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Table 1 Proportion of polymorphic SNPs, observed and expected heterozygosities, inbreeding coefficient and effective population size in Chinese and worldwide breeds

From: Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

 

Breed

Breed abbr.

Nt a

Nq b

Regionc

Combined data seti

Ne j

MAF d

Pne

Hof

Heg

F h

Chinese indigenous cattle breeds

Beisha

BSC

19

18

South

0.21

0.848

0.289

0.285

−0.015(0.015)

10

Tiantai

TTC

21

21

South

0.21

0.859

0.280

0.284

0.016(0.031)

59

Wenling Humped

WHC

20

19

South

0.22

0.893

0.300

0.297

−0.009(0.11)

72

Nandan

NDC

19

19

South

0.21

0.834

0.275

0.279

0.013(0.078)

67

Longlin

LLC

15

15

South

0.23

0.906

0.310

0.307

−0.011(0.406)

59

Dianzhong

DZC

30

30

South

0.26

0.924

0.331

0.339

0.024(0.005)

29

Wenshan

WSC

47

47

South

0.26

0.939

0.333

0.335

0.008(0.212)

152

Zhaotong

ZTC

43

42

South

0.28

0.965

0.366

0.365

−0.004(0.511)

85

Dabieshan

DBS

44

44

South

0.25

0.951

0.342

0.336

−0.019(0.001)

259

Nanyang

NYC

15

13

Central

0.27

0.943

0.356

0.349

−0.021(0.02)

105

Luxi

LXC

14

14

Central

0.28

0.962

0.361

0.368

−0.020(0.001)

221

Qinchuan

QCC

30

30

Central

0.28

0.972

0.370

0.364

−0.018(0.001)

235

Jinnan

JNC

55

55

Central

0.28

0.968

0.374

0.360

−0.038(0.001)

37

Tibetan

TIC

20

7

Plateau

0.25

0.904

0.362

0.335

–

–

Fuzhou

FZC

13

13

North

0.22

0.803

0.305

0.290

−0.051(0.05)

47

Mongolian

MGC

15

15

North

0.25

0.904

0.331

0.322

−0.026(0.001)

206

Yanbian Yellow

YYC

59

58

North

0.24

0.848

0.325

0.315

−0.032(0.001)

85

Improved cattle breeds

Chinese Caoyuan Red

CCR

26

26

North

0.25

0.849

0.331

0.316

−0.050(0.001)

63

Liaoyu White

LWC

20

20

North

0.26

0.867

0.334

0.326

−0.023(0.001)

422

Xinjiang Brown

XJB

47

47

North

0.22

0.769

0.313

0.288

−0.085(0.001)

29

Worldwide cattle breeds

Angus

AN

–

20

Scotland

0.30

0.971

0.395

0.386

−0.025(0.001)

 

Hereford

HFD

–

20

Wales

0.29

0.967

0.384

0.376

−0.022(0.001)

–

GIR

GIR

–

20

India

0.16

0.737

0.227

0.225

−0.010(0.005)

–

Sahiwal

SAHW

–

17

Pakistan

0.16

0.729

0.225

0.221

−0.019(0.012)

–

Mean

     

0.24

0.888

0.326

0.320

−0.019

118

  1. aTotal number of individuals sampled in each breed
  2. bNumber of individuals remaining after quality control, with a call rate > 0.95
  3. cSouth refers to south China, Central refers to central China, North refers to north China and Plateau refers to Tibet
  4. dMinor Allele Frequency
  5. eProportion of polymorphic loci within a breed
  6. fObserved heterozygosity
  7. gExpected heterozygosity
  8. hInbreeding coefficient (significant level)
  9. iPn, Ho, He, and F are calculated based on 7003 SNPs using bootstrapping method
  10. jRecent effective population size