Genome-Wide Analysis of Genetic Diversity and Selection Signatures in the Jiami Donkey

The Jiami donkey is an indigenous breed distributed on the Loess Plateau of northern Shaanxi Province, China. Owing to the rapid mechanization of agriculture, its population has declined substantially in recent decades, highlighting the need for effective conservation strategies. In this study, we performed whole-genome resequencing of 30 Jiami donkeys and integrated these data with 210 publicly available genomes from diverse domestic donkey breeds. After quality control, 23,752,978 high-quality biallelic SNPs were retained for downstream analyses. Population genetic analyses revealed that Jiami donkeys represent a genetically distinguishable indigenous population with relatively high genetic diversity, showing the lowest pairwise genetic differentiation from Dezhou donkeys (FST = 0.032), followed by Qingyang donkeys (FST = 0.034). Genome-wide selection scans using θπ, iHS, CLR, FST, θπ-ratio, and XP-EHH identified candidate genes associated with growth, reproduction, immunity, nervous system development, and environmental adaptation. Among these, NCAPG, SMG6, SCARF1, BTG4, ASTN2, and NLGN1 were highlighted as promising candidate genes. Functional enrichment analyses indicated that these genes were mainly involved in amino acid metabolism, epigenetic regulation, neuronal development, and cell adhesion. Collectively, these findings provide valuable genomic resources for understanding the evolutionary history of the Jiami donkey and support future conservation and genetic improvement of this indigenous breed.