Table 3. A partial list of candidate genes revealed by DCMS analysesa.

Chr.	Gene b	Position (kb)2	P-value	Skin color	Function/association (Reference)
1	DCT	145325;145275;	0.011;0.037;	Y;W;	Pathway: Melanogenesis, organism-specific biosystem, Pigmentation (Anno et al., 2010)
1	TYR	187125;	0.017;	Y;	Melanogenesis (Anno et al., 2010)
3	OSTM1	67325;65875;	<0.001;0.047;	Y;W;	Pigmentation (Anno et al., 2010)
5	OTX2	51375;	0.003;	W;	The developing retinal pigment epithelium (Nishihara et al., 2012)
11	MC1R	18275;18275;	<0.001;0.044;	Y;W;	The regulation of coat, skin and feather color (http://www.chickencolours.com/Pigment%20holes%20Paint%20Silkies.pdf)
12	MITF	15375;15425;	0.008;0.021;	Y;W;	Regulating the differentiation of pigment cells (Tsukiji et al., 2009)
20	ASIP	1425;	<0.001;	Y;	Pigmentation in skin (yellow) and feather (Nadeau et al., 2008)
20	EDN3	11175;	0.003;	Y;	Promoting melanoblast proliferation (Dorshorst et al., 2011)
24	BCO2	6125;6125;	<0.001;0.003;	Y;W;	The deposition of yellow carotenoids in the skin (Eriksson et al., 2008)

^aAll related genes are close to potential selection regions. See Supplementary Table S4

.

^bThis column presents the middle position of selection regions, the bold and italics represent the genes without detailed annotation in chicken.