Table 1.
Candidate regions and associated genes revealed by FST, hapFLK and XP-EHH selection signature analysis in the Bonga breed of sheep
| Approach | Chromosome | Genomic region (bp) | Number of significant SNPs | Genes present | |
|---|---|---|---|---|---|
| From | To | ||||
| FST | 5 | 46300001 | 47300000 | 168 | SPOCK1, KLHL3, HNRNPA0, ENSOART00000016824, MYOT, PKD2L2, FAM13B, WNT8A, NME5, BRD8, KIF20A, CDC23, GFRA3, CDC25C, ENSOART00000017740, ENSOART00000014602, ENSOART00000017768, KDM3B, REEP2, EGR1, ENSOART00000017967, HSPA9, CTNNA1, HB-EGF, SLC4A9 |
| X | 49700001 | 51100000 | IQSEC2, KDM5C, TSPYL2, GPR173, MAGED1, GSPT2, BMP15, SHROOM4, ENSOART00000006108, ENSOART00000010008, ENSOART00000006154, ENSOART00000010178, ENSOART00000010185, ENSOART00000006171, ENSOART00000006186 | ||
| hapFLK | 1 | 128490718 | 128525811 | 10 | APP |
| 2 | 119482589 | 119548236 | 7 | – | |
| 217377972 | 217398724 | 6 | – | ||
| 3 | 12453207 | 12568175 | 17 | ENSOART00000015088 | |
| 99126620 | 99326839 | 48 | SLC9A4, IL18RAP, IL18R1, IL1RL1 | ||
| 4 | 3548252 | 3582020 | 7 | – | |
| 8 | 41309054 | 41578812 | 41 | MANEA | |
| 63639731 | 63649616 | 4 | ECT2L | ||
| 9 | 86323485 | 86432306 | 18 | DECR1, NBN, OSGIN2 | |
| 11 | 21701005 | 21716773 | 8 | GLOD4, ENSOART00000004387, GEMIN4, ENSOART00000012524 | |
| 54540051 | 54638872 | 29 | RNF157, FOXJ1, EXOC7, ZACN, GALR2, SRP68, EVPL | ||
| 12 | 49122258 | 49208872 | 8 | ENSOART00000003233, TMEM240, ENSOART00000003483, VWA1, TMEM88B, ANKRD65, MRPL20, CCNL2 | |
| 13 | 6331437 | 6352500 | 7 | – | |
| 81406516 | 81586998 | 36 | DOK5 | ||
| 14 | 12372110 | 12484709 | 20 | ENSOART00000012708, FBXO31, ENSOART00000012902 | |
| 16 | 47181073 | 47266038 | 14 | – | |
| 60146782 | 60155318 | 2 | – | ||
| 18 | 8519837 | 8539965 | 2 | – | |
| 20 | 35706919 | 35768326 | 13 | CDKAL1 | |
| 24 | 17429910 | 17498671 | 12 | – | |
| X | 49938964 | 51146427 | 105 | ENSOART00000010008, MAGED1, GSPT2, ENSOART00000006154, ENSOART00000010178, ENSOART00000010185, ENSOART00000006171, BMP15, ENSOART00000006186 | |
| XP-EHH | 1 | 32315627 | 32543171 | 17 | – |
| 110286900 | 110307916 | 3 | ENSOART00000009796, CD244 | ||
| 2 | 217308731 | 217514986 | 14 | MARCH4, SMARCAL1, ENSOART00000021 | |
| 3 | 27572804 | 27685620 | 4 | TTC32, WDR35 | |
| 108990499 | 109273734 | 6 | – | ||
| 165291738 | 165524251 | 13 | AMDHD1, HAL, LTA4H, ELK3 | ||
| 4 | 5379251 | 5380178 | 2 | DDC | |
| 5 | 18474732 | 18604264 | 8 | SGTA, SLC39A3, DIRAS1 | |
| 51535099 | 51621099 | 4 | ARHGAP26 | ||
| 78895709 | 78945814 | 2 | SSBP2 | ||
| 6 | 74173229 | 74856423 | 8 | – | |
| 8 | 41273738 | 41354804 | 2 | – | |
| 74736476 | 74747842 | 2 | MTHFD1L | ||
| 12 | 34094639 | 34154274 | 7 | – | |
| 13 | 81349010 | 81625427 | 6 | DOK5 | |
| 21 | 18433779 | 18520811 | 5 | ENSOART00000008010 | |
| 22 | 24231560 | 24329956 | 12 | SORCS3 | |
| X | 50250146 | 50717975 | 16 | MAGED1, GSPT2, ENSOART00000006154 (BMP15 is downstream to the region) | |
Genes in bold are associated with either male or female reproduction and prolificacy