Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch

Abstract

In quantitative genetics, multivariate statistical approaches are increasingly used to describe genetic correlations in natural populations, yet the exact genetic relationship between phenotype and genotype is often unknown. Quantitative trait locus (QTL) analyses can be used to describe the molecular basis of this relationship. In salmonids, growth and development are important fitness traits that are phenotypically correlated with each other and with other life-history traits, and an understanding of the molecular basis of these relationships is valuable for future evolutionary studies. Here, a QTL analysis using an outbred cross was initiated to determine the molecular basis of phenotypic correlations between such growth traits in coho salmon (Oncorhynchus kisutch), an important fish species distributed throughout the North Pacific Ocean. Fifty-three QTL for growth rate, length and weight at eight time periods were located on seven linkage groups (OKI03, OKI06, OKI18, OKI19, OKI23, OKI24 and an unnamed linkage group) or associated with five unlinked markers (Omm1159, Omm1367/ i, Omy325UoG, OmyRGT55TUF and OtsG422UCD). One QTL for hatch timing was associated with the marker, Omm1241. All QTL were of minor effect, explaining no more than 20% of the observed variation in phenotypic value. Several instances of colocalization of QTL weight, length and growth rate were observed, suggesting a genetic basis for phenotypic correlations observed between these traits. This study lays the foundation for future QTL mapping efforts, for detailed examinations of the genetic basis of phenotypic correlations between growth traits, and for exploring the adaptive significance of growth traits in natural populations.

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

“…QTL for both weight and length were detected on Chr-12 (Sept. XX male) and Chr-10 and -17 (Dec. XY male). Overlapping weight and length QTL have also been found in other species of fish (Wang et al 2013;Sánchez-Molano et al 2011;McClelland and Naish 2010), and these results suggest that many genes have pleiotropic effects in the regulation of weight and length. The coupling of length and weight QTL is not surprising given that genetic correlations for these two traits are high (Fishback et al 2002), but interestingly, these traits appear largely uncoupled to genes influencing variation in condition factor.…”

Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

“…Specifically, F3 diploid crosses were created from a cultured line originally derived from an outbred cross between two populations in Washington State (McClelland and Naish 2010). F0 males were collected from Bingham Creek in Southwest Washington (47°15′N, 123°40′W).…”

Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)

“…Consequently, most identified QTL span a large chromosomal region, from which the identification of a causative gene(s) is problematic. Several studies have described QTL associated with growth and/or sexual maturation in salmonid species including Atlantic salmon [21–25], rainbow trout [26–29], coho salmon [30,31] and Arctic charr [24,32]. Yet, information regarding candidate genes located in these QTL regions is scarce for most species.…”