Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses

Wang Y. Tang C. Xue P. Yang N. Sun X. Serik K. Assanbayer T. Shamekova M. Kozhanov Z. Sapakhova Z. Khurramovich J.K. Zhou X. Kairat I. Muhatai G.
March 2025 Multidisciplinary Digital Publishing Institute (MDPI)

Genes
2025 #16 Issue 3

Background/Objectives: The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. Materials and Methods: A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite markers. Genetic diversity parameters (e.g., allele number, heterozygosity, F-statistics) were calculated using GeneAIEX (v.6.503) and Fstat software (v.2.9.4). Parentage analysis was conducted using Cervus software. Bayesian clustering analysis was performed using STRUCTURE software (v.2.3.4), and a phylogenetic tree was constructed based on Nei’s genetic distance to reveal the population genetic structure. Results: A total of 191 alleles were detected, with an average allele number of 11.969, observed heterozygosity of 0.481, and expected heterozygosity of 0.787. Parentage testing showed a cumulative exclusion probability (CEP) of 0.9652999 when one parent’s genotype was known and 0.9996999 when both parents’ genotypes were known, achieving an accuracy of 99%. Genetic differentiation analysis revealed moderate genetic divergence among populations (FST = 0.128) and moderate inbreeding levels (FIS = 0.396). Bayesian clustering analysis (K = 4) indicated that the Yanqi horse population could be divided into four genetic clusters, reflecting the impact of geographical isolation on genetic structure. Conclusions: The Yanqi horse conservation population exhibits moderate genetic diversity, high accuracy in parentage identification, and moderate genetic differentiation and inbreeding. The findings provide a scientific basis for the conservation and sustainable utilization of Yanqi horse genetic resources. Future efforts should focus on strengthening conservation measures, optimizing breeding strategies, and further investigating the genetic background using genomic technologies to ensure the sustainable development of the Yanqi horse population.

genetic diversity , genetic structure , microsatellite markers , paternity testing , Yanqi horse

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College of Animals Science and Technology, Tarim University, Alar, 843300, China
Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Tarim University, Alar, 843300, China
Key Laboratory of Tarim Livestock Science and Technology Corps, Tarim University, Alar, 843300, China
Physiology, Morphology and Biochemistry, Kazakh National Agrarian Research University, Almaty, 050010, Kazakhstan
Zootechnology and Veterinary Medicine, Toraighyrov University, Pavlodar, 140008, Kazakhstan
Institute of Plant Biology and Biotechnology, Breeding and Biotechnology Laboratory, Almaty, 050000, Kazakhstan
Horse Breeding Department, Kazakh Research Institute of Livestock and Forage Production, Almaty, 050000, Kazakhstan
Animal Husbandry and Biotechnology, Samarkand State University of Veterinary Medicine, Samarkand 140100, Uzbekistan

College of Animals Science and Technology
Key Laboratory of Tarim Basin Biological Resources Protection and Utilization
Key Laboratory of Tarim Livestock Science and Technology Corps
Physiology
Zootechnology and Veterinary Medicine
Institute of Plant Biology and Biotechnology
Horse Breeding Department
Animal Husbandry and Biotechnology

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