Genomic Selection in Dairy Goats (Capra hircus) using Genotyping by Sequencing

Genomic selection offers considerable advantages in ruminant dairy animals because the key traits of interest (milk volume, composition and reproductive traits) cannot be measured in males, the sex where opportunities for both increased selection pressure and decreased generation interval are greater. Historically, relatives’ information has been used to create breeding values (BLUP) and some degree of progeny testing has been used to increase accuracy. However, in large dairy goat enterprises, accurate pedigree recording at birth is fraught and this has encouraged use of DNA pedigrees based on microsatellites, albeit with additional cost. Genomic selection via GBLUP addresses both of these issues, while increasing accuracy, but the cost of genotyping using chip arrays is excessive and further compromised by large and inflexible setup costs. The alternative, genotyping by sequencing (GBS), has suffered from a variety of technical challenges including: increased complexity of data processing, a high proportion of missing genotypes, and low accuracy of genotype calls. All of these challenges have now been overcome and this technology has been implemented in a New Zealand dairy goat herd using a methodology that comprises approximately 80,000 SNPs for less than US$20/sample. The use of GBS has considerable implications for future goat genomic research especially if the technology is also used for high density genotyping (>200kb SNPs), due to the lack of a suitable HD chip.