Next-Generation Sequencing for Animals

A collaboration between Dr. David Burt of the Roslin Institute, Affymetrix, and multiple other researchers has yielded a high density 600K chicken genotyping microarray. Axiom® Genome-Wide Chicken Genotyping Array enables studies into the development of poultry lines that can better withstand a variety of stresses including emerging diseases, increased heat caused by climate change, and reduced quality and availability of feed and water. The array is the first chicken genotyping microarray of this size. The SNP content supports a range of studies, such as genetic selection, genome wide association studies, and high-resolution genetic mapping. Axiom® Genome-Wide Chicken Genotyping Array is available from Affymetrix for use across multiple populations of layers, broilers, and wild outbred non-commercial breeds for advanced genomic selection programs.

To identify relevant SNPs for the array, Dr. Burt's team first used next-generation sequencing (NGS) to screen and map genetic variations across 24 lines of broiler and layer chickens. This information was used to develop the high-density SNP genotyping array. From the resequencing, 78 million SNPs were segregated into those likely to be most interesting to breeders. Further selection narrowed the group to 1.8 million, while also ensuring that broiler and layer SNPs were equally represented. The SNP distribution was also adjusted for the extreme recombination variation rates in birds.

The team validated the 1.8 million SNPs using microarrays across all lines on multiple criteria including degree of polymorphism, genotype call rate, cluster separation, and reproducibility. They used principal component analysis to demonstrate that these markers can be used to classify chicken lines, resulting in tight groupings of brown egg layers, broilers, and white egg layers.

The initial project goal was to identify at least 100K polymorphic SNPs for each line of broilers and layers. The final result far exceeded those expectations, yielding 600K validated SNPs.