Potential of genotyping-by-sequencing for genomic selection in livestock populations

• DOI: 10.1186/s12711-015-0102-z
• Publication Date: 2015-02-28T03:54:21Z
• Authors: Gregor Gorjanc; Matthew A Cleveland; Ross D Houston; John M Hickey
• Keywords: SNP; Genomic Selection; SNP genotyping

Next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), provide alternatives to single nucleotide polymorphism (SNP) arrays. The aim of this work was evaluate the potential GBS compared SNP array genotyping for genomic selection in livestock populations. value quantified by simulation analyses which three parameters were varied: (i) genome-wide sequence read depth (x) per individual from 0.01x 20x or using genotyping; (ii) number genotyped markers 3000 300 000; and (iii) size training prediction sets 500 50 000 individuals. latter achieved distributing total available x 1000x, 5000x, 10 000x locus among varying With arrays, genotypes called data directly. GBS, reads that varied between loci individuals according a Poisson distribution with mean equal x. Simulated analyzed ridge regression accuracy bias predictions response under different scenarios. Accuracies comparable when large numbers used ~1x higher. very high at low When distributed individuals, maximized had markers. Similarly, same conditions due increasing both intensity. offers great developing populations because it makes possible cover fractions genome vary individual. Thus, is improved intensity increased larger candidates.