Comprehensive genomic analysis reveals population structure and conservation priorities of Chinese indigenous goats

Introduction Systematic genetic and conservation prioritization analyses are critical for the effective management and preservation of Chinese indigenous goat genetic resources, thereby facilitating the sustainable development of the goat industry. However, the genetic resources of Chinese indigenous goats, which comprise numerous breeds, have not yet been subjected to such comprehensive analyses. Methods In this study, we conducted the first large-scale whole-genome sequencing (WGS)-based genomic analysis of 25 representative indigenous goat breeds from 20 provinces and five climatic zones across China. WGS data from 214 individuals were utilized to investigate the analyses of population structure, inbreeding coefficient, and conservation prioritization. Genetic architecture was characterized using three methods. Results and Discussion Our results consistently identified four distinct genetic branches—Northern & Western (NW), Eastern (EA), Southwestern (SW), and Southeastern (SE)—which exhibit a strong correlation with their geographical distributions. Furthermore, genomic inbreeding coefficient analysis revealed that breeds from the SE and SW branches displayed significantly higher inbreeding levels compared to those from the NW and EA branches. Through the assessment of gene diversity (HT) and allelic diversity (AT), we established an optimized conservation priority list for Chinese indigenous goat breeds. Incorporating population structure analysis, the top three breeds of each genetic lineage were earmarked for priority protection. The NW branch includes Xinjiang Goat, Ziwuling Black Goat, and Hexi Goat; the EA branch comprises Huanghuai Goat, Jining Grey Goat, and Southern Shaanxi White Goat; the SE branch consists of Hechuan White Goat, Xiangdong Black Goat, and Hainan Black Goat; the SW branch encompasses Guizhou Black Goat, Guishan Goat, and Luoping Yellow Goat. In summary, our study provides novel insights into the impact of geographical barriers on the genetic relationships among Chinese indigenous goat breeds and facilitates the translation of genomic advancements into practical conservation strategies for livestock genetic resources.