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. 2020 Jul 29;52:43. doi: 10.1186/s12711-020-00560-8

Table 1.

Parameters of genetic diversity in the 115 examined cattle breeds with 46,678 SNPs

Breed Nd nA nA¯ mA mA¯ HO HE Hdef npA npA¯ nspA nspA¯ fpA F F¯ AR AR¯ Ho(SNPs) HE(SNPs) Νe5 Ne5¯ Ne50 Ne2000
Outgroups
 YAK 26 9193 1.60 0.232 0.099 − 1.350 79 70 0.406 1.056 1.29 0.030 0.029 54 123
 GIR 24 24,111 4.19 0.486 0.464 − 0.049 78 139 0.041 0.647 2.63 0.169 0.169 48 304 3966
 NDA 27 32,136 5.58 0.569 0.574 0.009 188 185 0.032 0.334 3.15 0.228 0.230 67 524 2737
Minor Asia
 ATER 17 41,775 7.26 0.733 0.725 − 0.011 147 158 0.031 0.106 4.17 0.321 0.317 40 349 4338
 ATBC 37 51,955 9.03 0.730 0.746 0.022 294 362 0.015 0.112 4.25 0.322 0.330 96 831 5040
 ATSR 17 40,859 7.10 0.713 0.719 0.008 152 185 0.034 0.142 4.12 0.310 0.313 40 337 4274
 ATSY 7 29,941 5.20 0.696 0.683 − 0.019 43 64 0.076 0.161 4.08 0.302 0.298 – – –
 TRG 8 31,406 44,046 5.46 7.65 0.740 0.695 − 0.064 28 191.7 65 234.8 0.069 0.071 0.117 4.10 4.18 0.327 0.308 15 64 125 2952
Greece and Cyprus
 CYP 12 27,328 4.75 0.629 0.627 − 0.004 32 55 0.115 0.261 3.41 0.271 0.271 18 119 2753
 AGT 6 17,302 3.01 0.593 0.504 − 0.178 17 23 0.206 0.329 2.74 0.244 0.218 – – –
 CRT 11 12,688 2.20 0.518 0.373 − 0.387 11 8 0.376 0.457 2.02 0.193 0.166 8 53 1753
 NSY 7 19,634 3.41 0.608 0.551 − 0.102 11 16 0.188 0.242 2.97 0.268 0.249 – – –
 GRB 41 49,079 8.53 0.701 0.742 0.056 142 208 0.021 0.108 4.18 0.314 0.334 85 618 4170
 KAS 4 17,185 2.99 0.656 0.520 − 0.261 23 19 0.141 0.261 2.99 0.270 0.224 – – –
 KEA 27 33,145 5.76 0.646 0.622 − 0.038 16 23 0.026 0.150 3.31 0.295 0.284 28 160 2791
 PRG 9 26,666 4.63 0.704 0.643 − 0.094 13 31 0.073 0.096 3.58 0.319 0.293 15 109 2950
 ROG 9 25,912 4.50 0.723 0.602 − 0.202 20 29 0.100 0.094 3.36 0.321 0.270 15 114 3099
 SYK 17 37,037 6.43 0.664 0.698 0.049 67 71 0.050 0.149 3.91 0.300 0.316 29 210 3429
 KTR 19 37,105 37,879 6.45 5.89 0.651 0.685 0.050 54 58.6 74 82.6 0.045 0.175 0.178 3.80 3.54 0.292 0.308 26 40 192 3441
South-east Europe
 RHS 17 41,278 7.17 0.741 0.734 − 0.009 70 104 0.034 0.058 4.22 0.334 0.332 38 308 3905
 MKB 22 45,364 7.88 0.721 0.744 0.031 106 156 0.025 0.076 4.27 0.326 0.337 51 425 3932
 SRB 20 44,355 7.71 0.726 0.742 0.021 101 120 0.028 0.063 4.27 0.329 0.337 46 396 4099
 PRE 29 44,126 7.67 0.752 0.733 − 0.025 73 92 0.025 0.028 4.12 0.343 0.335 58 420 3933
 RMB 17 42,940 7.46 0.757 0.738 − 0.025 105 127 0.032 0.027 4.28 0.343 0.335 40 345 3825
 SHB 17 39,748 6.91 0.727 0.724 − 0.004 84 104 0.039 0.062 4.13 0.331 0.329 34 275 3664
 DGB 21 36,322 6.31 0.729 0.700 − 0.041 30 41 0.052 0.053 3.86 0.335 0.322 31 228 3398
 DBB 25 37,724 6.55 0.725 0.703 − 0.031 34 41 0.038 0.060 3.87 0.334 0.324 34 257 3298
 MAB 43 51,066 8.87 0.738 0.745 0.010 148 180 0.013 0.042 4.20 0.339 0.342 97 712 3748
 LKB 27 44,381 7.71 0.743 0.729 − 0.020 85 105 0.024 0.034 4.10 0.340 0.333 54 406 3709
