determined. Differentially expressed miRNAs in chicken lung with avian influenza virus infection were identified by a deep sequencing approach. Alternate lengthening of telomere (ALT) mechanism in chicken cells was shown and analysis of telomeres-telomerase regulation and function in Mareks disease virus was conducted. Global gene expression and bioenergetic assessment was done on CEF and DF-1 cells. Proteomic profiling and function of chicken embryonic spleen exhibiting natural killing activity was studied. The developmental profile of claudin-3, -5, and -16 proteins in the epithelium of chick intestine was determined.The plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma was measured AgBase continued to support functional modeling in agricultural organisms. GOModeler--a computational tool for hypothesis-testing of functional genomics datasets was refined. Re-annotating functional genomics data was demonstrated as an essential step in systems biology modeling.<br /> <br /> Objective 2. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. <br /> <br /> Seven recombinant subunit fragments of the ± toxin polypeptide, which is the lethal exotoxin secreted by Clostridium septicum, were produced. A recombinant SV40 large T protein was produced that contains a poly-arginine transduction domain at the C-terminus of the protein such that it can penetrate across the plasma and nuclear membranes of somatic cells. Retinoic acid was shown to induce meiosis in avian primordial germ cells. <br /> <br /> Objective 3. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices.<br /> <br /> An investigation was completed on cardiac gene expression in growth-selected vs. non-selected birds and RH affected and non-affected birds using microarray, multigene CEQ and qRT PCR. Re-sequencing ADOL Lines 6 and 7 based on a pool of 6 individuals each, to 40X per line, on an ABI SOLiD machine was completed, and shed light on the SNP density and preservation of alleles in inbred lines. Extending BLUP methodologies to utilize pedigree and genomic information in a single step (ssGBLUP) was shown to solve the problems of ignoring phenotypic information from ungenotyped animals and limitations of single-trait evaluation and prediction bias. A panel of 120 SNP, closely linked to the 4 QTL for body weight, was developed and four<br /> generations of introgression of body-weight QTL have been completed. Allele-specific expression analysis revealed CD79B has a cis-acting regulatory element that responds to Mareks disease virus infection in chicken. Integrating the ChIP seq results with microarray analysis revealed 1722 genes that were within 2 Kb of the highest scoring Meq-binding peaks as well as being differentially expressed. Pathway analysis has suggested genes and molecular mechanisms for MDV-induced transformation. Data from challenging experiments suggested that there is a vaccine by host interaction altering vaccinal efficacy. A total of 172 SNPs distributed on chromosomes 1, 3, 15, and Z were detected significantly associated with MD by Marker-Trait Association analysis using a generalized linear mixed model taking into account the pedigree structures. Proteomic analysis of host responses to Marek's disease virus infection in spleens of genetically resistant and susceptible chickens was conducted. Glucocorticoid-regulated histone modifications and recruitment of the GR, Pit-1 and Ets1 transcription factors to the 5-flanking region of the chicken growth hormone gene was shown.Single nucleotide polymorphisms in candidate genes were associated with phenotypic traits in broiler chickens.We have identified the Wnt target gene Annexin A6 to play a positive role in the migration of neural crest cells, using a combination of gene perturbation experiments, in situ hybridization and immunohistochemistry. Systemic response of genetic lines of chickens that differ in their susceptibility to Campylobacter jejuni colonization was characterized. The impact of Salmonella enteritidis infection on liver transcriptome in broilers was profiled. Gene expression profiling differences were shown between resistant and susceptible broilers responding to Campylobacter jejuni infection.. Gene expression analysis and mechanism of action of chicken macrophage response to microorganism-derived nucleic acids was explored. We studied the characteristics of human miR-1 and miR-124 to create a miRNA target prediction program based on the common features of the interaction with their targets. We used an animal model combined with Gibb sampling to estimate genetic parameters for FCR and RFI in a pedigreed random mating broiler control population. An R package for fitting generalized linear mixed models in animal was developed. Persistence of accuracy of estimated breeding values in layers using marker and pedigree based relationship matrices, and the accuracy of genomic EBV using an evenly spaced low density SNP anel in broiler chickens was estimated. Proteomic evaluation was conducted on intestinal brush border membrane proteins. Expression of the peptide transporter, PepT1, in the yolk sac membrane and embryonic intestine was measured. Developmental mutants were characterized by SNP panels and gene expression, capture array and next-generation sequencing. Genetic mapping of regions associated with antibody response to sheep red blood cells in the chicken were mapped. Genome-wide analysis of chicken heterophil functional response to Salmonella in advanced intercross lines revealed associations with known resistance loci, and novel loci. Whole genome association analysis of idiopathic eosinophilic enteritis in brown egg layers identified important genomic regions. Genes affecting sperm mobility, ascites and stress response were identified and characterized. <br />

