Body size traits
Highly significant associations (adjusted P < 0.001) were observed for body size traits and SNPs on the four adaptive regions across datasets (WFA♀, WFA♂, T_BON, S_BON, and JDD; Table 1). The strongest associations between SNPs and body size traits (-LOG(10P) > 30) were with length (Fig. 2), weight, and girth and SNPs on chromosome 02 for the T_BON dataset; however, the S_BON and JDD datasets also showed significant associations for the same SNPs and traits (-LOG(10P) > 2). This result was similar to the findings of Hess et al. (2014) where they show that a SNP (Etr_5317), herein mapped to chromosome 02, had strongest association to body size traits at Bonneville Dam. In contrast, the WFA♀ and WFA♂ datasets had fewer total significant associations with body size traits across the four adaptive linkage groups. The WFA♀ and WFA♂ datasets significant associations to body size traits were concentrated on chromosome 02 and chromosome 04, and of these two linkage groups, chromosome 04 appeared to have the strongest associations with body size traits, and primarily with length and weight. For WFA♂, similar to the length and weight traits, male gonad size was also associated with chromosome 04 and chromosome 02 SNPs, which likely owes to the high intercorrelation observed among these traits. Overall, the results support strong association of SNPs with body size traits, primarily length and weight, compared to other intercorrelated traits (e.g., migration timing and migration distance). The chromosome that showed the highest association with body size was chromosome 02 at the BON and JDD sites. This chromosome 02 association with body size was consistent among sites both within and outside the Columbia River basin (Parkeret al. 2019).
The genotypes in the chromosome 02 adaptive region (SNP Etr_5317) in the T_BON sample were also predictive of average lengths, such that the average size of homozygotes for large body size alleles “AA”, heterozygotes “AC”, and homozygotes for small body size alleles “CC” were 677 mm, 627 mm, and 592 mm, respectively (Fig. 3b). Although the average body sizes differed across sites and sexes (WFA♀ were larger on average than WFA♂), the trends were consistent (Fig. 3b). Further, similar genotype and average length associations have been detected in Pacific lamprey collected from the Klamath River (634 mm, 602 mm, and 557 mm for the AA, AC, and CC genotypes at Etr_5317, respectively; Parker et al. 2019).