Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss)

Abstract

BackgroundSomatic growth is a complex process that involves the action and interaction of genes and environment. A number of quantitative trait loci (QTL) previously identified for body weight and condition factor in rainbow trout (Oncorhynchus mykiss), and two other salmonid species, were used to further investigate the genetic architecture of growth-influencing genes in this species. Relationships among previously mapped candidate genes for growth and their co-localization to identified QTL regions are reported. Furthermore, using a comparative genomic analysis of syntenic rainbow trout linkage group clusters to their homologous regions within model teleost species such as zebrafish, stickleback and medaka, inferences were made regarding additional possible candidate genes underlying identified QTL regions.ResultsBody weight (BW) QTL were detected on the majority of rainbow trout linkage groups across 10 parents from 3 strains. However, only 10 linkage groups (i.e., RT-3, -6, -8, -9, -10, -12, -13, -22, -24, -27) possessed QTL regions with chromosome-wide or genome-wide effects across multiple parents. Fewer QTL for condition factor (K) were identified and only six instances of co-localization across families were detected (i.e. RT-9, -15, -16, -23, -27, -31 and RT-2/9 homeologs). Of note, both BW and K QTL co-localize on RT-9 and RT-27. The incidence of epistatic interaction across genomic regions within different female backgrounds was also examined, and although evidence for interaction effects within certain QTL regions were evident, these interactions were few in number and statistically weak. Of interest, however, was the fact that these predominantly occurred within K QTL regions. Currently mapped growth candidate genes are largely congruent with the identified QTL regions. More QTL were detected in male, compared to female parents, with the greatest number evident in an F1 male parent derived from an intercross between domesticated and wild strain of rainbow trout which differed strongly in growth rate.ConclusionsStrain background influences the degree to which QTL effects are evident for growth-related genes. The process of domestication (which primarily selects faster growing fish) may largely reduce the genetic influences on growth-specific phenotypic variation. Although heritabilities have been reported to be relatively high for both BW and K growth traits, the genetic architecture of K phenotypic variation appears less defined (i.e., fewer major contributing QTL regions were identified compared with BW QTL regions).

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

“…Indeed, this is a major drawback of all family-based QTL studies, as these studies will likely only be able to sample a small proportion of all the genomic regions that influence a given phenotype in a population. However, previous rainbow trout studies have found QTL for growth on all of the chromosomes identified by this study (Wringe et al 2010;Magee 2011). In Atlantic salmon, Salmo salar, significant QTL for body weight were detected on AS-6 and -11, which are homologous to Chr-16 and -12/28 (Reid et al 2005).…”

“…In addition, quantitative trait locus (QTL) analyses have located multiple chromosomal regions that control the phenotypic variation (Laine et al 2013;Laghari et al 2013). For example, 10 linkage groups contain significant body weight QTL in rainbow trout, Oncorhynchus mykiss, from multiple strains (Wringe et al 2010). Other studies have shown that QTL can vary between strains and across rearing environments Magee 2011;Chiasson et al 2013).…”

“…If a region of the genome is highly conserved between two species, a gene falling within this conserved region in one species is assumed to fall within that same region in the second species. The model species threespine stickleback, Gasterosteus aculeatus, exhibits a high level of synteny with rainbow trout (Guyomard et al 2012) and previous studies have used this relationship to localize genes with rainbow trout QTL (Wringe et al 2010;Norman et al 2012). However, due to a recent whole-genome duplication in salmonids (Allendorf and Thorgaard 1984), two gene locations are expected in rainbow trout for each location identified in stickleback.…”

“…The offspring were derived from crosses made in September 2008 from a normal XY genotype male and a neomale (XX genotype), and halfsibling families made in December 2008, derived from an XY genotype male. We screened the families for variation at marker loci located on 11 linkage groups known to contain body weight QTL (Wringe et al 2010;Magee 2011). We then tested whether candidate genes known to be differently expressed between large and small fish in a microarray analysis of a subset of the fish from the same families (Kocmarek et al 2014(Kocmarek et al , 2015 used in the current QTL analysis localize with the chromosomal regions containing the QTL for body weight and length.…”

Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish

“…O'Malley et al [23] identified QTLs for body weight in rainbow trout on 10 different LGs. Wringe et al [24] used additional backcrossed families and SSR markers to confirm the O'Malley et al's results and found several major candidate growth genes (e.g., GH2 and Pax7). Reid et al [25] identified a QTL for body weight in two LGs (AS8 and 11) of Atlantic salmon, and reported that it was homologous to the growth QTL in rainbow trout.…”