Development and Characterisation of a Low Density (5K) Illumina Ovine SNP Chip

A low density ovine SNP chip has been developed providing a lower cost and higher throughput format to encourage commercial uptake. This chip will allow genomic selection in ram lambs via two stage selection with initial screening based on EBVs estimated from parental information then 10-30% of the highest ranking individuals being genotyped. For commercial use, the sires and key ancestors of these lambs would have been genotyped at 50K density and imputation utilised. Originally 6000 SNPs were selected so as to be equally spaced, Illumina type II assays, with a high minor allele frequency across breeds. This was optimised based on minimizing the sum of the squared differences from 0.5 of the breed MAFs, as estimated from the ISGC HapMap 50K dataset, coupled with a penalty factor based on distance from the centre of the relevant genome segment. The subsequent SNP chips were evaluated by genotyping 1729 individuals from a variety of New Zealand breeds and crosses. 5409 SNPs passed initial manufacturing QC and were included in the manifest. Of these, 5377 SNPs had a call rate above 98% and 5326 had a MAF above 0.1 across New Zealand breeds. The genotype repeatability was 99.99%. In validation tests, masking results from 50K genotyping, Beagle 3.0.4 was found to impute missing SNPs with 86.3, 91.4 and 95.2 percent accuracy for Perendales, Romneys and Coopworths respectively when no parent had been genotyped with the 50K chip. These percentages increased to 89.2, 94.6 and 95.9 where the sire had been genotyped.