Table 2.
Candidate selection signatures in BRH obtained from genome-wide SNP analysis in three Korean cattle breeds
| rs# | BTA | Position | GeneID | Value | p-value | Methods1) |
|---|---|---|---|---|---|---|
| rs133768410 | 2 | 17310348 | MGC139239 | 5.71 | 1.1E-08 | iHS |
| rs136606289 | 2 | 41998558 | GALNT13 | 5.55 | 2.9E-08 | iHS |
| rs109429220 | 2 | 46751065 | LYPD6 | 5.51 | 3.7E-08 | iHS |
| rs42400978 | 2 | 53245523 | ARHGAP15 | 5.81 | 6.4E-09 | iHS |
| rs110543441 | 4 | 77460068 | OGDH | 5.80 | 6.7E-09 | iHS |
| rs43709143 | 5 | 64646157 | SLC17A8 | 5.55 | 2.8E-08 | iHS |
| rs132649255 | 5 | 65021434 | ANO4 | 5.75 | 8.8E-09 | iHS |
| rs135611476 | 5 | 65566934 | UTP20 | 5.60 | 2.2E-08 | iHS |
| rs42500948 | 6 | 96900946 | C4orf22 | 5.40 | 6.5E-08 | iHS |
| rs137494018 | 6 | 102872168 | MAPK10 | 5.55 | 2.8E-08 | iHS |
| rs109162226 | 7 | 69865477 | SGCD | 5.60 | 2.1E-08 | iHS |
| rs43129125 | 7 | 74367220 | ATP10B | 5.53 | 3.1E-08 | iHS |
| rs110606217 | 7 | 92393984 | MBLAC2 | 5.66 | 1.5E-08 | iHS |
| rs133240533 | 7 | 98876412 | LNPEP | 5.67 | 1.4E-08 | iHS |
| rs133207591 | 8 | 101803833 | SVEP1 | 5.62 | 1.9E-08 | iHS |
| rs43576537 | 8 | 107367416 | PAPPA | 5.94 | 2.8E-09 | iHS |
| rs29019859 | 8 | 112426080 | CNTRL | 5.96 | 2.5E-09 | iHS |
| rs29026593 | 10 | 54537392 | NEDD4 | 6.30 | 2.9E-10 | Rsb |
| rs136684474 | 10 | 56267173 | UNC13C | 5.50 | 3.8E-08 | iHS |
| rs43637084 | 10 | 70168665 | SLC35F4 | 5.63 | 1.8E-08 | iHS |
| rs110040283 | 10 | 77239052 | SPTB | 5.42 | 5.9E-08 | iHS |
| rs43644105 | 10 | 81096899 | ACTN1 | 5.60 | 2.2E-08 | iHS |
| rs133082379 | 11 | 37504767 | EML6 | 5.77 | 8.1E-09 | iHS |
| rs134518946 | 12 | 48954111 | KLF12 | 5.74 | 9.7E-09 | iHS |
| rs43702054 | 12 | 54982565 | NDFIP2 | 5.81 | 6.1E-09 | iHS |
| rs133421541 | 13 | 19142912 | PARD3 | 5.86 | 4.6E-09 | iHS |
| rs137035050 | 13 | 20050038 | NRP1 | 5.40 | 6.8E-08 | iHS |
| rs41628263 | 13 | 37145268 | MKX | 5.47 | 4.4E-08 | iHS |
| rs133940147 | 18 | 14370567 | ANKRD11 | 0.31 | - | Fst |
| rs135905680 | 18 | 14512117 | SPG7 | 0.31 | - | Fst |
| rs136825205 | 18 | 14620678 | CDK10 | 0.29 | - | Fst |
| rs136080674 | 18 | 14635894 | VPS9D1 | 0.26 | - | Fst |
| rs136032320 | 18 | 14651461 | ZNF276 | 0.32 | - | Fst |
| rs110494166 | 18 | 14678403 | FANCA | 0.46 | - | Fst |
| rs135530868 | 18 | 14746515 | TCF25 | 0.44 | - | Fst |
| rs134499247 | 18 | 14760377 | MC1-R | 0.44 | - | Fst |
| rs134697549 | 18 | 14783535 | DEF8 | 0.45 | - | Fst |