Publications

Impact Statements

1. NC-1170 activities served as a platform for establishment of collaborative research teams including NC-1170, non-NC-1170 public and private sector researchers. NC-1170 activities were leveraged into additional, major support from poultry breeding companies and competitive federal programs, such as NIFA.
2. Bioinformatics tools were developed that enabled scientists to much more efficiently, rapidly and accurately apply systems biology approaches in the chicken. These tools were applied to advancing knowledge in Mareks disease.
3. A study showed the effectiveness of the cfos gene to reveal specific neural structures involved in sociality. Continued work in this area should uncover a neural network associated with specific emotional behaviors.
4. Studies on the genetics underlying male gonadal development and genetic mechanisms negatively impacting male fertility traits in the chicken are elucidating the underlying networks that influence a basic function of male fertility. This work will lead to a fundamental understanding of sperm mobility and its inter-relationship with selection for production.
5. The culture of PGCs will have significant applications in reproductive biology, developmental biology and transgenics. Understanding of the induction of meiosis in avian germ cells will provide new information/knowledge in reproductive biology of the domestic fowl.
6. Finding that YF class I molecules bind lipids of bacterial origin implies that YF antigen presentation may be a route by which chickens respond to the presence of pathogens, which might be an avenue for vaccination in the future. Genetic differences in the YF region might result in differences in the capacity of birds to respond to pathogens and hence typing and selection for YF haplotypes conferring resistance might be useful.
7. Completion of the sequencing of three BAC contigs that contain portions of the turkey MHC. facilitated identification and genetic mapping of additional MHC-associated genes and identified additional BAC clones for inclusion in the WGS effort. Completion of a survey of sequence variation in the B-locus of commercial and wild turkeys gave insight into variation that may be valuable in application in commercial turkeys or in conservation efforts.
8. The quality of the turkey genome map was greatly enhanced, and the BAC contig-based physical and comparative map has been essentially completed. The BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently published first draft sequence of the turkey genome. Interesting evolutionary trends have been detected that distinguish the turkey and chicken genomes.
9. ChIP seq analysis in DF-1-Meq cells confirmed Meq-DNA binding sites as well as revealed novel ones. Integration with microarrays analysis identified genes and biological pathways that may explain MDV-induced transformation.
10. Genomic selection was demonstrated as superior to state-of-the-art BLUP. However, the improvement is dependent on the genomic selection algorithm and probably the underlying genetic architecture of the trait.
11. Genetic variation was identified in commercial research chicken lines and statistical methodology was developed for the use of high-density SNP genotypes in genetic improvement, both of which are of potential value in genetic selection to improve commercial populations.
