Genotypic prediction of phenotypic traits and potential gene-interaction effects
In most of the trait associations, the representative candidate SNPs chosen on the four adaptive chromosomes (Etr_464, Etr_5317, Etr_1806, and Etr_4281 on chromosomes 01, 02, 04, and 22, respectively) represented above average genotype-by-phenotype associations of all 34 of the significant SNPs on these four chromosomes. In many cases, these four SNPs lie at the extreme end of the range of observed P values (Table S9).
Parker et al. (2019) found evidence for epistatic interactions that involved loci on chromosomes 01 and 04 (referred to previously as linkage groups D and B, respectively), which were found to represent the model with highest predictive ability for the female maturity trait (or ocean- and river-maturing ecotypes). We used single SNP locus representatives for each chromosome and conducted gene interaction tests for the maturity and body-size candidate loci following Parker et al. (2019, Supplemental Materials). For both traits, the model with highest support was a single locus model such that Etr_464 (chromosome 01) and Etr_5713 (chromosome 02) were the loci with highest predictive ability for the female maturity and adult total length traits, respectively (Table S10).