Genomic insights into the conservation and population genetics of two Chinese native goat breeds

Conservation and population genetic analyses uncover the conservation status, genetic architecture, selection signatures, and artificial introgression of two Chinese indigenous goat breeds in the context of 36 global breeds. Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats. Lay Summary Guangfeng and Ganxi goats are the only two indigenous goat breeds in Jiangxi Province, China. Their genetic diversity, population structure, selective sweep, and potential introgression are largely unknown. We analyzed 50K genotype data to clarify these issues from a global perspective. The results showed that Ganxi goats had a low level of genetic diversity, and Guangfeng goats had an introgression from Boer goats that led to increased genetic diversity. We reconstructed the subfamily structure of Jiangxi goats based on neighbor-joining trees, and proposed a reasonable conservation strategy to maintain the genetic variability of these breeds. Then, we detected a list of candidate genes under selection for fecundity, growth, immunity, and meat quality in Jiangxi goats. Finally, we identified some body development and reproduction-related genes that were introgressed from Boer into Guangfeng goats. Our study will provide guidelines for conservation and breeding programs for Jiangxi goats and highlights the potential effect of human-mediated introgression on economic traits in Chinese indigenous goats.

Automated summary

Conservation and population genetic analyses of two Chinese indigenous goat breeds, Guangfeng and Ganxi, provide insights into their conservation status, genetic structure, selection signatures, and artificial introgression. These analyses are conducted in comparison to 36 global goat breeds. The study also identifies candidate genes associated with fertility, growth, immunity, and meat quality in these two breeds, and highlights the potential benefits of introgression from exotic goats for improving performance and productivity. It offers guidelines for conservation and breeding programs for these breeds and emphasizes the impact of human-mediated introgression on economic traits in Chinese indigenous goats.