12. Identification of chicken microRNAs associated with avian influenza virus infection in chickens; chicken genes and signal pathways related to C. jejuni infection, and chicken genes associated with genetic resistance to C. jejuni colonization in chickens, may lead to the development of markers for improved resistance to these pathogens.
13. Regarding molecular mechanisms underlying chick neural crest development, our results demonstrate that Wnt and Snail2 signaling set up a cascade of gene regulation events to transform a precursor epithelial cell in the dorsal neural tube into a migratory neural crest cell. Identifying novel genes and understanding the mechanism by which Wnt and Snail2 regulates them, will illuminate how molecular networks that regulatechick embryonic development interact to generate a fully functioning animal.
14. Findings indicate epigenetic instability induced by MDV infection in MD resistant and susceptible chickens, including DNA methylation alterations in promoter regions of many genes and histone modifications. That many of these differences, particularly in response to MDV challenge, affect genes of the immune system or tumor progression and related pathways provides a strong rationale for pursuit of a hypothesis that epigenetic signatures are associated with MDV-induced tumorigenesis.
15. Demonstration of involvement of ETS-1 in GC regulation of the GH gene during embryonic development (first time shown in any species), enhances our understanding of growth regulation in vertebrates. Findings indicate that GC results in dynamic changes in histone modifications and transcription factor recruitment within the 5-flanking region of chicken GH gene.
16. Developing miRNA target programs based on specific features of a particular MiRNA class and its target interactions was demonstrated to be much more efficient than using generalized features, which will speed research in this area.
17. Identification of brush-border membrane-associated proteins in the small intestine is an important step in furthering scientific understanding of digestion and absorption in the chicken, and developing a better understanding of the molecular mechanism that regulates amino acid uptake during embryogenesis will lead to optimization of embryonic growth.
18. The oncogenic MDV genome (which is circular and has no need for a telomere-maintenance system) was shown to contain two copies of the chicken telomerase RNA gene as well as several sets of telomere repeats. This refines the hypothesis that the MDV is utilizing aspects of the telomere-telomerase system to integrate into the chicken genome at the site of telomeres, and that this contributes to aspects of the disease state  pathology, persistence and/or oncogenesis.
19. The developmental genetic mutations studied are common to poultry and a cause of sporadic embryo mortality, and are similar to a number of common human congenital malformations (affecting limb, heart, craniofacial features). The chicken provides a versatile model to contribute to our understanding of genes and genetic mechanisms important to skeletal, limb and organ development.
20. Comparative genomic analysis informs as to the chromosomal evolution of the chicken and turkey lineages. Genome organization at the chromosome level is important as a component of our understanding of the connection between genotype and phenotype (of cells, tissues and organisms).

