Association analyses suggest colour is regulated via an epistatic
interaction between two candidate loci
Mapping RADseq reads against reference genome resulted in 95% (± 0.6
SD) mapping rate, where an average of 9 million reads (± 5mio SD) were
utilized per individual. Catalogues construction resulted in the
discovery of 1165325 loci, with an average size of 185.7 sites and an
average coverage of 46.2x (± 20.9x SD). Filtering for minor allelic
frequency, presence in 80% of the dataset, and collecting one random
SNP per RAD-locus resulted in a panel of 19212 bi-allelic SNPs. The
distribution of RADseq reads across genomic regions of candidate loci
for coloration implied that our strategy indeed covered not only
flanking regions but also the coding sequence, despite not a single
locus in the coding sequence has survived the variant calling pipeline
(Table S5A and B). The search for structure at a meta-population level
identified two clusters, though neither were associated with colour,
family, or temporal stamp (Fig. S2-S3). Numbers varied between clusters,
with cluster 1 containing most of the samples. Association studies
jointly revealed a total of 2 markers concordantly associated with the
colour phenotype, which we will henceforth refer to as 602-G/C(log(p) = 6.32) and 3657-C/T (log(p) = 4.43) (Fig.
2; Table 2). Exploring the effect size of those associations revealed a
high predictive power for the colour “grey” either when genotypes are
analysed independently for each locus or jointly. Specifically,
independent genotype combinations showed that heterozygotes and
homozygotes for the least common allele to have between 70% and 90%
probability of being grey and between to 55% to 100% when genotypes of
both loci are interpreted together (Fig. 2). Notably, the probability
increase is explained by the number of copies of the less common allele
in each genotype (w-test= C in 602-G/C , w = 20.28, 2, p =
1.0e-05; T in 3657-C/T w = 20.29, p = 1.0e-05) (Table S6-S11)