Table 1.
Variants identified among 6 yak by Sanger sequencing of KIT exons (UMD3.1 Chromosome 6; Transcript ENSBTAT00000003498.5) with the genomic position with respect to ARS-UCD1.2 noted
| Position (bp) UMD3.1 | Position (bp) ARS-UCD1.2 | Variant ID | Ref | Alt | Black | Trim | Royal | Variant position (predicted consequence) based on ENSBTAT00000003498.5 |
|---|---|---|---|---|---|---|---|---|
| 71796285 | 70166659 | rs110394433 | T | G | G/G | G/T | T/T | Upstream Variant |
| 71796527 | 70166901 | . | TT | T | T/T | T/TT | TT/TT | Intron 1 Variant |
| 71868653 | 70205292 | rs109344937 | C | T | T/T | T/C | C/C | Synonymous Variant, Exon 2, c.177C>T, p.Thr59Thr |
| 71868885 | 70205524 | rs799246224 | C | T | T/T | T/C | C/C | Intron 2 Variant |
| 71871905 | 70208544 | . | A | G | G/Ga | G/A | A/A | Intron 2 Variant |
| 71872059 | 70208698 | rs109314357 | A | G | G/G | G/A | A/A | Synonymous Variant, Exon 3, c.483A>G, p.Thr161Thr |
| 71872160 | 70208799 | . | T | C | C/C | C/T | T/T | Missense Variant (Moderate), Exon 3, c.584T>C, p.Met195Thr |
| 71872250 | 70208889 | rs467478061 | A | ACTTCT | ACTTCT/ACTTCT | A/ACTTCT | A/A | Intron 3 Variant |
| 71873480 | 70210119 | rs109649112 | C | G | G/G | G/C | C/C | Intron 4 Variant |
| 71873703 | 70210342 | . | A | G | G/G | G/A | A/A | Intron 4 Variant |
| 71873749 | 70210388 | rs1116496751 | G | T | T/T | T/G | G/G | Intron 4 Variant |
| 71877765 | 70214407 | rs435078996 | C | T | T/T | T/C | C/C | Splice Region and Intron 5 Variant |
| 71877838 | 70214480 | . | G | A | A/A | A/G | G/G | Intron 5 Variant |
| 71882252 | 70218874 | rs109236495 | C | T | T/T | T/C | C/C | Intron 5 Variant |
| 71882552 | 70219174 | . | C | T | T/T | T/C | C/C | Intron 6 Variant |
| 71882595 | 70219216 | rs209891374 | T | G | T/T | T/G | G/G | Intron 6 Variant |
| 71884433 | 70221057 | rs108989845 | C | T | T/T | T/C | C/C | Intron 6 Variant |
| 71884478 | 70221102 | rs109078616 | G | A | A/A | A/G | G/G | Intron 6 Variant |
| 71884491 | 70221115 | rs109862472 | G | T | T/T | T/G | G/G | Intron 6 Variant |
| 71884601 | 70221225 | . | G | A | A/A | A/G | G/G | Intron 6 Variant |
| 71900932 | 70237545 | rs110595646 | T | C | C/C | C/T | T/T | Intron 7 Variant |
| 71901078 | 70237691 | rs109745851 | G | A | A/A | A/G | G/G | Intron 7 Variant |
| 71901286 | 70237899 | . | TG | T | T/T | TG/G | TG/TG | Intron 8 Variant |
| 71901298 | 70237911 | rs109723937 | AT | A | A/A | AT/A | AT/AT | Intron 8 Variant |
| 71902596 | 70239209 | rs110871960 | G | A | A/A | A/G | G/G | Intron 8 Variant |
| 71902723 | 70239336 | rs109921120 | C | G | C/C | C/G | G/G | Intron 8 Variant |
| 71904393 | 70241005 | . | T | C | C/C | C/T | T/T | Synonymous Variant, Exon 10, c.1644T>C, p.Tyr548Tyr |
| 71904433 | 70241045 | . | G | A | A/A | A/G | G/G | Intron 10 Variant |
| 71904863 | 70241475 | rs207688993 | T | C | C/C | C/T | T/T | Intron 11 Variant |
| 71905095 | 70241707 | rs378154728 | C | A | A/A | A/C | C/C | Synonymous Variant, Exon 13, c.1899C>A, p.Thr633Thr |
| 71906885 | 70243497 | rs110171094 | T | A | A/A | A/T | T/T | Intron 14 Variant |
| 71908561 | 70245173 | rs109891739 | T | C | C/C | C/T | T/T | Intron 14 Variant |
| 71908774 | 70245386 | rs110798632 | C | G | C/C | C/G | G/G | Intron 15 Variant |
| 71908788 | 70245400 | rs383702685 | G | GTTC | GTTC/GTTC | G/GTTC | G/G | Intron 15 Variant |
| 71909262 | 70245874 | rs110818069 | G | A | A/A | A/G | G/G | Synonymous Variant, Exon 16, c.2346G>A, p.Ala782Ala |
| 71909906 | 70246518 | rs110881216 | T | C | T/T | T/C | C/C | Intron 16 Variant |
| 71910036 | 70246648 | rs110901406 | A | AG | A/A | A/AG | AG/AG | Intron 16 Variant |
| 71910091 | 70246704 | . | G | A | A/A | A/G | G/G | Intron 16 Variant |
| 71913208 | 70249821 | . | G | A | A/A | A/G | G/G | Intron 17 Variant |
| 71913504 | 70250117 | . | C | G | G/G | G/C | C/C | Intron 18 Variant |
| 71913721 | 70250334 | rs1115157736 | G | A | G/G | G/A | A/A | Intron 19 Variant |
| 71914233 | 70250846 | . | G | T | T/T | T/G | G/G | Intron 20 Variant |
| 71914272 | 70250885 | rs109479879 | T | C | C/C | C/T | T/T | Intron 20 Variant |
| 71914295 | 70250908 | . | T | C | C/C | C/T | T/T | Intron 20 Variant |
| 71914316 | 70250929 | . | T | G | G/G | G/T | T/T | Intron 20 Variant |
| 71915311 | 70251924 | . | C | T | T/T | T/C | C/C | Synonymous Variant, Exon 21, c.2922C>T, p.His974His |
| 71915332 | 70251945 | . | G | A | A/A | A/G | G/G | 3′ UTR Variant |
| 71915337 | 70251950 | rs799571173 | T | C | C/C | C/T | T/T | 3′ UTR Variant |
| 71915355 | 70251968 | . | C | T | T/T | T/C | C/C | 3′ UTR Variant |
| 71915529 | 70252142 | rs801319071 | A | T | T/T | T/A | A/A | 3′ UTR Variant |
| 71915774 | 70252387 | . | G | A | A/A | A/G | G/G | 3′ UTR Variant |
Reference (Ref) and Alternative (Alt) alleles are defined with respect to UMD3.1. Variants without a variant ID are novel to this study. Observed genotypes of yak representing each coat color pattern (N = 2) are given with the exception of those marked in bold for which 33 animals were sequenced.
aTwo black yak were heterozygous (G/A) at this locus.