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Participants

See attached business meeting minutes.

Brief Summary of Minutes

See attached minutes file for 2011 annual report.

Accomplishments

NC-1170<br /> Accomplishments 2011<br /> <br /> Overall summary. <br /> <br /> The project has jointly (with NRSP-8) annually organized a very well-attended scientific session at the Plant and Animal Genomic meeting, which included invited international speakers and attracts many national and international scientists from outside of NC-1170, and including industry scientists. Project outputs have included the improvement of comprehensive genetic and physical maps for chicken and turkey; development and testing of novel techniques for gene transfer in chickens; greater insight into how genomic sequence variation affects phenotypic variation in poultry; and identification of QTL, specific genes and pathways associated with important biological traits in poultry. Research resources, such as poultry genetic lines and cells, and high-density SNP chips, have been developed and widely used across the stations. <br /> <br /> Examples of specific accomplishments in 2011 are listed below by project objective.<br /> <br /> Objective 1. Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. <br /> <br /> MHC class I target recognition, immunophenotypes and proteomic profiles for natural killer cells and monocytes within the spleens of day-14 of chick embryos were characterized. <br /> <br /> The miRNA targeting of the 225 bp insert in BG1*R4 allele of BG1 were identified. Additional genes were mapped to chicken chromosome 16.<br /> <br /> We have expanded the core turkey MHC sequence; measured MHC haplotype diversity within the species; and quantified expression of genes in the expanded MHC by examining immune system tissues. <br /> <br /> To enhance sequence coverage of the unassigned portion of the turkey genome we have sequenced pools of BACs from the CHORI and Texas A&M turkey BAC libraries using next-gen sequencing. Specifically, this effort identified BACs with end sequences that physically mapped to either the ChrUN portion of the 2.01 genome build or to the Z chromosome. <br /> <br /> To investigate the response to aflatoxin exposure, we are using RNA-Seq approaches to characterize the transcriptome level changes in the liver of birds exposed to AFB1 with and without probiotics (Lactobacilli).<br /> <br /> An introgression line is being generated by simultaneously introgressing four QTL alleles from the Virginia low-line into a Virginia high-line background. The introgression is being performed by marker assisted back-crossing to the high-line. A panel of 40 SNP, closely linked to the 4 QTL, was developed. Four generations of introgression have been completed.<br /> <br /> To employ GWMAS to address social and ethical concerns while at the same time demonstrating the power and limitations of GWMAS in a multi-generational selection experiment, we utilized 2 broiler and 3 layer lines with different selection objectives, but primary among the traits for selection were leg angle in broilers and livability in layers. <br /> <br /> We have completed re-sequencing ADOL Lines 6 and 7 based on a pool of 6 individuals each, to 44X per line, on an ABI SOLiD machine at Purdue. The KGB and DXL lines have been completed. <br /> <br /> We have developed software to call SNPs, find LD, Fst, Fis, and Tajima D from sequencing data. This software is being used as a pipeline to find signatures of selection for a number of traits, including aggression and MD resistance.<br /> <br /> Microarray analysis in early- and late passage (passage 4 and 18, respectively) of primary CEF cells was performed with 4X44K chicken oligo microarray. A total of 2149 differentially expressed genes were identified.<br /> To elucidate cellular and molecular mechanisms of resistance to C. jejuni colonization in chickens, two genetically distinct broiler lines (Line A (resistant) colonized less by C. jejuni compared to Line B (susceptible)) werei noculated with wild type (WT) or mutant (MT) C. jejuni or PBS at day of hatch. Total RNA was isolated from the bursa of Fabricius harvested at 1, 4, 24, and 36 hrs post-inoculation and a chicken whole genome 44K array was used to profile the host innate response to C. jejuni. <br /> <br /> We presented scenarios and basic principles of how HTC can be used in genomic selection,implemented using various techniques from simple batch processing to pipelining in distributed computer clusters.<br /> <br /> The analysis in several in vitro cell systems indicated that ALT is operating within immortalized cells as per the key markers: absence of telomerase activity, heterogeneous telomeric DNA profiles, and presence of APB foci.<br /> Results suggest that the telomerase and telomere-recombination (ALT) pathways may coexist in chicken cells; however, depending on the cell type, one or the other mechanism may dominate.<br /> <br /> Analysis of MDV integration through a temporal profile of immune cells and tumors was completed. <br /> <br /> Developmental mutants were studied through targeted capture array/next generation sequencing. We also employed whole embryo in situ hybridization to assess the expression patterns of genes within the causative regions during the relevant developmental stages and locations to assist in prioritizing candidate genes and to learn more about gene expression during chicken development.