Development of High Density Chicken Genotyping Array

Under a Defra-BBSRC funded LINK project between the Roslin Institute, Aviagen Ltd, Hy-Line International, Affymetrix Ltd. and in cooperation with the German Synbreed project funded by BMBF we are developing a high density (600K) chicken SNP genotyping array that will enable highly accurate GWAS, genomic selection, selection signature analysis and fine mapping of QTLs. We have re-sequenced a large number of chickens (n=243) from 24 different lines including commercial broiler and layer lines, and experimental inbred layer lines. By aligning the sequence reads to the new version of chicken reference genome (Gallus_gallus-4.0), we identified a staggering 78M SNPs that are segregating in one or more lines. This large number of SNPs was pruned on several steps to select 1.8M for validation. The key selection criteria included SNP quality scores, uniformity of distribution across the genome, equal representation of broiler and layer SNPs, and the predicted reproducibility of the SNPs in arrays. These SNPs were validated for their true reproducibility, stable Mendelian inheritance and polymorphism by genotyping on 288 individuals comprising of commercial broilers, layers and some outgroup individuals. The final panel of about 600K has been selected based on the validation results and with the key criteria of uniform distribution across the genome. Moreover, we have annotated the 1.8M SNPs to predict their genomic distribution and effects on protein coding; this information has also been used in selecting the final panel.