 SKB 14 35,556 6.18 0.717 0.707 − 0.013 33 48 0.048 0.070 4.00 0.328 0.325 25 205 3312
 MNB 19 41,711 7.25 0.731 0.730 − 0.001 65 81 0.032 0.045 4.16 0.336 0.335 41 337 3679
 BHB 18 30,993 5.38 0.687 0.642 − 0.070 21 44 0.064 0.113 3.47 0.311 0.291 23 154 3161
 HRB 28 48,122 42,800 8.36 7.44 0.745 0.745 0.001 106 82.2 147 106.5 0.020 0.027 0.051 4.26 4.10 0.340 0.341 68 51 583 3916
East Podolian
 HRI 28 40,285 7.00 0.709 0.704 − 0.007 25 58 0.039 0.074 3.88 0.323 0.322 49 322 3414
 HRP 24 29,711 5.16 0.679 0.639 − 0.063 16 31 0.092 0.129 3.38 0.306 0.289 26 149 2959
 UKP 21 31,176 34,188 5.42 5.94 0.689 0.656 − 0.051 27 22.6 38 43.4 0.053 0.109 0.103 3.50 3.61 0.313 0.298 29 36 161 2952
Tyrrhenian
 PODO 25 43,858 7.62 0.715 0.731 0.022 75 95 0.023 0.074 4.13 0.325 0.332 56 434 3756
 CINI 30 43,242 7.51 0.715 0.727 0.016 44 77 0.025 0.075 4.06 0.325 0.331 60 434 3882
 MOSI 29 37,742 6.56 0.690 0.688 − 0.002 26 46 0.021 0.112 3.75 0.312 0.311 51 300 3546
 RSIC 24 40,468 7.03 0.739 0.719 − 0.028 21 41 0.024 0.041 4.02 0.337 0.329 45 342 3632
 MOSA 28 39,565 6.87 0.719 0.707 − 0.017 22 39 0.037 0.068 3.91 0.325 0.320 53 349 3816
 SARD 30 44,722 7.77 0.710 0.726 0.022 76 90 0.021 0.059 4.08 0.326 0.333 66 533 3633
 SBRU 10 32,211 5.60 0.697 0.689 − 0.012 15 18 0.050 0.080 3.95 0.319 0.317 21 173 3226
 CORS 30 44,708 7.77 0.722 0.724 0.002 120 119 0.022 0.050 4.06 0.331 0.330 67 535 3572
 AGER 22 34,676 6.02 0.705 0.688 − 0.025 2 15 0.023 0.072 3.76 0.327 0.320 32 222 2966
 MARE 34 37,470 6.51 0.695 0.690 − 0.006 44 47 0.028 0.105 3.74 0.313 0.312 53 294 3367
 CHI 12 32,476 5.64 0.702 0.677 − 0.037 21 42 0.042 0.093 3.81 0.320 0.310 24 166 2928
 MPIS 15 21,614 3.76 0.639 0.539 − 0.185 7 8 0.152 0.173 2.82 0.286 0.246 15 86 2203
 CALV 24 28,886 5.02 0.640 0.617 − 0.036 4 19 0.057 0.172 3.24 0.288 0.280 29 146 2841
 MCH 21 37,548 6.52 0.711 0.696 − 0.021 39 50 0.040 0.077 3.86 0.320 0.314 45 282 3311
 RMG 18 34,890 6.06 0.677 0.667 − 0.014 158 153 0.032 0.127 3.69 0.307 0.300 34 191 3245
 GARF 23 26,502 4.60 0.645 0.618 − 0.044 13 16 0.077 0.156 3.21 0.294 0.283 22 121 2833
 PONT 13 25,804 4.48 0.631 0.599 − 0.055 3 18 0.103 0.170 3.20 0.287 0.274 17 104 2466
 MODE 23 35,203 6.12 0.705 0.687 − 0.026 27 31 0.045 0.069 3.75 0.324 0.315 35 239 3111
 CABA 22 36,019 6.26 0.715 0.693 − 0.031 21 22 0.027 0.052 3.81 0.329 0.319 38 258 3132
 REGG 26 38,053 6.61 0.724 0.699 − 0.036 52 56 0.046 0.049 3.83 0.333 0.322 45 293 3503
 PMT 16 39,962 6.94 0.737 0.719 − 0.026 171 171 0.033 0.029 4.12 0.339 0.327 36 294 3284
 BURL 24 36,125 37,025 6.28 6.43 0.713 0.696 − 0.023 11 45.1 19 55.7 0.047 0.077 0.087 3.81 3.79 0.335 0.327 40 44 267 3014
Alpine
 PRDO 23 33,445 5.81 0.685 0.673 − 0.017 15 17 0.038 0.088 3.64 0.314 0.309 38 250 2912
 OVAR 31 39,534 6.87 0.731 0.706 − 0.035 30 29 0.035 0.038 3.87 0.335 0.325 48 330 3409
