Table 1.
Positive selection: regions in the top 1% smoothed F ST values
| Region | BTA | SNP start pos | SNP end pos | Highest sFST | CNV [21] | Within cattle type** | Candidate genes | Cross reference |
|---|---|---|---|---|---|---|---|---|
| P1 | 2 | 47,857,335 | 48,065,161 | 0.387 | 1 | |||
| P2* | 2 | 71,565,086 | 72,885,823 | 0.498 | 1 | Hol | [24] | |
| P3 | 3 | 19,689,648 | 20,166,059 | 0.399 | 0 | Hol, Nor, Bro | CDC42SE1 | |
| P4 | 3 | 94,742,479 | 95,401,345 | 0.396 | 0 | |||
| P5 | 4 | 12,106,878 | 12,361,811 | 0.384 | 0 | |||
| P6 | 4 | 46,670,940 | 46,814,875 | 0.380 | 0 | [25] | ||
| P7 | 5 | 48,229,556 | 48,336,996 | 0.381 | 0 | [9, 12, 24] | ||
| P8 | 5 | 55,881,766 | 56,801,729 | 0.424 | 1 | Hol | STAT6, GLI1 | [24, 25] |
| P9 | 7 | 21,008,805 | 21,606,667 | 0.391 | 0 | Gue | ITGB1BP3 | [24, 25] |
| P10 | 7 | 47,299,497 | 47,859,329 | 0.433 | 3 | Lim | SPOCK, PPP2CA | [12] |
| P11* | 7 | 50,951,861 | 53,757,384 | 0.826 | 5 | Ang, Cha, Gue, Nor, Gir | CD14, CDC23, EGR1, MYOT, TMEM173 | [24] |
| P12 | 8 | 39,288,115 | 39,800,492 | 0.393 | 0 | CD274 | [24] | |
| P13 | 8 | 53,490,845 | 54,592,381 | 0.440 | 1 | Nor | [26] | |
| P14 | 8 | 58,649,674 | 58,727,004 | 0.380 | 0 | |||
| P15 | 8 | 61,543,379 | 62,874,750 | 0.464 | 1 | |||
| P16 | 8 | 69,691,214 | 70,488,061 | 0.493 | 0 | Ang | POLR3D, PPP3CC | |
| P17 | 8 | 73,617,355 | 73,704,634 | 0.382 | 0 | |||
| P18 | 10 | 36,488,829 | 37,051,537 | 0.416 | 0 | Her | CHP | [25] |
| P19 | 12 | 27,935,604 | 29,508,940 | 0.439 | 1 | Hol | [24, 25] | |
| P20 | 13 | 34,119,211 | 35,054,048 | 0.402 | 0 | ZEB1 | ||
| P21 | 13 | 48,893,096 | 49,816,619 | 0.408 | 0 | Guz | [9] | |
| P22 | 14 | 24,603,090 | 25,298,972 | 0.395 | 0 | Nor | PLAG1, XKR4, MOS | [10] |
| P23 | 14 | 36,715,710 | 37,511,658 | 0.444 | 0 | Gue | [24] | |
| P24 | 14 | 38,919,669 | 39,027,008 | 0.383 | 0 | Gue | ||
| P25 | 14 | 42,121,450 | 42,376,970 | 0.389 | 0 | |||
| P26 | 14 | 45,478,315 | 46,437,276 | 0.430 | 0 | [24] | ||
| P27 | 16 | 40,318,965 | 40,656,961 | 0.390 | 0 | |||
| P28 | 16 | 40,886,797 | 41,149,860 | 0.383 | 0 | |||
| P29 | 16 | 41,564,542 | 42,407,997 | 0.440 | 0 | Jer | ||
| P30 | 16 | 43,250,880 | 43,501,100 | 0.390 | 0 | [27] | ||
| P31* | 16 | 44,277,286 | 45,534,177 | 0.510 | 2 | PIK3CD | ||
| P32 | 18 | 11,298,096 | 11,959,392 | 0.409 | 0 | Bro | IRF8 | [24] |
| P33 | 18 | 14,171,624 | 14,702,657 | 0.423 | 0 | ACSF3, SPATA2L | [10] | |
| P34 | 20 | 13,714,109 | 15,135,107 | 0.429 | 0 | [24] | ||
| P35* | 20 | 71,629,018 | 71,967,622 | 0.508 | 0 | |||
| P36* | 21 | 83,766 | 2,416,432 | 0.564 | 0 | Gue | ||
| P37* | 21 | 31,681,776 | 33,273,658 | 0.530 | 1 | Her | ||
| P38 | 21 | 45,793,883 | 45,979,589 | 0.391 | 0 | |||
| P39 | 21 | 68,349,152 | 68,943,249 | 0.448 | 0 | Ang | HSP90AA1, PPP2R5C | |
| P40 | 24 | 24,114,816 | 24,452,344 | 0.383 | 1 | Nor | ||
| P41 | 29 | 51,452,986 | 52,452,986 | 0.382 | 1 | |||
| P42 | 30 | 33,064,381 | 50,329,406 | 0.810 | 0 | IRAK1, BCAP31, CETN2, GAB3, IKBKG, KIR3DL2, MTM1, SRPK3 | ||
| P43 | 30 | 53,439,167 | 57,258,157 | 0.711 | 0 | BTK | ||
| P44 | 30 | 68,834,838 | 71,300,049 | 0.861 | 0 | CYLC1 | [12] | |
| P45 | 30 | 72,360,206 | 79,580,964 | 0.844 | 0 | [12] | ||
| P46 | 30 | 84,352,052 | 85,706,219 | 0.764 | 0 | IL2RG | [12] | |
| P47 | 30 | 96,229,383 | 100,603,158 | 0.699 | 0 | ALAS2, SMC1A, LOC524601, SPIN2, VSIG4 | ||
| P48 | 30 | 130,500,087 | 132,116,040 | 0.670 | 0 | RS1 |
*Regions containing smoothed FST (sFST) in the top 0.1%.
**Regions at sFST top 1% of within taurine and within zebu breeds. Full table of within cattle type results for candidate regions under positive selection is on Additional file 6: Table S3. Ang – Angus; Bro – Brown Swiss, Cha – Charolais, Gue – Guernsey, Jer – Jersey, Her – Hereford, Hol – Holstein, Lim – Limousin, Nor – Norwegian Red, Guz – Guzera, Nel – Nelore.