The Genetic Diversity and Population Structure of Native Horse Breeds in Xinjiang, China

Chi Tang¹Baoyu Yang¹Gulibaheti Dawulietihan²Li Xue²Shuyuan Liu³Yinamujiang Yalimaimaiti⁴Qingzheng Wang¹Na Yang¹Xiaoyuan Sun¹Yaru Wang¹Ailifeire Wumaier¹Serik Khizat⁵Tolegen Assanbayev⁶Zhassulan Kozhanov⁷Attokurov Kursantbek⁸Obdunov Elmurat⁸Hangsen Li¹Aikebaier Reheman¹Xiaoling Zhou¹Wumaierjiang Aizimu¹Kairat Iskhan^5*Gemingguli Muhatai^1*

• ¹Tarim University, Aral, China
• ²Independent researcher, Fuyun, China
• ³Independent researcher, Balikun, China
• ⁴Independent researcher, Yining, China
• ⁵Kazakh National Agrarian University, Almaty, Kazakhstan
• ⁶Toraighyrov University, Pavlodar, Kazakhstan
• ⁷Kazakh Research Institute for Livestock and Fodder Production LLP, Almaty, Kazakhstan
• ⁸Osh State University, Osh, Kyrgyzstan

Xinjiang is known for the rich diversity of its native horse breeds, making it one of the most affluent regions in China. The horse industry in Xinjiang is growing fast, with native horse breeds prized for their high adaptability and tolerance to roughage. However, the introduction of external breeds and industrial changes are challenging for the conservation of these native horse breeds. Moreover, the population structure of Xinjiang horse breeds is unknown, hindering conservation efforts. Therefore, this study provides the first Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds (taxa) using 10X whole genome sequencing (WGS). The study analyzed the genetic diversity, population structure, and genetic distance of the horse breeds. The findings revealed a high population genetic diversity among Xinjiang native horse breeds. These breeds exhibited significant genetic differences from other horse breeds from Europe, Central and Western Asia, and China. Additionally, Xinjiang native horse breeds showed evidence of frequent gene flow, particularly in northern Xinjiang, where the breeds are more closely related. This study elucidates the distribution pattern, evolutionary characteristics, and genetic diversity of Xinjiang native breeds. The findings can offer theoretical support for establishing core conservation groups of local germplasm, cultivating new breeds, and exploring the characteristics of Xinjiang native horse germplasm resources.