Genetic diversity analysis of eight indigenous goat breeds (groups) in China using AFLP markers

Eight goat breeds from Chengdu, Lezhi, Jintang, Baiyu, Yingshan, Hejiang, Jiangan, and Jialing in Sichuan, China were analyzed for genetic diversity using AFLP markers. A total of 261 individuals were analyzed using eight selective AFLP primer combinations which generated 174 discernible fragments, of which 80 were polymorphic with an average of 27.15 bands per primer pair. Shannon's gene diversity index among breeds ranged from 0.0888 to 0.2289, and the highest and the lowest gene diversity index among breeds were the Yingshan Black goat (0.2289) and the Baiyu Black goat (0.0888) respectively. The genetic distance (DR) among eight goat breeds were calculated by Rogers' genetic distance. Based on the analytical results, systematic trees were constructed by using the unweighted pair-group method with arithmetic average (UPGMA) and the neighbor joining (NJ) methods. Eight breeds were divided into two main clusters by using cluster analysis, one of which including two subclusters. The clustering results agreed well with the origin of the goats and geographic distribution. The results implied that AFLP markers were informative and could provide significant insights for genetic diversity research and genetic resource conservation of indigenous goats.