Genetic introgression of Boer goat into indigenous goat breeds in the Three Gorges Area of China.

• Nanjiang Yellow, Yichang White, Black-boned goats showed high degree of inbreeding. • Differentiation degree between Black-boned and other indigenous goats were the largest. • Genetic introgression of Boer goat was found in indigenous goats in Three Gorges Area. • Protection of Yichang White, Youzhou Black and Macheng Black goats are imminent. Genetic diversities of indigenous goat breeds in the Three Gorges Area are at risk due to the increasing crossbreeding with exotic breed with the improved traffic conditions. Fourteen single nucleotide polymorphisms markers were used to analyze genetic diversities, differentiation, and genetic introgression of six goat breeds including five indigenous goat breeds: Nanjiang Yellow goat, Youzhou Black goat, Yichang White goat, Black-boned goat, and Macheng Black goat in the Three Gorges Area, and an exotic breed, namely, Boer goat. The results showed that for six goat breeds, the genetic diversity of Black-boned goat was the highest and that of Boer goat was the lowest, and that for five indigenous goat breeds in the Three Gorges Area, the genetic diversity of Nanjiang Yellow goat was the lowest. Nanjiang Yellow goat, Yichang White goat, and Black-boned goat showed inbreeding phenomenon (F is > 0). Genetic introgression of Boer goat was found in Macheng Black goat, Yichang White goat, and Youzhou Black goat populations. In addition, these indigenous goat breeds are confronted with the problems of mixed genetic relationships. This study revealed the necessity and urgency of breed resources conservation of Macheng Black goat, Yichang White goat and Youzhou Black goat. [ABSTRACT FROM AUTHOR]