Microsatellite based genetic diversity and population structure of nine indigenous Chinese domestic goats

Determination of genetic diversity and population structure plays an important role in supporting genetic improvement programs and future conservation plans. In this study, 352 individuals representing nine Chinese indigenous goat populations distributed in China were genotyped at 15 microsatellite loci. The mean number of alleles (MNA) per breed ranged from 3.867 (Matou goat, MT) to 5.400 (Ujumqin white goat, UW), the expected heterozygosity (He) varied from 0.482 (Hainan black goat, HNB) to 0.659 (UW). Allelic diversity and heterozygosity measures in the studied populations were much lower than Chinese Cashmere and meat type goats. Global F statistics revealed 9.8% of total variance explained among breeds while 90.2% of variance was due to diversities within breeds. Three major population clusters were observed broadly conforming to geographical locations of different goat populations. Three-dimensional scatterplot derived from three largest principal components supported the observed phylogeny based on genetic distance estimations. Goats from Northern China and Island region were distinct while strong admixture was observed among goat populations from Central China. The study revealed market orientation and geographical distances among populations might have contributed to the genetic structure and population sub-division among Chinese indigenous goats. Our study provided a new insight into understanding the genetic diversity and structure of Chinese indigenous goat breeds, and will be helpful to determine the strategies for breeding and conservation programs.