Abstract：Abstract Domestic goats (Capra hircus) are evolved from wild goats, and there are good adaptability, wide distribution and abundant breed resource for goats in China. Natural and artificial selection for long time may lead to differences in polymorphism and differentiation between goats of South and North of China. To study genetic diversity and origin as well as differentiation of goats in South and Northwest of China, D-loop region of 69 individuals belonging to 5 goat breeds distributing in South-China were sequenced and analyzed combing with 33 sequences from 3 goat breeds distributing in Northwest of China. The results showed that content of A+T and G+C in South and Northwest were 60.1%, 39.9% and 60.0%, 40.0%, respectively, indicating no apparent difference in base composition between the 2 areas. The average haplotype diversity (Hd) and nucleotide diversity (π) of goats in South China were 0.954±0.005 and 0.019 57±0.002 10, respectively, while they were 0.919±0.106 and 0.019 08±0.001 15 for goats in Northwest; Fs of all data sets were large negative value (P＜0.05) while values of sum of squared deviation (SSD) and raggedness had no significant difference (P＞0.05), which indicated nucleotide mismatch distribution had not deviated from population expansion model, and at 13th、37th、61st nucleotide, there was a peak for each site; NJ (neighbor-joining) tree showed 2 lineages: A and B, and all goats of South and Northwest distributed in the 2 lineages. Furthermore, lineage B divided into 2 sub-clade, B1 and B2, implying persistently differentiation. Media-joining network showed the same result to the NJ tree, and further pointed out H1 was the highest frequency haplotype appearing. When it comes to genetic distance, it was 0.022 and 0.019 within population for goats of South and Northwest. These results suggested that genetic diversity of goats in South area was slightly higher than in Northwest, although a little lower than that in past several years; events of population expansion had arisen for the whole haplotype group as well as A and B lineages; C. aegagrus was the wild ancestor for domestic goats of South and Northwest of China referred in this study. This research offers theoretical support for further understanding origin, differentiation and genetic diversity of goats which distributed in South and Northwest of China, and provide theoretical basis for protecting native breeds.
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