Table 4.
Sequence polymorphisms in ASIP, MC1R, and TYRP1.
| Gene symbol | Location in the gene | Variant | Reference | Effect on protein | Phenotype–genotype |
P-value | ||
|---|---|---|---|---|---|---|---|---|
| White | Black | Brown | ||||||
| MC1R | Promoter (1802 bp from ORF | g.535236C > T | This study | Non-coding | 4CC | 4CT | 4CT | 0.0005 |
| MC1R | Promoter (557 bp from ORF) | g.536482G > A | This study | Non-coding | 2GG, 2GA | 1GG, 2GA, 1AA | 2GG, 2GA | 0.6208 |
| MC1R | Promoter (420 bp from ORF) | g.536623G > A | This study | Non-coding | 4GG | 3GG, 1GA | 3GG, 1GA | 0.4033 |
| MC1R | 5′UTR | g.537027G > A | This study | Non-coding | 4GG | 3GG, 1GA | 3GG, 1GA | 0.4033 |
| MC1R | 5′UTR | g.537028A > T | This study | Non-coding | 4AA | 3AA, 1AT | 3AA, 1AT | 0.4033 |
| MC1R | Exon | g.537961C > T; c.901C > T | Almathen et al., 2018 | Missense; p.Arg301Cys | 3CT, 1TT | 4CC | 4CC | 0.0042 |
| MC1R | 3′UTR | g.538058G > A | This study | Non-coding | 4GG | 2GG, 2GA | 4GG | 0.0718 |
| ASIP | Exon 2 | g.174495T_del; c.23T_del | Almathen et al., 2018 | Frameshift; p.24X | 4TD | 4DD | 2TT,2TD | 0.0009 |
| ASIP | Exon 2 | g.174497A > G; c.25A > G | Almathen et al., 2018 | Synonymous | 4GA | 4AA | 2GG, 2GA | 0.0009 |
| ASIP | Exon 4 | g.178388C_del | This study | Frameshift; p.253X | 4CC | 2CC, 2CD | 3CC, 1CD | 0.178 |
| TYRP1 | Intron 1 (72 bp before exon 2 | g.6544484G > A | This study | Non-coding | 4GG | 3GG, 1GA | 4GG | 0.3359 |
| TYRP1 | Intron 2 (26 bp after exon 2) | g.6544049T > C | This study | Non-coding | 2TT, 2TC | 4TT | 1TT, 3TC | 0.0438 |
| TYRP1 | Intron 3 (13 bp before exon 4) | g.65372260_g.65372261insCA | This study | Non-coding | 1insCA/insCA | None | None | 0.3359 |
| TYRP1 | Intron 4 (90 bp after exon 4 | g.6537183T > C | This study | Non-coding | 2TT, 2TC | 3TT, 1TC | 1TT, 3TC | 0.3512 |
| TYRP1 | 3′UTR | g.6529345A > T | This study | Non-coding | 3AA, 1AT | 3AA, 1AT | 3AA, 1AT | 1 |
Sequence variants were discovered by sequencing the three genes in 4 white, 4 black, and 4 brown dromedaries. Sequence positions correspond to dromedary whole genome assembly: GCA_000767585.1 PRJNA234474_Ca_dromedarius_V1.0.; MC1R scaffold ID: NW_011592664.1, ASIP scaffold ID: NW_011591043.1 and TYRP1 scaffold ID: NW_011591511.1; Numbers in columns White, Black, Brown denote the number of animals with the corresponding genotype; ORF, open reading frame; D, deletion; P-value for genotype–phenotype association was determined by contingency analysis in JMP using Chi-square (see Supplementary Figure S2).