Genotyping-By-Sequencing (GBS) in Sheep: Comparison to SNP Chips and Whole Genome Sequencing

Recent advances in next generation sequencing technology have increased the output/cost to a level that where genotyping-by-sequencing (GBS) in livestock and plant crops as well as aquaculture species can be considered. GBS has the potential to be a cost effective, reproducible and high-throughput SNP genotyping method.  To establish the accuracy and reproducibility of GBS, and to allow forward genotyping capability, SNPs located in GBS targeted genome regions were included on the sheep High Density (HD) Illumina SNP chip. This HD SNP chip was recently developed by the International Sheep Genomics Consortium (ISGC; www.sheephapmap.org) in conjunction with Farm^IQ (www.farmiq.co.nz).  Here we compare genotype calls between the two genotyping methods as well as whole genome sequencing (between 10x -20x genome coverage). We found that GBS called 82.3% of the GBS-targeted SNPs that were on the HD chip. Utilizing the HD SNP chip genotype calls as the “gold standard”, 91% of SNP genotypes derived from whole genome sequencing (~20x coverage) were in concordance with the HD SNP chip. However the homozygous calls were 99% in concordance compared to only 74% for the heterozygous calls. The primary reason for non-concordance between systems was low reliability of SNP genotypes due to lack of sequencing depth in the affected GBS and WGS SNP calls.