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).