Table 1.
Summary of major candidate regions identified from the 150-kb windowed heterozygosity (HP) and fixation index (FST) values for each breed comparison (see Supplementary Tables S9–S27 for summary values of all candidate genes).
| Gene | Chromosome | Position (Mb) | Association | Candidate SNP position | PolyPhen Scores1 | Selected breed |
|---|---|---|---|---|---|---|
| PDE6B | 6 | 116.7–116.85 | Decreased vision | XM_027971363.1:c.C2284A/p.L762M | 0.606 | All five native breeds |
| XM_027971363.1:c.G2994C/p.A982P | 0.973 | |||||
| PANK2 | 13 | 50.325–50.55 | – | – | ||
| GMDS/FOXC1 | 20 | 50.1–50.325 | – | – | ||
| T | 8 | 87.525–87.825 | Short tail | XM_004011450.4:c.G334T/p.G112W | 0.998 | Altay Duolang |
| BMPR-IB | 6 | 29.175–29.625 | Litter size | XM_027970721.1:c.A746G/p.Q249R | 0.381 | Hu |
| RXFP2 | 10 | 29.4–29.55 | Absence of horns | – | – | Duolang Hu |
| HOX gene cluster | 4 | 68.7–68.925 | Development of axial skeleton | – | – | Mongolian |
| CYP17 | 22 | 22.425–22.575 | Hypoxia adaptability | NC_019479.2:g.22521501G > T | – | Tibetan |
| MSRB3 | 3 | 153.975–154.125 | Ear size | – | – | Duolang |
| DNAJB5 | 2 | 53.1–53.25 | Heat tolerance | – | – | Duolang |
1PolyPhen Scores were predicted by PolyPhen-2 software (Polymorphism Phenotyping V2), which indicated possible impact of an amino acid substitution on the structure and function of a protein.