Figure 2.

Genome-wide association study (GWAS) results for flesh colour in Chinook salmon. (a) Manhattan plot of all loci (SNPs) analysed for association with flesh pigmentation in an F₂ family of Chinook salmon derived from the backcrossing of two flesh colour populations. SNPs located above the red line indicate genome-wide significance based on Bonferroni correction (p < 4.60 × 10⁻⁶). (b) The quantile–quantile plot obtained from the analysis. (c) The significant peak found on Chromosome 30 in more detail with the grey bar indicating the position of the carotenoid-associated gene (BCO2-l) that aligned next to the most significant SNP. (d) The phenotype association for genotypes GG and GT at the most significant SNP (S10010_28050034; p = 9.18 × 10⁻²², R² = 0.66). Points are jittered horizontally and vertically for visualization. (Online version in colour.)