Comprehensive genomic analysis of genetic diversity, body size, and origins of the Hetian Gray donkey

Abstract

Abstract Background The Hetian Gray donkey, characterized by its large stature and gray coat color, is a relatively recently identified breed. This breed plays an important role in local agricultural practices and cultural heritage. However, with the widespread adoption of mechanization, its use as a draft animal has gradually diminished. Additionally, the insufficient development of its meat and milk products has contributed to a continuous decline in its population, making its conservation increasingly urgent. Despite its significance, research on the origin and ancestral composition of the Hetian Gray donkey remains limited, which is essential for developing effective conservation strategies. To address this, whole-genome resequencing data of 208 donkeys from seven Chinese indigenous donkey breeds, Equus africanus somaliensis, and Equus kiang were analyzed to investigate the relationships between the Hetian Gray donkey and other breeds in the present study. The findings of this study will provide valuable scientific evidence for preserving the genetic diversity and unique characteristics of the Hetian Gray donkey. Results The analysis revealed that wild donkeys had no significant impact on the formation of the Hetian Gray donkey. Among the breeds studied, the Xinjiang donkey and the Guanzhong donkey exhibit the closest genetic affinity with the Hetian Gray donkeys. Additionally, genome-wide selection signature analysis between the Hetian Gray donkey and the Xinjiang donkey identified positive selection for genes associated with body size traits. Conclusion In summary, the results confirm that geographical distance plays a crucial role in determining the genetic relationships among the Hetian Gray donkey and other populations. The Xinjiang donkey and the Guanzhong donkey played an important role in the formation of the Hetian Gray donkey, and genes related to body size were positively selected during development of the breed.

Keywords

• Hetian Gray donkey
• Genome resequencing
• Origin
• Population genetic structure
• Selection signature