Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations.

Roger L Vallejo,Sixin Liu,Gregory D Wiens,Guangtu Gao,James E Parsons,Alvaro G Hernandez,Jason P Evenhuis,Timothy D Leeds,Kyle E Martin,Timothy J Welch,Breno O Fragomeni,Yniv Palti

doi:10.3389/fgene.2017.00156

Abstract

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.

Highlights

Bacterial cold water disease (BCWD) inflicts substantial mortality and economic losses in salmonid fish aquaculture (Nematollahi et al, 2003; Barnes and Brown, 2011)
For both BCWD phenotypes and across genotyping platforms and populations, the mean heritability estimated with wssGBLUP (0.32) was slightly higher than that estimated with BayesB (0.27)
Previous studies detected quantitative trait loci (QTL) for BCWD resistance on chromosomes Omy1 (Vallejo et al, 2014a; Palti et al, 2015b), 2 (Vallejo et al, 2014a; Liu et al, 2015b), 7 (Quillet et al, 2014; Vallejo et al, 2014a; Palti et al, 2015b), 12 (Vallejo et al, 2014a; Liu et al, 2015b), 17 (Johnson et al, 2008; Campbell et al, 2014; Quillet et al, 2014), 26, and 28 (Liu et al, 2015b) which were not detected in this study. These conflicting results in QTL mapping can be expected due to several reasons including: (1) QTL effects can be population and/or family specific with unique extent/phase of linkage between QTL and marker alleles; and (2) they can represent false positive results due to limitations and weaknesses of experimental-design and power of analysis as we describe here. This genome-wide association studies (GWAS) is the most comprehensive genome-wide scan for QTL associated with BCWD resistance performed to date in two commercially-relevant rainbow trout breeding populations, using two whole-genome single nucleotide polymorphism (SNP) genotyping platforms and two multiple-regression GWAS models

Summary

Introduction

Bacterial cold water disease (BCWD) inflicts substantial mortality and economic losses in salmonid fish aquaculture (Nematollahi et al, 2003; Barnes and Brown, 2011). We revealed the complex genetic architecture of BCWD resistance (Vallejo et al, 2010) and identified several moderate-large effect quantitative trait loci (QTL) for this trait in the NCCCWA odd- and evenyear rainbow trout selective-breeding populations (Wiens et al, 2013; Vallejo et al, 2014a; Liu et al, 2015b; Palti et al, 2015b). Sequencing-by-genotyping methods that do not require a priori marker discovery or a reference genome sequence and are capable of concurrent marker discovery and genotyping in many individuals were developed for genetic analyses (Davey et al, 2011) One such technique is restrictionsite-associated DNA (RAD) sequencing (Miller et al, 2007; Baird et al, 2008). The method of RAD genotyping by sequencing has been widely used in salmonid species for SNP discovery, generating linkage maps, QTL mapping, genome-wide association studies (GWAS) and for evaluating genome-enabled selection (Hecht et al, 2012, 2013; Houston et al, 2012, 2014; Miller et al, 2012; Hale et al, 2013; Narum et al, 2013; Brieuc et al, 2014; Campbell et al, 2014; Gonen et al, 2014; Palti et al, 2014, 2015b; Liu et al, 2015a,b; Vallejo et al, 2016)

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