Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation

Abstract

Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree-based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low-density novel genotype-by-sequence assay was designed and incorporated into the scheme. Through the use of a static high- and dynamic low-density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.