Brief Summary of Minutes of Annual Meeting

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 Objective 1, Develop high resolution integrated maps to facilitate the identification of poultry genes and other DNA sequences of economic importance 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. 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. 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. 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. Objective 2, Develop methods for locating new genetic variation in poultry by gene transfer and chromosome alteration 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. 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. 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. Objective 3, Develop, compare, and integrate emerging technologies with classical quantitative genetics for improvement of economic traits in poultry 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. 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. 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. 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. 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. 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.