Whole-genome analysis reveals genetic diversity and selection pressure in Sichuan donkey

Sichuan donkeys are small-statured donkeys native to the plateau and mountainous regions of southwestern China. They are well-suited for transportation tasks in mountainous terrain and exhibit remarkable adaptability to the harsh environment, characterized by low temperatures and hypoxia. Adaptation to the local environment has shaped their unique genomic characteristics and is an important source of genetic variation. However, the genome-wide landscape of Sichuan donkeys remains undescribed.

In this study, we obtained whole-genome sequencing data from 17 Sichuan donkeys and combined this data with published data of 99 donkeys from 9 other donkey breeds. We aimed to elucidate the population structure, genetic diversity, genetic differentiation, and selection pressure of Sichuan donkeys at the whole-genome level. Population structure and genetic diversity analysis showed that Sichuan donkeys were less influenced by the hybridization of foreign donkey breeds. They maintained a relatively pure lineage of Chinese native donkeys and exhibited higher genetic diversity. The study also found that Sichuan donkeys were genetically closest to Tibetan and Yunnan donkeys. Although their effective population size around 1000 years ago was smaller compared to Tibetan and Yunnan donkeys, it was still larger than that of other donkey breeds. Moreover, selective signature analysis (θπ, CLR, F_ST, θπ-ratio) identified several candidate genes associated with hypoxia adaptation (EGLN3, RORA, CACNA2D3) and cold adaptation (NCOA2, SLC1A1, PAM, PLPPR1, and ZNF668). The most important finding is that EGLN3 shows different nucleotide diversity, Tajima'D value, and haplotype in donkeys living at different altitudes, suggesting it may be an important candidate gene for Sichuan donkeys to adapt to the cold hypoxic environment in the plateau.

This study clarified the genetic diversity, genetic differentiation, and effective population size of Sichuan donkeys by comparing them with other donkey breeds. Our findings contribute to deeper understanding of the high-altitude adaptability of Sichuan donkeys, and provide valuable information for the conservation and breeding of the breed.