| rs134353733 | 18 | 14822319 | DBNDD1 | 0.42 | - | Fst |
| rs134777248 | 18 | 14837991 | GAS8 | 0.45 | - | Fst |
| rs110992941 | 18 | 56911576 | MYH14 | 5.93 | 3.0E-09 | iHS |
| rs134697162 | 19 | 12260224 | BCAS3 | 5.44 | 5.3E-08 | iHS |
| rs135696145 | 19 | 20017811 | LYRM9 | 5.60 | 2.1E-08 | iHS |
| rs136501883 | 19 | 22171727 | TUSC5 | 5.38 | 7.6E-08 | iHS |
| rs134894253 | 19 | 30230290 | MYHC-EMBRYONIC | 5.81 | 6.3E-09 | iHS |
| rs137391775 | 19 | 62330716 | PRKAR1A | 5.85 | 4.8E-09 | Rsb |
| rs110514303 | 19 | 62455237 | MGC159964 | 5.87 | 4.4E-09 | Rsb |
| rs42699274 | 19 | 63125174 | CEP112 | 5.95 | 2.6E-09 | Rsb |
| rs134090120 | 20 | 25504490 | NDUFS4 | 5.43 | 5.7E-08 | iHS |
| rs41958923 | 20 | 67969388 | ADAMTS16 | 5.67 | 1.4E-08 | iHS |
| rs109923642 | 22 | 5154690 | TGFBR2 | 6.00 | 2.0E-09 | iHS |
| rs41995876 | 22 | 11649096 | MYD88 | 5.70 | 1.2E-08 | iHS |
| rs41995842 | 22 | 11695319 | OXSR1 | 5.76 | 8.6E-09 | iHS |
| rs42002387 | 22 | 11768489 | SLC22A13 | 5.80 | 6.5E-09 | iHS |
| rs42000489 | 22 | 15346591 | SEC22C | 5.45 | 5.1E-08 | iHS |
| rs41640857 | 22 | 15696637 | GTDC2 | 5.47 | 4.6E-08 | iHS |
| rs133373037 | 22 | 19323943 | GRM7 | 5.77 | 8.0E-09 | iHS |
| rs108990174 | 22 | 37747536 | C3orf49 | 5.91 | 3.5E-09 | iHS |
| rs110659486 | 22 | 39026908 | CADPS | 5.96 | 2.6E-09 | iHS |
| rs42008596 | 22 | 39238249 | PTPRG | 5.90 | 3.7E-09 | iHS |
| rs134422044 | 22 | 46906743 | CACNA2D3 | 5.43 | 5.7E-08 | iHS |
| rs133683877 | 23 | 28565821 | TRIM26 | 5.52 | 3.4E-08 | Rsb |
| rs42047398 | 24 | 30362703 | AQP4 | 5.41 | 6.2E-08 | iHS |
| rs133648402 | 24 | 34562142 | GATA6 | 5.57 | 2.5E-08 | iHS |
| rs135865261 | 24 | 40481765 | LAMA1 | 5.51 | 3.6E-08 | iHS |
| rs136017859 | 26 | 21660800 | C26H10ORF6 | 6.11 | 9.8E-10 | Rsb |
| rs109276863 | 26 | 21677036 | SEMA4G | 6.46 | 1.0E-10 | Rsb |
| rs41586295 | 27 | 42253264 | UBE2E2 | 5.94 | 2.9E-09 | Rsb |
| rs29020432 | 28 | 29117568 | PLA2G12B | 6.15 | 7.5E-10 | Rsb |
| rs110736939 | 28 | 33155536 | KCNMA1 | 5.78 | 7.5E-09 | Rsb |
| rs134941983 | 28 | 35362739 | ANXA11 | 6.11 | 9.7E-10 | Rsb |
BRH, Brindle Hanwoo; SNP, single-nucleotide polymorphism; BTA, Bos taurus; Rsb, cross population extended haplotype homozygosity; iHS, integrated haplotype score; Fst, fixation index.
1)
For selection signature analysis Rsb, iHS, and Fst was conducted. Markers of Rsb and iHS were passed genome-wide significance level (p-value = 8.77×10−8). The Fst was estimated on the basis of the Wright F statistic and passed the Fst threshold 0.03.