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 SNP	genes containing a plumage-associated SNP	genes within 20 kb of a plumage-associated SNP	scaffolds with genes within 20 kb of a plumage-associated SNP
throat	523 (100)	56 (0)	17	18	81	11
eye line	98 (46)	60 (38)	2	10	19	2
eye spot	113 (49)	55 (41)	3	11	23	3
auricular	228 (37)	18 (0)	4	10	34	4
wing bar	125 (10)	10 (0)	3	0	7	2
expected	39 (<1)	16 (<1)