The Genetic Architecture of Spawning Date and the Associations Among Life History Traits and Growth in Rainbow Trout (Oncorhynchus mykiss)
I investigated the genetic architecture of spawning date through quantitative trait locus (QTL) and candidate gene analyses and correlations among life history traits in a commercial hatchery strain of rainbow trout that has been under strong selection for spawning date. I first tested whether differentiation at the population level was occurring between early and late spawning broodstock at genetic loci throughout the rainbow trout genome. I detected significant genetic heterogeneity at microsatellite loci between females with early and late spawning dates within a season and this genetic differentiation was pronounced enough to assign females to the correct spawning group with an average accuracy of 76%. Many loci exhibiting significant differences in allele frequencies co-localize to genomic regions containing QTL for spawning date and other life history traits and potential candidate genes related to circadian rhythms and the brain-pituitary-gonadal axis (BPG axis). I next tested for associations among life history and growth traits by examining whether selection for spawning date based on the genetic markers associated with this trait results in differential growth, embryonic developmental rate and age of maturation. Families produced through selection of genetic markers associated with late spawning had significantly faster developmental rates and increased precocious male maturation. Co-localization of the two QTL detected for developmental rate to the same markers known to be associated with spawning date in this strain suggests that some of the co-variation between spawning date and developmental rate has a genetic basis. Furthermore, faster developmental rate conferred a growth advantage up to 13 months post fertilization within families and body size was a significant predictor of the propensity to mature early both within and across families. Finally, I tested whether variation in 9 candidate genes belonging to the clock gene system and BPG axis is associated with variation in spawning date. I detected 255 SNPs and 45 INDEL’s within the coding and non-coding regions of candidate genes. SNPs from three genes belonging to the clock gene system (bmal, clock1b, dec2) showed nominally significant associations with spawning date, providing further evidence that circadian genes play an important role in the circannual rhythms of salmonids.