Is Genotyping By Sequencing a Viable Alternative to Existing Methods for Genomic Selection and GWAS?

Genotyping by sequencing (GBS) is emerging as an alternative technology to array based genotyping for genomic selection and genetic mapping.  A method, based on GBS allele read depths, was developed to give unbiased estimates of genomic relationship matrices (GRM). This overcomes issues with missing genotypes and poor genotype calling accuracy due to low coverage when SNP density and samples numbers per lane are maximised. The GRM produced can be interrogated to estimate: breed composition, pedigree, traceability, inbreeding and co-ancestry as well as be included directly in existing mixed models to estimate breeding values. Crucially, the methodology is extremely cost competitive compared to array based technologies, particularly at high densities, which typically involve low numbers of samples and high set-up costs. This opens up major opportunities for application in minor agricultural species and studies of natural populations. Imputation, genome sequence or reference imputation data are not required and the method can be extended to multi-marker/haplotype based methods if an assembled genome is available. Furthermore, with genotyping costs comparable to existing DNA based parentage assays, opportunities are arising to genotype multiple tiers in elite breeding schemes leading to rapid increases in genetic gain.