Application of Genotyping-by-Sequencing (GBS) in Livestock and Aquaculture Species

Advances in next generation sequencing technology have increased the output/cost ratio to a level where cost effective genotyping-by-sequencing (GBS) in livestock, plants and aquaculture species is now a reality. High-throughput GBS methodology produces SNP genotypes that are supported by varying depth of sequence reads, dependent on the number of samples and proportion of the genome assayed within a lane of sequencing. Although more samples per lane improves cost effectiveness, a balance is needed to achieve the required sequence read depth to support the SNP genotypes for use in downstream applications such as genetic diversity and differentiation, parentage assignment, inbreeding estimation, genomic selection and genome wide association studies. Here we present parentage assignments in deer and salmon (species with genome sizes of ~3Gb) that utilises GBS data, filtered for likely genotyping artefacts, and using an unbiased genomic relationship matrix adjusted for sequence read depth at each individual SNP location.