Résumé
The association of molecular variants to phenotypic variation is a main
issue in biology, often tackled with genome-wide association studies
(GWAS). GWAS are challenging, with increasing, but still limited use in
evolutionary biology. We used redundancy analysis (RDA) as a complimentary
ordination approach to single- and multi-trait GWAS to explore the
molecular basis of pigmentation variation in brown trout (Salmo trutta)
belonging to wild populations impacted by hatchery fish. Based on 75,684
single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait
GWAS allowed us to extract 337 independent “colour patterning loci” (CPLs)
associated with trout pigmentation traits, such as the number of red and
black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of
40 brown trout linkage groups indicating a polygenic genomic architecture
of pigmentation, (ii) were found associated with 218 candidate genes,
including 197 genes formerly mentioned in the literature dealing with skin
pigmentation, skin patterning, differentiation or structure notably in a
close relative, the rainbow trout (Onchorhynchus mykiss), and (iii)
related to functions relevant to pigmentation variation (e.g., calcium-
and ion-binding, cell adhesion). Annotated CPLs include genes with
well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also
markers associated with genes formerly found expressed in rainbow or brown
trout skins. RDA was also shown useful to investigate management issues,
especially the dynamics of trout pigmentation submitted to several
generations of hatchery introgression.