Development of a High Density (600K) Illumina Ovine SNP Chip and Its Use to Fine Map the Yellow Fat Locus

Abstract

Developed by the International Sheep Genomics Consortium (ISGC) in conjunction with FarmIQ (www.farmiq.co.nz), the Ovine Infinium® HD SNP BeadChip includes 603,350 callable SNPs, the majority equally spaced across the genome and selected from groups differing in their minor allele frequency across an international sample of breeds. The chip also contains SNPs reported in the literature as affecting function, those that change protein structure, and those on the OvineSNP50 BeadChip. For sheep researchers the HD chip, in combination with other genotyping tools, will provide the basis for the next generation of genomic selection and has been designed to enable researchers to customise or update it with new SNP discoveries. As a proof of concept for the use of the HD chip in fine mapping studies, we investigated the causative genetic variant of yellow fat, an undesired trait in sheep carcasses. Consumers associate yellow coloured fat in meat with sick and jaundiced animals and consequently carcasses displaying yellow fat are downgraded at the processing plant resulting in reduced payment for these animals. Previous work has suggested that a variant causing a truncation mutation in the BCO2 gene is responsible for the yellow fat phenotype however this mutation is not associated with all yellow fat cases and is also sometimes heterozygous while the observed mode of inheritance is recessive.