 REND 24 33,939 5.90 0.687 0.671 − 0.024 11 23 0.053 0.092 3.63 0.314 0.308 44 233 3181
 BPUS 24 38,621 6.71 0.717 0.703 − 0.021 25 31 0.032 0.052 3.88 0.330 0.324 42 321 3335
 PUST 24 31,615 5.49 0.701 0.667 − 0.052 16 17 0.059 0.075 3.57 0.321 0.306 32 197 3075
 SIC 26 39,920 6.94 0.732 0.714 − 0.025 28 39 0.032 0.035 3.97 0.336 0.328 49 355 3562
 PIN 29 38,594 6.71 0.714 0.701 − 0.020 27 39 0.024 0.066 3.84 0.332 0.326 50 309 3408
 TGV 50 38,939 6.76 0.700 0.690 − 0.014 36 45 0.023 0.071 3.72 0.322 0.318 67 344 3187
 MWF 46 35,855 6.23 0.710 0.675 − 0.053 21 25 0.039 0.058 3.58 0.327 0.311 45 252 3128
 OBV 35 36,925 6.42 0.695 0.682 − 0.020 17 26 0.028 0.074 3.68 0.319 0.313 66 333 3390
 BBV 50 35,287 6.13 0.656 0.643 − 0.020 10 15 0.010 0.100 3.39 0.301 0.296 65 233 2797
 DFV 50 40,079 6.96 0.692 0.684 − 0.013 26 41 0.012 0.075 3.69 0.320 0.316 98 445 3123
 FGV 50 37,494 6.51 0.704 0.682 − 0.031 15 36 0.032 0.067 3.65 0.325 0.316 64 311 3148
 VOG 18 34,749 6.04 0.721 0.688 − 0.048 12 22 0.039 0.045 3.80 0.331 0.317 33 245 3128
 ABO 22 33,385 5.80 0.706 0.666 − 0.061 21 18 0.040 0.054 3.60 0.325 0.306 37 240 3005
 MON 28 31,738 5.51 0.691 0.647 − 0.068 11 15 0.065 0.083 3.43 0.318 0.298 36 209 3003
 TAR 37 37,339 36,709 6.49 6.38 0.692 0.680 − 0.018 18 20.5 47 30.0 0.022 0.079 0.070 3.66 3.67 0.318 0.314 65 56 342 3228
France
 R DBI 29 26,163 4.55 0.606 0.578 − 0.048 25 34 0.174 0.200 2,99 0.277 0.265 28 127 2615
 SAL 26 36,384 6.32 0.668 0.667 0.000 26 40 0.043 0.117 3.62 0.305 0.305 58 321 2942
 AUB 22 37,489 6.51 0.691 0.685 − 0.008 32 49 0.028 0.079 3.79 0.317 0.314 51 349 2840
 LIM 48 42,891 7.45 0.708 0.705 − 0.003 65 75 0.015 0.066 3.85 0.326 0.325 106 563 3274
 CHR 39 43,444 7.55 0.720 0.719 − 0.001 67 63 0.018 0.061 3.97 0.335 0.335 88 482 3340
 PAR 17 36,898 6.41 0.724 0.701 − 0.033 52 53 0.035 0.044 3.93 0.333 0.322 34 262 3242
 BAQ 33 40,280 7.00 0.706 0.700 − 0.009 53 73 0.021 0.065 3.83 0.325 0.322 69 426 3291
 GAS 22 37,288 38,387 6.48 6.67 0.699 0.687 − 0.018 49 48.9 65 58.9 0.028 0.071 0.087 3.80 3.73 0.320 0.314 49 67 317 3071
Iberian
 MNRQ 30 26,609 4.62 0.637 0.605 − 0.054 28 27 0.173 0.166 3.12 0.292 0.277 29 128 2868
 MALL 30 20,486 3.56 0.556 0.521 − 0.067 14 26 0.211 0.276 2.65 0.247 0.236 19 81 2456
 NGAN 14 35,429 6.16 0.660 0.702 0.059 56 67 0.053 0.143 3.96 0.301 0.320 28 221 3208
 CANA 30 31,527 5.48 0.645 0.614 − 0.051 16 36 0.151 0.158 3.24 0.292 0.279 31 168 2801
 MARI 22 30,016 5.21 0.656 0.622 − 0.055 22 42 0.116 0.147 3.30 0.299 0.284 27 148 2686
 ALEN 10 29,018 5.04 0.654 0.655 0.001 98 86 0.080 0.166 3.67 0.297 0.294 19 136 3104
 BAR 14 32,044 5.57 0.659 0.663 0.006 29 54 0.051 0.145 3.68 0.301 0.302 31 199 2738
 MARO 19 35,039 6.09 0.687 0.677 − 0.014 40 65 0.037 0.108 3.73 0.313 0.309 45 265 3147
 SYG 11 30,662 29,205 5.33 5.07 0.670 0.667 − 0.004 43 31.3 35 43.2 0.063 0.129 0.169 3.75 3.32 0.305 0.303 20 28 149 2802
