Using Axiom® SNP Arrays to Enhance the Chicken Genetic Map and Improve the Genome Assembly

In 2004, chicken was the first agricultural genome to have a genome assembly, which has greatly enhanced poultry as a major agricultural food source as well as a model organism.  Despite continued efforts that have employed the latest technologies (e.g., Illumina Moleculo, PacBio) and more, the assembly suffers from gaps and the lack of assigned sequences to 8 microchromosomes.  To address primarily the latter issue, genetic mapping is being employed.  Specifically, targeting contigs of 2 Kb or larger, SNPs were identified in the East Lansing reference panel and a custom Axiom SNP array was designed.  The status of the chicken genome and genetic map, as well as the process in designing the SNP array will be discussed.