Genome-wide association study and genomic predictions for resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing

Abstract

ABSTRACTPiscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming. Current treatments have been ineffective for the control of the disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) which were experimentally challenged against P. salmonis were sequenced using ddRAD sequencing. A total of 4,174 SNP markers were identified in the population. These markers were used to perform a GWAS and testing genomic selection models. One SNP related with iron availability was genome-wide significantly associated with resistance to P. salmonis defined as day of death. Genomic selection models showed similar accuracies and predictive abilities than traditional pedigree-based best linear unbiased prediction (PBLUP) method.