<br /> <br /> A key cytogenomic finding of the chicken:turkey species comparison was the stability of the two genomes relative to each other, with a number of inversions and placement of the centromere more terminally in turkey chromosomes than the chicken orthologs.<br /> <br /> Study of the Japanese quail genome affirmed multiple NOR loci (three versus one in both turkey and chicken) and showed cytogenetic linkage of one of the NORs with the MHC.<br /> <br /> Electrophoretic mobility shift assays demonstrated that the isoforms differ in their ability to bind Pit-1 binding sites on the cGH promoter. From our results, we conclude that Pit-1 isoforms differ in their ability to activate the chicken GH promoter, and this may be due to differences in their DNA-binding abilities.<br /> <br /> Our results indicate that like in mice, Shh must be down-regulated in order to allow for OE evagination and RP formation and that a specific dosage of FGF8 is required for proper development of RP.<br /> <br /> By testing temporal transcriptome changes using three representative chicken lines with different resistance to MD, we identified 163 candidate genes for MD-resistance and 175 candidate genes for MD-susceptibility over the three time points.<br /> <br /> We utilized microarrays to screen miRNAs that were sensitive to Mareks disease virus (MDV) infection. QRT-PCR analysis confirmed the microarray data and revealed expression patterns of some miRNAs in tumor samples. Chicken miRNA gga-miR-15b, which is reduced in infected susceptible chickens and splenic tumors, controls the expression of ATF2 (activating transcription factor 2). ATF2 is significantly increased in the same group. <br /> <br /> Using immunoblotting technique we noted that chicken macrophages express a variety of DUBs, while our bioinformatic search identified only eight of these enzymes, demonstrating usefulness of this targeted proteomic technique in comparison to complementary bioinformatic tools that can be used alongside proteomics.<br /> <br /> We have developed and deployed Genome2Seq, a tool that rapidly looks up genome co-ordinates generated from RNA-Seq data and returns genes and Gene Ontology (GO) annotation when the co-ordinates map to annotated genes and a fasta sequence files when co-ordinates do not map to previously annotated genes. <br /> <br /> Two existing AgBase ID mapping tools (ArrayIDer and AffyIDer) are being reconfigured to handle a larger number of accession types and combined for ease of use. In addition to developing these tools we are also providing online support for functional modeling and access to biocomputing (including high performance computing) via request through AgBAse.<br /> <br /> We have developed guidelines for providing standardized gene nomenclature for chicken genes. We are liaising with NCBI to ensure that chicken nomenclature is displayed in NCBIs Entrez Gene database and are working to expand this collaboration to include eChickAtlas and Ensembl.<br /> <br /> Chickspress is being developed as a tissue specific compendium of gene expression for chicken gene products.<br /> <br /> Via BirdBase we are creating a comparative genome browser for bird genomes, initially including the three public bird genomes (chicken, turkey, zebra finch). <br /> <br /> To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9x coverage) from two independent libraries.<br /> <br /> We have obtained deep next generation sequence data for the DF1 and DT40 chicken cell lines.<br /> <br /> Objective 2. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. <br /> <br /> Many unique experimental lines of poultry were developed, maintained and characterized; and shared among researchers.<br /> <br /> A non-cytolytic Clostridium alpha toxin vaccine, engineered to lack the cytolytic 28 amino acid domain in the middle of the polypeptide, was developed and tested to protect against turkey cellulitis. <br /> <br /> We combined trisomy mapping with array Comparative Genomic Hybridization (aCGH) to identify additional GGA 16 sequences among unassigned genomic sequence contigs.<br /> <br /> Working on adult chicken anatomy we have developed almost 700 terms (and definitions) to describe adult chicken musculoskeletal system and integument.<br /> <br /> Objective 3. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices.<br /> <br /> The expression of nutrient transporters and digestive enzymes in the yolk sac membrane and embryonic intestine were defined. <br /> <br /> Proteomic analysis of chicken breast muscle demonstrated differential protein expression with varied growth rate and water-holding capacity. <br /> <br /> Integration of nutritional phenotypes, duodenal transcriptomics and plasma metabolites in divergently selected broiler chickens (high vs. low feed efficiency lines) at 35 and 42 days of age demonstrated likely mechanisms linking feed efficiency phenotypes with their genotypes.