Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

BMC Genomics

Table 1 Summary of genotyped animals and genetic diversity compared between nine goat populations

Breed	Alpine	Boer	Boer	Cashmere	LaMancha	Nubian	Rangeland	Saanen	Toggenburg
Origin	Canada	Australia	Canada	Australia	Canada	Canada	Australia	Canada	Canada
Abbreviation	AL	BA	BC	CA	LA	NU	RA	SA	TO
Sample size	403	61	67	48	81	54	66	318	53
Purpose	Milk	Meat	Meat	Fiber	Milk	Milk/Meat	Meat	Milk	Milk
P_N ^a	0.946	0.969	0.924	0.981	0.939	0.902	0.995	0.945	0.911
H_O ^a	0.385	0.365	0.363	0.384	0.384	0.338	0.413	0.379	0.353
H_E ^a	0.388	0.356	0.357	0.372	0.382	0.335	0.411	0.382	0.336
D_ST	0.307	0.281	0.284	0.293	0.303	0.269	0.323	0.302	0.263
F_EH ± SD	0.103 ± 0.058	0.141 ± 0.043	0.156 ± 0.048	0.104 ± 0.044	0.108 ± 0.046	0.214 ± 0.051	0.039 ± 0.036	0.117 ± 0.056	0.179 ± 0.055
F_VR ± SD	0.006 ± 0.063	−0.029 ± 0.065	−0.014 ± 0.064	−0.027 ± 0.053	−0.001 ± 0.079	−0.004 ± 0.082	−0.001 ± 0.033	0.005 ± 0.090	−0.041 ± 0.223
F_LEUT ± SD	0.006 ± 0.093	−0.028 ± 0.087	−0.014 ± 0.105	−0.027 ± 0.080	0.000 ± 0.134	−0.005 ± 0.146	0.000 ± 0.034	0.006 ± 0.138	−0.027 ± 0.373
F_ROH ± SD	0.031 ± 0.019	0.047 ± 0.015	0.057 ± 0.016	0.021 ± 0.009	0.039 ± 0.018	0.057 ± 0.018	0.009 ± 0.009	0.033 ± 0.019	0.046 ± 0.018
F_PED ± SD	0.021 ± 0.040	NA	0.002 ± 0.016	NA	0.044 ± 0.050	0.017 ± 0.034	NA	0.040 ± 0.042	0.054 ± 0.053

P _N proportion of polymorphic SNPs, H _E and H _O expected and observed heterozygosity, respectively, D _ST average pairwise genetic distance, SD standard deviation, NA not available, F _EH , F _VR , F _LEUT , F _ROH and F _PED inbreeding coefficients based on excess of homozygosity, VanRaden, Leutenneger, runs of homozygosity and pedigree, respectively
^aestimates for the three Australian breeds were previously reported by Kijas et al. [24] using the same dataset

ISSN: 1471-2164