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Table 3 Genomic regions identified as being under divergent selection in six cattle breeds in South Africa and their associated QTL

From: Genome-wide scan for selection signatures in six cattle breeds in South Africa

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

  1. aBreed abbreviations and names: AFR Afrikaner, NGU Nguni, DRA Drakensberger, BON Bonsmara, ANG Angus and HOL Holstein
  2. b Nb Number