Microsatellite analysis revealed the genetic diversity and population structure of 18 native black goat breeds in China

¹Southwest University, Chongqing, China
²Chongqing Tengda Animal Husbandry Co., Ltd, Chongqing, China
³College of Animal Science and Technology, Southwest University, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China

Correspondence: yanguo Han, Tel: 86-02368251196, Fax: 86-02368251196, Email: hyg2015@swu.edu.cn

Received: 3 April 2025 • Revised: 8 May 2025 • Accepted: 17 June 2025

Abstract

Objective
In China and Southeast Asia, black goats command higher selling prices. However, the blind breeding practices carried out by farmers pose a threat to the original genetic diversity of the population. Therefore, the objective of this study is to conduct a systematic detection of the genetic diversity of native black goat breeds, aiming to provide a reference for the protection and improvement of these valuable native black goat breeds.
Methods
Genetic diversity and population structure of 18 black goat breeds were estimated by utilizing 16 microsatellite markers. Subsequently, data analysis was carried out with the assistance of software like Phylip, Fstat, Arlequin, Structure. For the purpose of visualization, ITOL and Structure Selector were used to present the results in a visual manner.
Results
The mean number of alleles (MNA) per population ranged from 4.75 to 9.56, with an average of 6.38. The observed heterozygosity (HO) of each breed ranged from 0.46 to 0.68, all of which were lower than the expected heterozygosity (HE). The inbreeding coefficient (FIS) of the 18 breeds ranged from -0.003 to 0.376. Among them, the FIS values of Meigu goat (MG), Yimeng black goat (YM), Yunling goat (YL), Guizhou black goat (GZ) and Ziwuling black goat (ZWL) were significantly higher than those under random rearrangement (p < 0.05). All pairwise Fixation index (FST) between the Chinese black goat populations reached a significant level (p < 0.05). Finally, the results of Bayesian model-based clustering and a neighbor-joining tree based on Nei's genetic distance showed these eighteen breeds can be further classified into seven genetic clusters.
Conclusion
All breeds showed high genetic diversity. MG had excessive inbreeding, and CZ and LZ were at risk of losing original genetic traits. Similar geographical and climatic conditions might lead to similar genetic materials in different breeds.

Keywords: genetic diversity; microsatellites; population structure; black goats