Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction Site Associated DNA Sequencing

Abstract

Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site−associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs.

Genetic variation underlying resistance to infectious hematopoietic necrosis virus in a steelhead trout (Oncorhynchus mykiss) population

“…Phenotypic correlation between mortality and DTD was calculated at the family level because all individuals with a DTD measure were susceptible to the virus. Heritability estimates for mortality and DTD are designated in italics on the diagonal with 95% confidence intervals approaches (Palti et al 1999, 2001, Trobridge et al 2000, Arkush et al 2002, Miller et al 2004, Liu et al 2013, low density quantitative trait loci (QTL) mapping (Khoo et al 2004, Barroso et al 2008) and genome-wide association studies (Campbell et al 2014), new tools available for Oncorhynchus mykiss, including a draft genome (Berthelot et al 2014) and a 57K single nucleotide polymorphism (SNP) chip (Palti et al 2015), will facilitate molecular-based studies on a more extensive portion of the genome. …”

Applications of genotyping by sequencing in aquaculture breeding and genetics

“…), and infectious hematopoietic necrosis (Campbell et al . ) and bacterial cold water disease (Campbell et al . ; Liu et al .…”

Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

“…These techniques have been applied in several studies of aquaculture species to generate high-density linkage maps ( e.g. , Palaiokostas et al 2013a,b; Gonen et al 2014; Palaiokostas et al 2015) and perform genome-wide association studies (GWAS) in a cost-efficient manner (Campbell et al 2014). A flexible and easily streamlined variation of RAD sequencing, named 2b-RAD sequencing, utilizes type IIB restriction enzymes to cleave genomic DNA upstream and downstream of the target site (Wang et al 2012).…”