Whole genome SNP panels for genotyping experimental chicken lines - a vital BBSRC resource

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The project will identify genome-wide panels of SNPs in each of our 10 chicken lines at IAH. Objective 1 - To genotype the 10 IAH chicken lines with 6144 SNPs and determine informative SNPs for each pairwise line comparison. When samples have been successfully genotyped each assay will be examined and analyzed for genotype calls based on call rate, heterozygosity and cluster score. Finally a panel of informative SNPs will be generated for all pairwise line combinations to ensure they are divergently monomorphic for each informative SNP. Objective 2 - Examine linkage disequilibrium within each line for all genotypes. Once all SNPs have all been genotyped we will analyze the haplotype structure for each line using Haploview. This will provide a measure of the non-random association of alleles at different loci on a chromosome-wide level. Objective 3 - Make the data available in a publicly accessible database. With collaborators at the Wellcome Trust Centre for Human Genetics (Oxford) we will set up a chicken SNP resource that will provide a public database of genome wide SNPs that will present a means of disseminating this resource to the scientific community, both within and beyond the BBSRC.

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