<br /> <br /> We used qPCR to determine that reduced protein levels in sperm are not reflected at the level of the testis transcriptome. We performed RNAseq on testis RNA and over 3000 genes are significantly altered for expression, and we have identified SNPs in 300 of those genes that are differentially represented with respect to mobility phenotype.<br /> <br /> We have identified informative SNPs in HTR2B, UTS2D, and AGTR1. SNPs in the former three genes have been applied to different experimental lines and found to show strong association with ascites phenotype.<br /> <br /> Employing immobilization stress, and examining a second vasotocin receptor subtype, the VT4R, we have found that it participates in the avian stress response.<br /> <br /> Between HGFL and LGLL lines, in overlapping windows of 100 SNP along autosomes, we have identified several potential genomic targets of divergent selection and putative candidate genes subjected to divergent selection within these regions.<br /> <br /> High-throughput proteomic analysis in chicken lung with avian influenza virus infection was conducted by MASS spectrometry. <br /> <br /> Using simulation, it was found that RBF had better ability (higher predictive correlations and lower predictive mean square errors) of predicting merit of individuals in future generations in the presence of non-additive effects than a linear additive model, the Bayesian Lasso.<br /> <br /> We evaluated the effects of directional selection based on estimated genomic breeding values (GEBVs) for a quantitative trait.<br /> <br /> Comparison between a structural equation model (SEM) with the selected structure and a Multiple Trait Animal Model using deviance information criterion indicated that the SEM is more plausible. Coupling prior knowledge with the output provided by the inductive causation algorithm allowed further learning regarding phenotypic causal structures when compared to standard mixed effects SEM applications.<br /> <br /> Screening for allele-specific expression (ASE) in response to MDV infection, a simple and novel method was used for identifying polymorphic cis-acting regulatory (genetic) elements, which may contain strong candidate genes with specific alleles that confer MD genetic resistance. <br /> <br /> The DNA-binding sites and the genes that are directly regulated by Meq, the likely MDV oncogene, were defined. <br /> <br /> Sequence datasets of the genomes of lines 6 and 7 were further defined. <br /> <br /> A vaccine by chicken line interaction affecting vaccine protective efficacy was identified. <br /> <br /> One SNP accounting for more than 6% of the disease/non-disease variation in MD infection was determined. <br /> <br /> We have further characterized the functional role of the Wnt target gene Annexin A6 during neural crest cell development. <br /> <br /> A global microarray was used to measure gene expression in spleen and peripheral blood leukocytes (PBL) from the same 40 birds, either infected or not with E. coli. Birds showing severe pathology had a greater induction of gene response than repression. DAVID analysis identified many terms related to immune response and metabolic processes. In addition to the differentially expressed genes and networks identified in individual tissues, the combined bi-analysis of two tissues from the same birds gave insights into potential systemic signaling between tissues.<br /> <br /> TLR15 RNA expression was found to be increased in response to APEC challenge in the bursa of broilers.<br /> <br /> Heat-stressed chicks were found to have significantly lower blood hemoglobin, hematocrit, carbon dioxide partial pressure, and higher pH and saturated oxygen, than control chicks. There were several interactions of genetic line with heat treatment effects.<br /> <br /> A total of 65 single nucleotide polymorphisms (SNPs) were identified in chicken FTO, and 18 tested SNPs were significantly associated with traitsof body weight, body composition and fatness.<br /> <br /> A high-density SNP study detected a number of genomic regions showing association with egg defects, some of which explain a sizeable proportion of genetic variance.<br /> <br /> A QTL region on chromosome 4 was found to explain a large proportion of the genetic variance for the mean (30%) and uniformity (up to 16%) for egg weight.<br /> <br /> A high-density SNP study of markers associated with body weight (BW) and hen house production (HHP) showed that both traits are highly polymorphic with no major QTL. <br /> <br /> A steady decline of accuracy was observed as the number of generations with low-density (LD) genotyped dams increased, which suggests that some dams may need to be strategically high-density (HD) genotyped to maintain accuracy close to that achieved using HD platforms.<br /> <br /> Comparison of the accuracy of genotype imputation using different methods suggested that a combined approach using the best features of the methods may be needed to optimally utilize the information and maximize accuracy within defined computing resources.<br /> <br /> We continue to provide training, outreach and support for poultry researchers via AgBase to ensure that they are able to better leverage their functional genomics data to understand key economic traits for poultry.<br />

