Table 2. Details of the genes in which the SNPs used in this study were identified.

	Gene	Abbr.	A/Z	nSNP	I/E	MAF	He	FST	Function
Pigmentation	Micropthalmia-associated transcription factor	MITF	A	2	I	0.10	0.20	0.006	A critical regulator of pigment cell development and survival (Widlund and Fisher, 2003)
	Melanocortin-1 receptor	MC1R	A	1	E	0.07	0.13	0.007	Main role as a switch affecting the type of melanin pigment produced by the melanocytes (for example, Mundy et al., 2003)
	Myosin-Va	MyoVA	A	1	I	0.17	0.29	0.010	Involved in transport of pigment-containing granules (melanosomes) to peripheral sites (Fukuda et al., 2002)
	Pallidin	Pldn	A	1	I	0.05	0.09	0.021	Involved in the biogenesis of melanosomes (Falcón-Pérez and Dell'Angelica, 2002)
	Tyrosinase-related protein-1	TYRP1	Z	1	I	0.07	0.13	0.009	Converts dopaquinone, a eumelanin and pheomelanin precursor, into eumelanin (April et al., 1998; Nadeau et al., 2007)
Vision	Rhodopsin	Rhod	A	3	I	0.48	0.59	0.014	A photoreceptor protein, which acts as a signal transducer in the rod outer segments of animal eyes. (Lamb, 1986)
	Ultraviolet-sensitive opsin	UV opsin	A	1	I	0.42	0.43	0.116	A visual pigment with its absorption maximum in the UV range. Forms the basis for UV vision (Yokoyama et al., 1998; Wilkie et al., 2000)
FM	Follistatin	FST	Z	1	E	0.42	0.44	0.146	A BMP antagonist, expressed in the growing feather bud (Patel et al., 1999)
Other	5-Aminolaevulinate synthase (Ala-synthase)	ALASY	A	2	I	0.43	0.55	0.022	The first and rate-controlling enzyme of haeme biosynthesis (Maguire et al., 1986)
	Aldolase-B	ALDOB	Z	2	I	0.32	0.22	0.023	An important enzyme for fructose and glucose metabolism (Ito et al., 1998)
	CEPUS	CEPU	A	1	I	0.16	0.25	0.021	A secreted type of neural glycoprotein belonging to the immunoglobulin-like opioid-binding cell adhesion molecule (OBCAM) subfamily (Kim et al., 1999)
	Transforming growth factor-β2	TGFBb	A	1	I	0.10	0.19	0.024	Has a role in growth, development, repair, inflammation and immunity (Clark and Coker, 1998)
	Tropomyosin	Tropom	A	2	I	0.12	0.46	0.035	Binds to actin filaments and regulates the interaction of the filaments with myosin in response to Ca2+ (Wegner, 1979)
	Very low-density lipoprotein receptor	VLDR2	Z	1	E	0.32	0.42	0.026	Associated with the metabolism of fat and cholesterol. Similar to the low-density lipoprotein (LDL) receptor (Takahashi et al., 1992)

Abbreviations: A, autosomal gene; Abbr., abbreviation used in text; E, the SNP locus is in an exon of the gene; FM, feather morphogenesis-associated gene; H_e, expected heterozygosity; I, the SNP locus is in an intron in or near the gene; MAF, minor allele frequency; n_SNP, number of SNPs in the gene region used in the study; Z, sex-linked gene. The haplotype frequencies of loci with more than one SNP are listed in Supplementary Appendix 3.