Utilisation of the Ovine HD SNP Chip for Meat Quality Traits in NZ Composite Terminal Sire Breeds

FarmIQ (www.farmiq.co.nz) a joint New Zealand government and industry Primary Growth Partnership programme, in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) released the Ovine Infinium^®HD SNP BeadChip in 2013.  FarmIQ commissioned the HD Chip as part of its mission to add value to red meat by improving linkages between animals’ meat yield and quality, and what happens on the farm and in the processing plant.

The ISGC together with FarmIQ developed the HD SNP chip following the re-sequencing of 73 diverse breeds from around the world and utilised the recently released sheep genome assembly (OARv3.1). The chip contains ~600 000 SNPs; although majority (~90%) of SNPs have MAF>0.10, there are also rare genetic variants and ~53,000 SNPs that are known to affect proteins included.

The FarmIQ programme has now used this HD chip for genome wide association studies and multi-breed genomic predictions for meat quality traits in New Zealand composite terminal sire breeds. Preliminary results suggest genomic prediction accuracies will be similar to measuring the trait on the animal itself and most meat quality traits also have several loci of large effect.