Table 2.
Results of the FST-outlier analysis performed contrasting 15 “grey” cattle breeds with each of the four selected “non-grey” cattle breeds (Angus, Charolais, Holstein, and Limousin). Only loci detected as significant (q-value < 0.05) in at least 15 pair-wise contrasts out of 60 are presented.
| CHR | SNP ID | No. OF SIGNIFICANT CONTRASTS | |||||||
|---|---|---|---|---|---|---|---|---|---|
| ANGUS | CHAROLAIS | HOLSTEIN | LIMOUSIN | OVERALL | POSITION (ARS-UCD1.2) | CONSIDERED INTERVAL | GENES | ||
| 2 | Hapmap49624-BTA-47893 | 0 | 0 | 0 | 15 | 15 | 6760630 | 6510630-7010630 | PMS1, ORMDL1, OSGEPL1, ANKAR, ASNSD1, SLC40A1, LOC100848294, WDR75 |
| 4 | Hapmap53144-ss46525999 | 0 | 0 | 15 | 0 | 15 | 76874783 | 76624783-77124783 | MYO1G, LOC112446527, PURB, MIR4657, H2AFV, PPIA, ZMIZ2, LOC112446406, OGDH, TMED4, DDX56, NPC1L1, NUDCD3, LOC104972146, CAMK2B, YKT6 |
| 14 | BTB-01532239 | 2 | 10 | 9 | 0 | 21 | 22781305 | 22531305-23031305 | XKR4, TRNAT-AGU |
| 14 | BTB-01530788 | 3 | 9 | 10 | 9 | 31 | 22867321 | 22617321-23117321 | XKR4, TRNAT-AGU, TMEM68, TGS1 |
| 14 | BTB-00557532 | 6 | 10 | 9 | 11 | 36 | 22986080 | 22736080-23236080 | XKR4, TRNAT-AGU, TMEM68, TGS1, LYN |
| 14 | Hapmap46986-BTA-34282 | 2 | 3 | 2 | 9 | 16 | 23630896 | 23380896-23880896 | CHCHD7, SDR16C5, SDR16C6, PENK, LOC112449660, IMPAD1 |
| 14 | Hapmap46735-BTA-86653 | 2 | 12 | 0 | 13 | 27 | 23725488 | 23475488-23975488 | SDR16C6, PENK, LOC112449660, IMPAD1 |
| 14 | ARS-BFGL-NGS-36089 | 1 | 5 | 0 | 10 | 16 | 24019648 | 23769648-24269648 | LOC112449660, IMPAD1 |
| 14 | Hapmap30932-BTC-011225 | 0 | 11 | 0 | 8 | 19 | 25082860 | 24832860-25332860 | LOC107133116, TOX, TRNAC-GCA |
| 14 | BTB-01280026 | 4 | 9 | 0 | 4 | 17 | 25354206 | 25104206-25604206 | TOX, TRNAC-GCA |
| 14 | Hapmap27934-BTC-065223 | 0 | 10 | 0 | 5 | 15 | 25472332 | 25222332-25722332 | TOX |
| 26 | ARS-BFGL-NGS-11271 | 2 | 0 | 13 | 0 | 15 | 23039524 | 22789524-23289524 | LDB1, PPRC1, LOC112444554, NOLC1, LOC112444524, LOC101902227, LOC785229, ELOVL3, PITX3, GBF1, NFKB2, PSD, FBXL15, CUEDC2, LOC112444535, MIR146B, MFSD13A, ACTR1A, SUFU, TRIM8 |