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
| 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