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

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: Genome resequencing; Hetian Gray donkey; Origin; Population genetic structure; Selection signature.

Fig. 1

Geographic distribution of the studied Chinese donkey breeds showed in a partial map of China. HT and XJ indicate Hetian Gray donkeys and Xinjiang donkeys in the Xinjiang Uygur Autonomous Region (purple), respectively; YN, Yunnan donkeys in Yunnan province (pink); GZ, Guanzhong donkeys in Shaanxi province (light green); GL, Guangling donkeys in Shanxi province (deep green); DZ, Dezhou donkeys in Shandong province (blue); HBH, Huaibei Gray donkeys in Anhui province (yellow)

Fig. 2

NJ tree of the Hetian Gray donkey and other studied donkey breeds. YN indicates Yunnan donkeys; HT, Hetian Gray donkeys; DZ, Dezhou donkeys; GL, Guangling donkeys; GZ, Guanzhong donkeys; XJ, Xinjiang donkeys; HBH, Huaibei Gray donkeys; kiang, Equus kiang; somali, Equus africanus somaliensis

Fig. 3

PCA for the studied donkey breeds. A and B showed the results of 3D and 2D PCA, respectively. YN indicates Yunnan donkeys; HT, Hetian Gray donkeys; DZ, Dezhou donkeys; GL, Guangling donkeys; GZ, Guanzhong donkeys; XJ, Xinjiang donkeys; HBH, Huaibei Gray donkeys; kiang, Equus kiang; somali, Equus africanus somaliensis

Fig. 4

ADMIXTURE analysis for the studied donkey breeds. (A) Cross-validation for each run in ADMIXTURE analysis. (B) ADMIXTURE analysis results of the studied donkey breeds. YN indicates Yunnan donkeys; HT, Hetian Gray donkeys; DZ, Dezhou donkeys; GL, Guangling donkeys; GZ, Guanzhong donkeys; XJ, Xinjiang donkeys; HBH, Huaibei Gray donkeys; WD, Wild donkeys

Fig. 5

LD decay of the studied donkey breeds. The studied populations are indicated with different colors. YN indicates Yunnan donkeys; HT, Hetian Gray donkeys; DZ, Dezhou donkeys; GL, Guangling donkeys; GZ, Guanzhong donkeys; XJ, Xinjiang donkeys; HBH, Huaibei Gray donkeys

Fig. 6

The estimation of IBD shared between the Hetian Gray donkey and other Chinese indigenous donkey breeds. YN, Yunnan donkeys; DZ, Dezhou donkeys; GL, Guangling donkeys; GZ, Guanzhong donkeys; XJ, Xinjiang donkeys; HBH, Huaibei Gray donkeys

Fig. 7

Manhattan plot of the F_ST values between the Hetian Gray donkeys and the Xinjiang donkeys. The F_ST values are calculated for each 50 kb autosomal window. Adjacent chromosomes were indicated with different colors to make a better distinction of the borders

Fig. 8

The migration of the Guanzhong donkey along the Silk Road trade routes showed in a partial map of China. The red dot indicates Xi’an city; the orange dot, Hetian area; the white line, the Silk Trade Routes within China; The red dashed line, the possible migration route of the Guanzhong Donkey; Shaanxi province, Gansu province and the Xinjiang Uygur Autonomous Region are represented in green, light green, and light blue, respectively