Table 3.
Genomic regions identified as being under divergent selection in six cattle breeds in South Africa and their associated QTL
| Breedsa | BTA | UMD3.1 coord. (bp) | Nbb of SNPs | Size (kb) | SmoothedF ST | Candidate genes | QTL |
|---|---|---|---|---|---|---|---|
| AFR vs. HOL, NGU vs. HOL | 3 | 35,255,950–35,785,053 | 5 | 529.10 | 0.28 | KCNA2, CYM PROK1, PROK1, LAMTOR, SLC16A4, UBL4B | Milk fat percentage, milk protein percentage, body weight, height, somatic cell count |
| AFR vs. HOL | 3 | 121,025,205–121,374,825 | 4 | 349.62 | 0.44 | – | Shear force, fat thickness at the 12th rib |
| BON vs. HOL | 3 | 99,004,471–99,111,024 | 3 | 106.55 | 0.39 | SCP2, SLCA17, NDUFA12, SEMA4A | Calf size, carcass weight, clinical tick-resistance mastitis, marbling score, calving index |
| DRA vs. HOL | 3 | 7,957,960–8,391,057 | 3 | 433.10 | 0.25 | NOS1AP | Non return rate, body weight, longissimus muscle area, milk protein percentage, marbling score |
| AFR vs. HOL, NGU vs. HOL | 5 | 4,472,786–4,598,476 | 4 | 125.69 | 0.42 | – | Tenderness score, teat placement, shear force |
| AFR vs. HOL, NGU vs. HOL | 5 | 114,085,555–114,594,935 | 3 | 509.38 | 0.48 | ERC1, FBXL14, WNT5B, ADIPOR2 | Hip height, rump length, calving ease, height, ovulation, type, rump angle |
| BON vs. HOL | 5 | 107,242,527–107,451,881 | 4 | 209.35 | 0.36 | OVOS2 | Ovulation rate, calving ease, marbling score, height, milk yield, milk fat |
| NGU vs. HOL | 7 | 71,038,040–71,240,079 | 4 | 202.04 | 0.25 | EBF1 | Somatic cell count, milking speed, tick resistance, heel depth, social separation–vocalisation |
| DRA vs. HOL | 7 | 46,109,256–46,700,828 | 4 | 591.57 | 0.34 | CXCL14, SLC25A48, FBXL21, LECT2, TGFBI | Stillbirth, milking speed, body weight, parasites, milk beta-casein percentage |
| AFR vs. HOL, DRA vs. HOL | 9 | 105,263,583–105,587,941 | 3 | 324.36 | 0.50 | SFT2D1, BRP44L, RPS6KA2 | Chest depth, scrotal circumference, milk yield, milk alpha-casein percentage, milk protein yield |
| BON vs. HOL, NGU vs HOL | 9 | 15,767,136–15,991,964 | 3 | 224.83 | 0.37 | MYO6, IMPG1 | Clinical mastitis, weaning weight, longissimus muscle area, residual feed intake, milk fat yield |
| NGU vs. HOL | 9 | 46,632,366–47,246,008 | 4 | 613.64 | 0.43 | PREP | Clinical mastitis, marbling score, milk protein yield |
| DRA vs. HOL | 14 | 81,125,493–81,269,892 | 3 | 144.40 | 0.40 | – | Stature, body weight carcass weight, behaviour, height |
| AFR vs. HOL | 16 | 73,143–933,282 | 8 | 860.14 | 0.31 | FMOD, PRELP, OPTC, ATP2B4, LAX1, ZC3H11A, SNRPE, REN, TMEM51 | Milk protein yield, height, carcass weight, length of productive life |
| BON vs. HOL, NGU vs. HOL | 16 | 49,386,191–49,867,758 | 3 | 481.57 | 0.41 | DNAJC16, CASP9, CELA2A, CTRC, EFHD2, TMEM51 | Abomasum displacement, milk, carcass weight, calving ease, bone percentage |
| AFR vs. HOL | 18 | 1,094,150–1,422,084 | 5 | 327.93 | 0.47 | DDX19A, DDX19B, AARS, EXOSC6, MRCL, PDPR, GLG1 | Weaning weight-maternal milk |
| DRA vs. HOL, BON vs. HOL | 18 | 1,212,743–1,486,363 | 4 | 273.62 | 0.35 | PDPR, GLG1 | Weaning weight-maternal milk |
| NGU vs. HOL | 18 | 14,757,060–14,758,700 | 3 | 487.73 | 0.28 | CHMP1A, SPATA2, CDK10, FANCA, SPIRE2, TCF25, MC1R | Dystocia, somatic cell score, longissimus muscle area, fat thickness at the 12th rib, carcass weight, stillbirth, skin pigmentation |
| NGU vs. HOL | 19 | 42,896,570–42,897,840 | 4 | 478.76 | 0.32 | HSPB9, WIPF2, CDC6, RARA, IGFBP4, TNS4, CCR7, SMARCE1, K KRT222, KRT24-27 | Intramuscular fat, average daily milk yield, milk capric acid percentage, lauric acid, myristic acid, milk c14 index, hair development |
| AFR vs. HOL | 20 | 11,932,262–12,017,779 | 3 | 85.52 | 0.41 | – | Body weight, average daily gain, longissimus muscle area, somatic cell score |
| AFR vs. HOL, NGU vs. HOL | 21 | 43,246,618–43,399,424 | 4 | 152.81 | 0.30 | – | Somatic cell score, calving ease, carcass weight |
| DRA vs. HOL | 21 | 59,640,020–59,787,612 | 3 | 147.59 | 0.26 | SERPINA3-8 | Calving ease, gastrointestinal nematode burden, weaning weight, body weight (birth), height (mature and yearling) |
| ANG vs. HOL | 22 | 32,930,704–33,076,318 | 3 | 145.61 | 0.28 | FRMD4B | Non return rate, calf size, somatic cell |
| NGU vs. HOL | 23 | 2,019,985–2,247,046 | 3 | 227.06 | 0.34 | – | Milk protein yield, height, carcass weight, percentage live sperm after thawing |
| ANG vs. HOL | 23 | 49,809,003–49,945,187 | 4 | 136.18 | 0.46 | – | Body weight, dry matter intake |
| AFR vs. ANG, NGU vs. ANG, DRA vs. ANG, BON vs. ANG | 24 | 54,588,817–54,593,951 | 393.07 | 0.45, 0.29, 0.25, 0.25 | DCC | Gastrointestinal nematode burden, body weight, calving ease, udder attachment, feed conversion ratio, body weight | |
| AFR vs. HOL | 27 | 35,734,689–36,117,365 | 4 | 382.68 | 0.26 | – | Dystocia, marbling score, clinical mastitis |
aBreed abbreviations and names: AFR Afrikaner, NGU Nguni, DRA Drakensberger, BON Bonsmara, ANG Angus and HOL Holstein
b Nb Number