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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