Quantitative Trait Loci for Spawning Date and Body Weight in Rainbow Trout: Testing for Conserved Effects Across Ancestrally Duplicated Chromosomes

Abstract

We incorporated 69 microsatellite loci into an existing data set of 132 markers to test for quantitative trait loci (QTLs) affecting spawning date and body weight in a backcross between two outbred strains of rainbow trout (Oncorhynchus mykiss). Twenty-six linkage groups were identified and synteny of duplicated microsatellite markers was used to confirm 13 homeologous chromosome pairs. Gene-centromere data were used to localize the centromeres for 13 linkage groups whose orientations were previously unknown. We applied a combination of interval mapping and single marker analysis to the segregating maternal and paternal alleles at 201 microsatellite loci. Four spawning date QTLs with suggestive evidence for an additional two QTLs were detected in female trout spawning at 3 and 4 years of age. Similarly we detected three QTLs for body weight in females at 2 years of age plus four suggestive QTLs for this trait. We found marginal evidence that three pairs of ancestral homeologues contained detectable QTLs for the same trait. In one of the three pairs of homeologues, the duplicated QTL regions mapped to the same relative chromosomal location, while the exact localization of the QTL position in one of the other pairs was difficult to infer since it was based on data from a male-derived map. The existing data were unable to refute a hypothesis that duplicated functional genes will be maintained within the telomeric regions of salmonids due to preferential male-mediated crossing over in this region. Two of the four spawning date QTLs were detected on linkage groups with unknown homeologous relationships. QTLs with possible pleiotropic effects on both spawning date and body size were localized to two linkage groups.

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

“…Many of these studies have identified QTL or significant associations between markers on Omy5 and life-history traits such as spawn timing [47,65,68], smoltification [42,46] and development rate or early maturation [17,66,67,70]. Thus, this study supports previous suggestions that the LD block on chromosome Omy5 represents a 'master control region' influencing residency and anadromy in O. mykiss [46,72] and is a parallel selected region [21] that has experienced repeated selection in multiple populations.…”

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

“…QTL mapped in coho have previously been mapped to homologous linkage groups in other salmon species (Martyniuk et al, 2003;O'Malley et al, 2003;Reid et al, 2005). One QTL for body weight day 293 after fertilization was mapped to RT21 in rainbow trout (Martyniuk et al, 2003); this rainbow trout linkage group is homologous to coho linkage group OKI19 that contains QTL for body weight at all ages measured in this study.…”

QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus)

“…The BW QTL with the greatest effect in Atlantic salmon was detected in a region of AS-8 that shows homology to RT and AC linkage groups RT-24 and AC-13, respectively (Somorjai, 2001;O'Malley et al, 2003). Unfortunately, the QTL regions in these studies were localized in the male mapping parent, making it difficult to ascertain the exact chromosomal location of the QTL region, for reasons discussed previously.…”

“…Three of the significant QTL for BW identified in Atlantic salmon that occur on linkage groups AS-1, AS-8, and AS-11 may be homologous to BW QTL regions in RT and AC (Somorjai, 2001;Martyniuk et al, 2003;O'Malley et al, 2003). AS-1 shows homology to a pair of RT chromosomes (RT-27 and RT-31) that represent ancestral homeologues (Woram et al, 2003).…”

“…The regression of log FL 3 onto log BW was approximately linear (r 2 X0.83 in all three families) and the coefficient of slope (b) was approximately 3 (b ¼ 2.89-3.35). Due to the high correlation between FL and BW, and in order to allow for comparisons to QTL for BW and K in RT (O'Malley et al, 2003) and AC (Somorjai et al, 2003), only BW and K were used for QTL analysis. Sampling methods precluded the sexing of the progeny.…”