Publications

See attached file.

Impact Statements

1. Platform for establishment of collaborative research teams including researchers from NC-1170, and non-NC-1170 public and private sectors.
2. Leveraged NC-1170 support and collaborations into additional, major support from poultry breeding companies and competitive federal programs, such as NIFA.
3. Increased scientific knowledge of the chicken and turkey genomes and their organization, more effective research utilizing newly developed bioinformatic tools, enhanced understanding of gene function and expression, identification of genes affecting economically important traits in poultry, and technology transfer to the poultry breeding industry of enhanced tools to apply genomic selection in commercial lines.
4. Senescence-associated genetic alterations in chicken cells can provide valuable knowledge of cellular growth characteristics.
5. Studies suggest that just as there exist two receptors, corticotropin releasing hormone 1 and 2 receptors (CRH1R and CRH2R) involved in the stress response, there are also two vasotocin receptors (VT2R and VT4R) in the chicken involved in the stress response since the latter two receptors have been found in corticotropes of the anterior pituitary. Having four receptors involved in stress gives flexibility regarding how an animal, such as the chicken, responds to a particular stressor.
6. We are elucidating the underlying networks that influence a basic function of male fertility. This work will lead to a fundamental understanding of sperm mobility and its inter-relationship with selection for production.
7. The work in Ascites is also directed at a fundamental understanding of the genetics and physiology of ascites and how selection can be augmented to reduce susceptibility.
8. MDV is a major cause of mortality leading to substantial economic losses to the poultry industry. Interestingly, the oncogenic MDV genome (which is circular and has no need for a telomere-maintenance system) contains two copies of the chicken telomerase RNA gene as well as several sets of telomere repeats. We hypothesize the MDV is utilizing aspects of the telomere-telomerase system to integrate into the chicken genome at the site of telomeres, and that this contributes to aspects of the disease state  pathology, persistence and/or oncogenesis.
9. The developmental genetic mutations studied are common to poultry and a cause of sporadic embryo mortality, and are similar to a number of common human congenital malformations (affecting limb, heart, craniofacial features). The chicken provides a versatile model to contribute to our understanding of genes and genetic mechanisms important to skeletal, limb and organ development.
10. Genome organization at the chromosome level is important as a component of our understanding of the connection between genotype and phenotype (of cells, tissues and organisms). The chromosomes are the vehicles for transmission of the sequence information to daughter cells (mitotic and meiotic) and define via their hierarchical structure expression patterns and also control aspects of genome stability which impact life or death decisions for cells at the molecular level. Comparative genomic analysis informs as to the chromosomal evolution of the chicken and turkey lineages.
11. MHC-B haplotypes are known to confer valuable traits to chickens raised for meat and eggs. The findings from the studies underway will provide a greater understanding of genes within MHC-B and how they contribute to desirable traits in chickens. The work on MHC-Y is providing insights into how YF class I may contribute to desirable traits and may help by providing a means for selection of particular MHC-Y haplotypes. Additional genes with roles in fitness are newly mapped to GGA16.
12. We have identified several potential genomic targets of divergent selection and putative candidate genes subjected to divergent selection in experimental chicken lines.
13. The transcriptomic data suggested that improved FE is associated with high cell growth and proliferation, and less apotosis, upregulation of glycolysis, efficient N digestion and retention, and renal function for N recycling. The metabolomic analysis also showed the strong association between plasma glutamate and N recycling. The metabolomic data reveals the posttranscriptional and posttranslational mechanisms associated with transcriptomics, and therefore can directly link feed efficiency phenotypes to their respective genotypes.
14. Studies demonstrate the feasibility of application of techniques of molecular genetics to analysis of variation in structure, function and gene expression within the chicken genome.
15. We identified genes and pathways associations with important biological traits in chickens.
16. We identified genetic variation in commercial research chicken lines, and developed statistical methodology for the use of high-density SNP genotypes in genetic improvement, both of which are of potential value in genetic selection to improve commercial populations.
17. As the high- and low- body weight lines from VT display large phenotypic differences in a wide range of metabolic as well as immunological traits, they are a valuable resource as a model for studying the genetics underlying important traits in agriculture as well as human and veterinary medicine.