North-west Europe
 BPN 15 33,384 5.80 0.726 0.689 − 0.054 28 46 0.055 0.047 3.83 0.336 0.319 26 200 3033
 NOR 30 34,001 5.91 0.698 0.664 − 0.052 38 61 0.055 0.091 3.55 0.322 0.307 43 234 3072
 MAN 20 34,940 6.07 0.683 0.664 − 0.029 23 22 0.032 0.123 3.64 0.320 0.312 44 244 2941
 BBB 45 39,395 6.84 0.698 0.690 − 0.010 40 46 0.028 0.103 3.72 0.328 0.325 67 329 3110
 LKF 22 31,859 5.53 0.678 0.658 − 0.030 10 25 0.057 0.129 3.54 0.316 0.307 34 187 2810
 HF 50 37,888 6.58 0.696 0.685 − 0.016 14 29 0.011 0.127 3.65 0.334 0.329 72 279 2877
 GNS 16 28,903 5.02 0.634 0.623 − 0.016 89 65 0.039 0.175 3.36 0.292 0.286 29 159 2606
 JSY 49 31,507 5.47 0.624 0.619 − 0.007 20 28 0.020 0.185 3.23 0.287 0.286 74 223 2641
 HER 41 36,659 6.37 0.653 0.676 0.034 55 64 0.028 0.229 3.57 0.320 0.332 79 227 2286
 SHR 13 25,626 4.45 0.566 0.575 0.016 4 15 0.039 0.300 3.12 0.267 0.274 27 128 2131
 KRY 14 27,681 4.81 0.678 0.644 − 0.053 57 67 0.083 0.144 3.46 0.317 0.300 22 131 2698
 DXT 16 31,660 5.50 0.625 0.667 0.062 32 26 0.065 0.202 3.64 0.292 0.312 31 185 2841
 GLW 40 34,358 5.97 0.635 0.652 0.025 24 36 0.047 0.186 3.45 0.296 0.304 82 275 2744
 AAN 48 35,756 6.21 0.659 0.668 0.014 30 42 0.026 0.188 3.53 0.317 0.322 83 249 2617
 HGL 27 28,798 5.00 0.606 0.605 − 0.001 33 47 0.045 0.231 3.18 0.281 0.282 57 181 2524
 NRC 34 36,853 6.40 0.702 0.686 − 0.023 20 39 0.033 0.101 3.70 0.333 0.325 57 268 3016
 SERC 24 35,396 6.15 0.690 0.678 − 0.018 32 35 0.069 0.113 3.68 0.325 0.320 47 239 2839
 FJL 22 35,464 6.16 0.700 0.680 − 0.030 67 74 0.083 0.093 3.72 0.319 0.310 42 242 2946
 FIAY 42 37,043 6.44 0.686 0.677 − 0.014 19 46 0.018 0.111 3.61 0.323 0.318 65 281 2942
 FINE 20 38,958 6.77 0.692 0.711 0.026 78 100 0.048 0.097 3.99 0.317 0.324 41 321 3608
 FINW 35 38,966 6.77 0.696 0.693 − 0.004 59 81 0.040 0.095 3.77 0.317 0.316 56 316 3372
 FINN 18 32,166 5.59 0.719 0.670 − 0.073 27 42 0.067 0.069 3.64 0.327 0.305 27 190 3140
 YARO 20 36,065 34,908 6.27 6.06 0.707 0.686 − 0.029 58 34.9 69 47.0 0.068 0.080 0.142 3.78 3.58 0.324 0.315 39 57 246 3265

Nd, number of genotyped animals; nA and nA¯, total and mean number of observed alleles within subpopulation; mA, nA/5756 (number of blocks); HO, average observed heterozygosity within subpopulation; HE, average expected heterozygosity within subpopulation; npA and npA¯, number and mean number of private alleles; nspA and nspA¯, number and mean number of alleles present only in two subpopulations; fpA, average frequency of private alleles, F and F¯, inbreeding coefficient per breed and per group; AR and AR¯, number and mean value of allelic richness; Ho(SNP) and HE(SNP), observed and expected heterozygosity within subpopulation by SNPs; Ne5 and Ne5¯, effective population number for five generations back per breed and per group; Ne50 and Ne2000, effective population number for fifty and two thousand generations back