Table 1. Candidate regions for signature of positive selection in EASZ.
| BTA | Position of most significant SNPs (bp) | Candidate region intervals (bp) | Candidate genes | Test | Ref | Median ΔAZ |
|---|---|---|---|---|---|---|
| 2 | 125,585,810 | 125,585,810 – 126,058,677 | Uncharacterised | Fst | 16 | −0.003 |
| 3 | 101,942,771 | 101,442,771 – 102,442,771 | TMEM53 | Rsb | 16 | −0.132 |
| C1orf228 | 19 | |||||
| RNF220 | ||||||
| 4 | 47,216,521 | 47,195,467 – 47,539,595 | ATXN7L1 | Fst | 16 | 0.016 |
| 19 | ||||||
| 42 | ||||||
| 4 | 52,138,962 | 51,927,595 – 52,308,430 | _ | Fst | 19 | −0.051 |
| 42 | ||||||
| 44** | ||||||
| 45** | ||||||
| 5 | 57,977,594 | 57,477,594 – 58,477,594 | OR6C4 | Rsb | 19 | −0.003 |
| OR2AP1 | 18 | |||||
| 43** | ||||||
| 5 | 60,556,520 | 60,056,520 – 61,056,520 | SNRPF | Rsb | 19 | 0.049 |
| CCDC38 | 16 | |||||
| 18 | ||||||
| 5 | 76,286,670 | 75,786,670 – 76,786,670 | CARD10 MFNG | iHs | 0.043 | |
| 7 | 52,419,683 | 52,224,595 – 52,720,797 | UBE2D2 | Fst | 19 | 0.07 |
| 11 | 62,629,106 | 62,129,106 – 63,129,106 | _ | Rsb | 0.008 | |
| 12 | 27,181,474 | 26,681,474 – 27,681,474 | _ | Rsb | 19 | −0.188 |
| 12 | 29,217,254 | 28,717,254 – 29,717,254 | RXFP2 | Rsb | 19 | −0.038 |
| 16 | ||||||
| 17 | ||||||
| 12 | 35,740,174 | 35,240,174 – 36,240,174 | EFHA1 | Rsb | −0.084 | |
| 13 | 46,472,930 | 46,433,697 – 46,723,493 | ADARB2 | Fst | 18 | 0.022 |
| Uncharacterised | ||||||
| 13 | 58,099,969 | 57,848,276 – 58,207,174 | bta-mir-296 | Fst | 18 | 0.051 |
| 43** | ||||||
| 14 | 24,437,778 | 24,482,969 – 25,254,540 | XKR4 | Fst | 43** | −0.042 |
| 46 | ||||||
| 19 | 27,444,684 | 27,369,763 – 27,763,447 | ALOX12 | Fst | 19 | −0.012 |
| RNASEK | ||||||
| BAP18 | ||||||
| BCL6B | ||||||
| SLC16A13 | ||||||
| SLC16A11 | ||||||
| CLEC10A | ||||||
| 19 | 42,696,815 | 42,196,815 – 43,196,815 | KLHL10 | Rsb | 42 | −0.004 |
| KLHL11 | ||||||
| ACLY | ||||||
| 22 | 2,655,659 | 2,314,019 – 2,788,566 | – | Fst | 0.035 | |
| 23 | 28,281,915 | 27,781,915 – 28,781,915 | TRIM39-RPP21 | iHs | 19 | –0.004 |
| LOC512672 | 18 | |||||
| uncharacterised | ||||||
| 24 | 4,461,406 | 4,118,163 – 4,474,760 | CYB5A | Fst | 0.006 | |
| 29 | 1,898,171 | 1,398,171 – 2,398,171 | Uncharacterized | iHs | 18 | 0.022 |
| X | 9,201,028 | 8,582,093 – 9,248,137 | bta-mir-2483 | Fst | −0.113 | |
| X | 40,738,704 | 39,942,044 – 43,999,854 | Metazoa_SRP | Fst | 46 | −0.05 |
| X | 85,589,749 | 84,566,018 – 85,993,719 | DGAT2L6 | Fst | 46 | −0.034 |
| IGBP1 |
Ref: Reference number for previous studies reporting overlapping regions with the identified candidate regions. **Commercial breeds studies. ΔAZ: The average excess/deficiency in Asian zebu ancestry at each SNP calculated by subtracting the average estimated Asian zebu ancestry of the SNP from the average estimated Asian zebu ancestry of all SNPs. Bold (deviation by plus or minus 1 s.d. from the genome-wide mean ΔAZ).