A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population

Reiner, Gerald; Tramberend, Kirsten; Nietfeld, Florian; Volmer, Klaus; Wurmser, Christine; Fries, Ruedi; Willems, Hermann

doi:10.1186/s12863-020-0814-0

Table 2 List of candidate genes after extracting non-synonymous colour genes and their association with coat colour in red deer populations from Reinhardswald and others. All figures originally referring to the bovine genome were recalculated so as to fit to the recently published genome sequence CerEla1.0 of Cervus elaphus

From: A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population

Cervus elaphus							not Reinhardswald		Reinhardswald		Bos taurus
CEC	chr_pos	gene	prot_len	pos	aa variant	SNP	brown	white	brown	white	BTA	chr-pos
3	47,510,875	ADAMTS20	1915	1134	p.1134 V > I	0 = G,1 = A	GG,AG	GG,AA	AA,AG	AA,AG	5	37,227,378
3	47,511,824	ADAMTS20	1915	1204	p.1204I > T	0 = C,1 = T	CT, TT	CC, TT	CC,CT	CC,CT,TT	5	37,228,964
12	126,879,585	APC	2851	2720	p.2720 T > I	0 = G,1 = A	GG,AG	AA,AG	AA,AG,GG	AA,AG,GG	10	1,118,743
30	26,850,856	ATP7B	1505	604	p.604D > Y	0 = C,1 = A	AA,AC	AA	AA, AC	AA	12	21,442,340
5	124,958,667	DPH1	438	273	p.273Q > R	0 = A,1 = G	AG	GG,AG	GG,AG	AA,GG,AG	19	23,643,044
1	30,427,888	DRD2	445	323	p.323A > T	0 = C,1 = T	TC, TT	TC, TT, CC	CT,TT	CC,CT,TT	15	24,305,495
7	4,579,141	DST	5653	918	p.918A > V	0 = C,1 = T	TT,TC	CC,TT	CC,CT	CC,CT,TT	23	3,499,604
7	4,697,844	DST	5653	3005	p.3005 N > S	0 = A,1 = G	GG,AG	AA,GG	AA,AG	AA,AG	23	3,584,163
5	8,504,491	HPS4	681	64	p.64 V > I	0 = G,1 = A	GG,AG	AA, GG	AG,GG	GG	17	68,389,531
5	8,509,383	HPS4	681	143	p.143I > V	0 = T,1 = C	CC, CT, TT	CC, CT, TT	CT,TT	CT,TT	17	68,383,336
5	8,515,161	HPS4	681	298	p.298S > L	0 = G,1 = A	AG, GG	AA, GG	AG,GG	AG,GG	17	68,377,269
5	gap	HPS4	681	571	p.571A > V	0 = C,1 = T	CC, TC	CC, TT	CT,CC	CT,CC	17	68,372,291
23	26,036,482	ITGB1	798	670	p.670I > V	0 = A,1 = G	AG, GG	AG,GG	AG,GG	GG	13	20,282,477
3	35,496,676	KRT75	543	35	p.35A > T	0 = G,1 = A	GG, AG	AA,GG	AG,GG	AA,AG,GG	5	27,630,776
1	70,321,949	MYO7A	2293	1779	p.1779R > Q	0 = G,1 = A	GG,AG	AA,GG	AG,GG	AA,AG,GG	15	57,402,107
11	4,864,962	NOTCH1	2900	40	p.40 V > A	0 = A,1 = G	SNP not confirmed by Sanger sequencing				11	104,015,685
11	4,865,366	NOTCH1	2900	59	p.59P > R	0 = G,1 = C	CC,GC	CC	CC,CT,GG	CC,CT,GG	11	104,015,279
21	458,420	RECQL4	1218	600	p.600G > R	0 = G,1 = A	AA, AG	GG,AA	GG	GG	14	1,617,571
12	53,771,046	SLC24A5	501	177	p.177A > V	0 = G,1 = A	GG, AG	AA, AG	AG	AA	10	62,475,788
1	55,722,734	TUB	508	163	p.508A > V	0 = G,1 = A	GG,AG	AA,AG	AA,AG,GG	AA,AG	15	45,040,996
2	na	TYR	530	291	p.291G > R	0 = C,1 = T	CC, CT	TT,CC	CT, CC	TT	29	6,451,778

CEC Cervus elaphus chromosome, chr_pos position on the Cervus elaphus chromosome (in bp), gene name of the gene, prot_len length of the corresponding protein, pos position of the amino acid substitution in the protein, aa variant amino acid variant, brown/white genotype(s) of the brown and white animals, respectively; gap: gap in CerEla1.0, na not annotated. In a first step, all genes were tested with 3 brown and 3 white animals from the Reinhardswald and 3 brown and 3 white animals not from the Reinhardswald. TYR was tested with 194 brown and 11 white samples from the Reinhardswald and 21 brown and 9 white animals not from the Reinhardswald

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