Genomic Analyses Reveal Distinct Genetic Architectures and Selective Pressures in Chinese Donkeys
Abstract BackgroundDonkey (Equus asinus) is an important livestock animal in China because of its nourishment and medical value. After a long period of natural and artificial selection, the variety diversity and phenotype of donkey are very rich. However, due to the lack of genome-wide studies, its genomic value remains unclear.ResultsWe clarified the genetic and demographic characteristics of Chinese donkeys and the selective pressures on them by analyzing 78 whole genomes from 12 breeds. We found that Gunsha donkey had the lowest nucleotide diversity, longest length, and largest number of runs of homozygosity. Phylogenetic analysis revealed obvious geographical distribution trends in Chinese donkeys. In selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small body donkey groups, we identified selective signals, including NCAPG and LCORL, to be related to rapid growth and large body size.ConclusionOur findings improve the understanding of the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.