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Table 1 Genetic diversity parameters of 23 goat populations included in AlpInit, Alp1Step, and Alp2Step datasets

From: Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds

Breed label N nA mA npA (nrA) mpAf Ho He Hdef
AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step AlpInit Alp1Step Alp2Step
FR_CMA 52 48 33 58450 58037 54400 10.35 10.28 9.64 70 (192) 92 (247) 140 (273) 0.01 0.02 0.02 0.83 0.83 0.83 0.81 0.81 0.80 −0.02 −0.02 − 0.03
IT_VLD 24 24 17 51751 51751 45941 9.17 9.17 8.14 140 (179) 154 (196) 142 (220) 0.04 0.04 0.06 0.76 0.76 0.74 0.78 0.78 0.76 0.03 0.03 0.03
CH_SAA 64 39 38 48967 46885 45864 8.67 8.31 8.12 81 (136) 78 (135) 107 (169) 0.03 0.03 0.04 0.76 0.74 0.76 0.75 0.77 0.75 −0.01 0.04 − 0.01
CH_VAL 43 43 31 44043 44043 42644 7.80 7.80 7.55 68 (128) 71 (143) 84 (171) 0.06 0.06 0.06 0.73 0.73 0.73 0.72 0.72 0.72 −0.01 − 0.01 − 0.01
CH_NVR 42 42 37 55837 55837 54918 9.89 9.89 9.73 90 (180) 100 (193) 130 (249) 0.02 0.02 0.02 0.79 0.79 0.78 0.78 0.78 0.78 0.00 0.00 0.00
CH_TSG 37 37 28 58643 58643 53361 10.39 10.39 9.45 99 (183) 111 (200) 98 (184) 0.03 0.03 0.03 0.81 0.81 0.81 0.80 0.80 0.79 −0.01 − 0.01 − 0.03
CH_TGB 31 31 22 39223 39223 36651 6.95 6.95 6.49 41 (59) 43 (67) 50 (98) 0.04 0.04 0.06 0.73 0.73 0.72 0.71 0.71 0.70 −0.03 − 0.03 − 0.03
CH_APP 29 29 19 39237 39237 35852 6.95 6.95 6.35 45 (77) 47 (87) 43 (113) 0.05 0.05 0.07 0.72 0.72 0.72 0.70 0.70 0.69 −0.03 − 0.03 − 0.04
CH_BOT 23 23 19 42695 42695 41167 7.56 7.56 7.29 37 (75) 40 (79) 43 (98) 0.07 0.07 0.08 0.77 0.77 0.77 0.74 0.74 0.74 −0.04 −0.04 − 0.04
CH_PEA 31 31 31 50873 50873 50873 9.01 9.01 9.01 64 (108) 68 (125) 92 (188) 0.03 0.04 0.04 0.81 0.81 0.81 0.78 0.78 0.78 −0.04 −0.04 −0.04
CH_GST 49 49 38 52107 52107 50723 9.23 9.23 8.99 105 (171) 116 (187) 139 (225) 0.05 0.05 0.05 0.79 0.79 0.79 0.78 0.78 0.77 −0.02 −0.02 −0.02
CH_CHA 123 50 50 60731 56987 54484 10.76 10.10 9.65 70 (154) 71 (120) 67 (135) 0.01 0.01 0.02 0.80 0.80 0.79 0.79 0.79 0.79 −0.01 − 0.01 − 0.01
IT_ORO 23 23 20 46994 46994 44199 8.32 8.32 7.83 85 (137) 91 (150) 105 (175) 0.04 0.04 0.05 0.74 0.74 0.73 0.74 0.74 0.73 0.00 0.00 −0.01
IT_ABL 24 24 20 59640 59640 56520 10.57 10.57 10.01 188 (281) 205 (297) 225 (368) 0.03 0.03 0.03 0.82 0.82 0.83 0.82 0.82 0.81 −0.01 −0.01 − 0.02
IT_CMA 158 50 48 66261 62074 54050 11.74 11.00 9.57 124 (287) 91 (248) 50 (162) 0.01 0.01 0.03 0.81 0.82 0.82 0.82 0.82 0.79 0.01 0.01 −0.03
IT_VLP 24 24 20 60047 60047 57493 10.64 10.64 10.18 157 (293) 171 (315) 191 (363) 0.03 0.03 0.03 0.82 0.82 0.82 0.82 0.82 0.82 0.01 0.01 0.00
IT_PSR 22 22 19 54825 54825 52094 9.71 9.71 9.23 128 (209) 139 (222) 150 (269) 0.03 0.03 0.03 0.81 0.81 0.81 0.80 0.80 0.80 −0.01 −0.01 − 0.01
AT_BLB 34 34 28 60302 60302 58164 10.68 10.68 10.30 155 (308) 170 (332) 189 (377) 0.02 0.02 0.03 0.82 0.82 0.82 0.81 0.81 0.81 −0.01 − 0.01 −0.02
AT_CHA 22 22 22 50588 50588 50588 8.96 8.96 8.96 38 (91) 48 (105) 68 (121) 0.03 0.03 0.03 0.81 0.81 0.81 0.79 0.79 0.79 −0.02 −0.02 −0.02
AT_PNZ 27 27 22 55553 55553 51791 9.84 9.84 9.17 149 (273) 164 (291) 158 (306) 0.03 0.03 0.04 0.79 0.79 0.78 0.79 0.79 0.78 0.00 0.00 0.00
AT_TAP 28 28 24 44555 44555 43262 7.89 7.89 7.66 87 (186) 96 (197) 129 (235) 0.05 0.05 0.06 0.76 0.76 0.77 0.74 0.74 0.74 −0.03 − 0.03 − 0.04
SI_DRZ 133 50 50 64369 58802 55097 11.40 10.42 9.76 383 (520) 290 (439) 301 (482) 0.03 0.03 0.04 0.78 0.79 0.79 0.80 0.79 0.79 0.02 0.01 0.00
AT_STP 32 32 27 65543 65543 63180 11.61 11.61 11.19 301 (495) 326 (545) 382 (607) 0.02 0.02 0.03 0.85 0.85 0.85 0.84 0.84 0.83 −0.01 −0.01 −0.02
  1. N sample size
  2. nA total number of observed Alleles within subpopulation
  3. mA mean number of alleles per block
  4. npA number of private Alleles
  5. nrA number of alleles present only in two subpopulations (this and anyone other)
  6. mpAf mean frequency of private Alleles
  7. Ho average observed Heterozygosity
  8. He average expected Heterozygosity
  9. Hdef Heterozygosity deficiency (He-Ho)/He