Table 1.

The number of SNPs significantly associated with the five plumage characters. Results derive from the linear mixed model output from GEMMA. The number of SNPs expected (under the null model of no association) to show significant associations for the large dataset (393 755 SNPs) at α = 0.000001 (−log10(α) = 6) and α = 0.0001 (−log10(α) = 4) are less than 1 and 39, respectively. For the smaller dataset (154 683 SNPs), with AR2 = 0.8 (i.e. markers with higher imputation confidence), the expectation is less than 1 and 16, respectively. Numbers in bold indicate that the number of SNPs found exceed the number expected under the null. Throat colour had the largest number of significantly associated genomic regions, suggesting a more polygenic genetic architecture for this carotenoid-based trait than for the four melanin-based traits.

trait# SNPs in full dataset, α = 0.0001 (0.000001)# SNPs in smaller dataset with AR2 > 0.8, α = 0.0001 (0.000001)scaffolds containing a plumage-associated SNPgenes containing a plumage-associated SNPgenes within 20 kb of a plumage-associated SNPscaffolds with genes within 20 kb of a plumage-associated SNP
throat523 (100)56 (0)17188111
eye line98 (46)60 (38)210192
eye spot113 (49)55 (41)311233
auricular228 (37)18 (0)410344
wing bar125 (10)10 (0)3072
expected39 (<1)16 (<1)