Brief Summary of Minutes of Annual Meeting

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.

NC-1170 Accomplishments 2010 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. Examples of specific accomplishments in 2010 are listed below by project objective. Objective 1. Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. 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. 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. 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. Objective 3. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. 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 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.