Table 2.
Balancing selection: regions in the bottom 1% smoothed F ST values
| Region | BTA | SNP start pos | SNP end pos | Lowest | CNV [21] | Within cattle type** | Candidate genes | Cross reference |
|---|---|---|---|---|---|---|---|---|
| B1 | 4 | 110,295,764 | 111,378,106 | 0.070 | 2 | |||
| B2 | 4 | 111,742,866 | 112,562,902 | 0.076 | 2 | CNTNAP2 | ||
| B3 | 5 | 19,457,756 | 19,898,237 | 0.075 | 0 | ATP2B1 | ||
| B4 | 5 | 76,719,327 | 77,207,435 | 0.067 | 0 | PKP2 | ||
| B5 | 6 | 2,883,313 | 4,231,143 | 0.059 | 6 | CCNA2, ANXA5 | ||
| B6 | 6 | 12,490,545 | 13,266,473 | 0.062 | 1 | CAMK2D | ||
| B7 | 6 | 54,759,464 | 55,199,755 | 0.062 | 4 | |||
| B8 | 6 | 61,590,746 | 61,892,976 | 0.076 | 0 | APBB2 | ||
| B9 | 6 | 118,252,961 | 118,649,364 | 0.061 | 0 | Guz | ||
| B10 | 7 | 65,205,183 | 65,242,121 | 0.079 | 0 | GLRA1 | ||
| B11 | 7 | 98,598,188 | 99,371,157 | 0.050 | 3 | ERAP2, LNPEP | ||
| B12 | 11 | 11,993,676 | 13,090,823 | 0.072 | 0 | DYSF | ||
| B13 | 11 | 16,914,701 | 17,716,204 | 0.074 | 2 | |||
| B14 | 12 | 70,094,561 | 76,785,743 | 0.059 | 6 | ABCC4 | ||
| B15 | 14 | 53,550,213 | 54,231,380 | 0.066 | 2 | Nel, Guz, Jer | ||
| B16 | 16 | 16,039,261 | 17,069,240 | 0.076 | 1 | FAM5C | ||
| B17 | 16 | 19,740,336 | 20,450,779 | 0.073 | 0 | ESRRG | ||
| B18 | 16 | 36,476,830 | 37,151,556 | 0.068 | 1 | XCL2 | ||
| B19 | 17 | 8,512,165 | 8,575,700 | 0.079 | 0 | |||
| B20 | 21 | 69,852,429 | 70,269,531 | 0.054 | 0 | Guz | ||
| B21 | 22 | 1,504,583 | 1,623,884 | 0.078 | 1 | SEC61G, NEK10 | ||
| B22* | 23 | 24,242,547 | 31,194,961 | 0.025 | 30 | Ang, Cha, Her, Lim | BOLA (MHC) genes, TNF, AGER, NCR3, C2, CFB, LY6G6F, BTNL2, IL17A, IL17F, CLIC1, CSNK2B, MOG | [12, 24] |
| B23 | 23 | 32,608,468 | 33,237,258 | 0.069 | 1 | Cha | ALDH5A1, TDP2, GMNN | |
| B24 | 26 | 46,663,802 | 47,234,109 | 0.055 | 0 | Cha |
*Regions containing smoothed FST (sFST) in the bottom 0.1%.
**Regions at sFST bottom 1% of within taurine and within zebu breeds. Full table of within cattle type results for candidate regions under balancing selection is on Additional file 7: Table S4. Ang – Angus; Bro – Brown Swiss, Cha – Charolais, Gue – Guernsey, Jer – Jersey, Her – Hereford, Hol – Holstein, Lim – Limousin, Nor – Norwegian Red, Guz – Guzera, Nel – Nelore.