Table 2.
Potential candidate genes and previously detected QTL within detected selective sweep regions within breeds
| Breeda | BTA | UMD3.1 coordinate (bp) | Number of SNPs | Size (kb) | Candidate genes | QTL |
|---|---|---|---|---|---|---|
| ANG | 1 | 89,563,554–89,734,339 | 6 | 170.79 | KCNMB3, PIK3CA, ZMAT3 | Body length, withers height, hip width |
| DRA | 1 | 115,420,906–115,619,350 | 5 | 198.44 | – | Non return rate, calving ease |
| BON | 3 | 62,887,463–63,196,635 | 6 | 309.17 | GNG5, RPF1 | Milk protein percentage, marbling score, dystocia |
| AFR | 4 | 102,570,116–103,100,577 | 6 | 530.46 | MTPN | Parasites, marbling score, fat thickness, |
| DRA | 5 | 28,859,701–29,043,711 | 5 | 184.01 | HOXC12, HOXC13 | Udder height, intramuscular fat, milk yield, longissimus muscle area |
| DRA & BON | 5 | 109,333,059–109,478,057 | 6 | 145.00 | WC1, WC1.3 | Calving ease, milk fat, ovulation rate, milk yield, marbling score |
| BON | 6 | 102,546,791–102,779,196 | 8 | 232.41 | ZNF280B,NUCB2, KBTBD1 | Interval to first oestrus after calving, marbling score |
| HOL | 7 | 63,608,866–63,778,905 | 6 | 170.04 | ATOX1, G3BP1, GLRA1 | Somatic cell count, milking speed, tick resistance, heel depth, feed conversion ratio |
| 7 | 72,882,903–73,126,315 | 8 | 243.41 | – | Somatic cell count, milking speed | |
| BON | 8 | 24,844,168–25,057,606 | 6 | 213.44 | KIAA1797 | First service conception rate, fat thickness, body weight, somatic cell and marbling score |
| AFR | 10 | 40,135,969–40,460,414 | 5 | 324.45 | – | Milk protein yield, milk fat, strength and body weight |
| ANG & HOL | 10 | 70,871,943–71,022,679 | 7 | 150.74 | OTX2 | Milk protein yield, teat length, tick resistance, social separation walking and running |
| HOL | 13 | 12,076,103–12,276,846 | 6 | 200.74 | – | Body weight, somatic cell count, teat placement |
| 13 | 15,456,721–15,683,571 | 6 | 226.85 | – | Body weight, somatic cell count, teat placement, udder depth | |
| NGU | 13 | 78,430,096–78,793,099 | 8 | 363.00 | KCNB1, PTGIS | Residual feed intake, body weight (slaughter), weaning weight, teat length |
| ANG & HOL | 16 | 45,425,579–45,874,144 | 7 | 448.57 | AJAP1 | Abomasum displacement, residual feed intake, carcass weight, bone percentage, calving ease |
| BON | 16 | 51,195,450–51,357,613 | 6 | 162.16 | PDPN | Abomasum displacement, residual feed intake, carcass weight, body weight (weaning and birth), calving ease |
| HOL | 18 | 44,880,710–45,044,333 | 6 | 163.62 | DNAH2, TMEM88, GUCY2D | Calf size, subcutaneous fat thickness, gastrointestinal nematode burden, residual feed intake, somatic cell |
| HOL | 19 | 27,734,700–28,060,683 | 9 | 325.98 |
ALOX15B
ALOX12B |
Calf size, residual feed intake, milk fat yield |
| BON | 24 | 34,248,516–34,415,701 | 6 | 167.19 | RBBP8 | Stillbirth, udder depth, interval to first oestrus after calving, oleic acid content, weaning weight, somatic cell height |
aBreed abbreviations and names: AFR Afrikaner, NGU Nguni, DRA Drakensberger, BON Bonsmara, ANG Angus and HOL Holstein