18. Actions of Pit1 on pituitary gene expression are complicated by the existence of functional isoforms that differ in their ability to regulate transcription. Therefore, future investigations of genetic polymorphisms in the Pit1, GH and TSH genes should incorporate the possibility that the polymorphisms might result in expression of different Pit1 isoforms with altered transcriptional activity or that the Pit1 response elements in target genes may have differential selectivity for a Pit1 isoform.
19. Using temporal gene expression, we identified important genes involved in MD-resistance or susceptibility and found several biofunctions related with immune response that we believe play an important role in MD-resistance. Important, the methylation fluctuation and mRNA expression change of CD4 gene and miRNAs induced by MDV infection suggested a unique epigenetic mechanism existed in MD-susceptible chickens.
20. Our results demonstrate that Wnt signaling sets up a cascade of gene regulation events to transform a precursor epithelial cell in the dorsal neural tube into a migratory neural crest cell. Identifying novel genes, and their regulation by Wnt, will illuminate how the molecular networks that regulate chick embryonic development interact in order to generate a fully functioning animal; and underscores the importance of dismantling cellular junctions in order to permit neural crest cell emigration.
21. The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes.
22. Our map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes.
23. Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently completed first draft sequence of the turkey genome.
24. Our studies of the turkey MHC have significantly advanced our understanding of this important immunological locus in poultry. We have assembled three regions of the MHC in the turkey and have identified additional linked genes. These studies will allow for the incorporation of MHC variation in disease-related studies.
25. Additional sequencing of turkey large insert libraries and BAC pools has significantly improved coverage of the turkey genome and the quality of the genome build. A new assembly and annotation is anticipated in the next few months.
26. Application of RNA-Seq approaches to characterize the transcriptome-level changes in the liver and spleen of birds exposed to aflatoxin (AFB1) with and without probiotic treatment (Lactobacilli) is revealing new information of gene regulation and splicing variation.
27. We have produced the complete Clostridium septicum ±-toxin that lacks the cytolytic 28 amino acid domain in the middle of the polypeptide. When assayed for cytotoxicity this peptide doesnt lyse cells. In a vaccination trial, the non-cytolytic alpha-toxin (NCAT) alone and the NCAT Bacterin +/- adjuvant provided 60-65% protection. This suggests that a formulation of bacterin alone with no adjuvant could be used as a cost effective vaccine.
28. Developing omics and bioinformatics capabilities for poultry and extending our capacity to understand the effect of deubiquitinating enzymes in infection/innate immunity are expected to elucidate new mechanisms for managing Salmonella enterica. By leveraging new sequencing technologies, we will ensure that poultry researchers can translate their large scale data into gains for the industry. This will be enhanced as the capacity to link between genotype and phenotype is developed for poultry.
29. Developing standardized gene nomenclature and a comparative bird genome browser will facilitate comparative genomics for poultry while a tissue and developmental stage specific expression atlas provides a more detailed understanding of gene expression to assist with functional modeling.
30. Identification of potential candidate sequences for GGA 16 mapping.
31. Identification of chicken genes and signal pathways that are related to C. jejuni colonization in chickens.
32. Identification of candidate proteins associated with genetic resistance to avian influenza virus infection.
33. A shared set of genes and SNPs that exhibit ASE in response to MDV infection have been identified between experimental layers and broilers, which suggests common pathways and possibly causative polymorphisms for MD response.
34. The SNPs exhibiting ASE can be used as genetic markers in MD resource populations to directly test whether the associated genes confer genetic resistance.
35. Integration of ASE, ChIP seq, and gene profiling identified 97 high confidence genes for MD genetic resistance
36. The advancement in understanding of host genetics influence over vaccine efficacy is of importance in vaccine development and usage.
37. The identified SNP (along with other reported markers) conferring MD resistance can be integrated in Marker-assisted Selection to improve genetic resistance to MD in chickens.
38. HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of marker panels to realized genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans
39. Nonparametric RBF regression is a useful counterpart for dealing with situations where non-additive gene action is suspected, and it is robust irrespective of mode of gene action.
40. Coupling prior knowledge with the output provided by the IC algorithm allowed further learning regarding phenotypic causal structures when compared to standard mixed effects SEM applications.
41. Developing a better understanding of the molecular mechanism that regulates nutrient uptake during embryogenesis will lead to optimization of embryonic growth and potentially post-hatch growth.

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Brief Summary of Minutes

Please see attached "Copy of Minutes" file for NC1170's complete 2012 annual report.

Accomplishments

Publications

Impact Statements

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