In this study, we analyzed the whole genome sequence of 78 donkeys from 12 breeds. According to their body sizes, 12 donkey breeds were divided into groups of small donkeys (Xinjiang, Tibetan, Qinghai, Haibeihui, Taihang, and Gunsha donkeys), medium donkeys (Jiami and Qingyang donkeys), and large donkeys (Biyang, Dezhou, Guanzhong, and Guoluo donkeys). The genetic diversity of these animals may reflect various evolutionary events, including bottlenecks during domestication, introgression, recent cross-breeding, and artificial selection. Gunsha donkey showed reduced levels of nucleotide diversity compared to the other breeds, which is likely the result of intensive artificial selection in China. The nucleotide diversity of the other 11 donkey breeds was similar, which may be explained by unknown historical demography such as population expansion or introgression and a degree of inbreeding or a smaller effective population size. The length and number of homozygosity (ROH) among different donkey breeds were analyzed. ROH was first described by Gibson (32) and defined as contiguous homozygous genotype segments in the genome that are present in an individual because of the transmission of identical haplotypes from parents to their offspring (33–35). Inbreeding can increase the homozygosity of a population; as the level of inbreeding increases, the possibility for becoming homozygous for harmful recessive genes also increases, which may lead to decreases in reproduction, viability, and phenotypes of the offspring (36). The segment and number of ROH in Gunsha donkey were longer and larger, respectively, than those in other donkey breeds, possibly because of strong artificial selection and recent excessive inbreeding of Gunsha donkeys. Qinghai donkey had the shortest and smallest number of ROHs among the 12 donkey breeds. This may be because of the following reasons: 1. Qinghai donkey inbreeding may have been low in the large area of Qinghai and 2. Qinghai donkey was not the only or most important economic and transportation animal in the local area, and thus the intensity of natural and artificial selection may be relatively low. A lower inbreeding coefficient and lower selection pressure may be underlying factors causing Qinghai donkey to have the smallest number of and shortest ROH.
Population structure and phylogenetic analyses can improve the understanding of the evolutionary process of certain species or breeds. As there is no complete chromosome-level reference genome available, no population genomic analyses have examined the genetic ancestry and population structure of Chinese donkey. In our study, we selected representative breeds of Chinese donkey to analyze their relationships. According to the NJ tree, Mongolian wild ass was the outer group, and Chinese donkey breeds were clustered into three branches according to their geographic region. These mainly included the East China Plain, loess plateau, and plateau area donkeys. The results of PCA showed that only the first PC separated Gunsha and Jiami donkey from the other donkey breeds, whereas other PCs could not separate the breeds. Admixture analysis did not distinguish between each donkey breed and different ancestral types. The reason that clear results were not obtained by PCA and admixture analysis may be that most individuals were of mixed ancestry. With the rapid development of civilization, donkeys were rarely used as a means of transport; however, domestic donkeys have been widely used for their meat and medicinal value. This has led to the artificial migration, hybridization, and breeding of Chinese donkeys. Such mixed results can be explained by mixed ancestry between donkey breeds. The degree of genetic diversity among Chinese donkey breeds may not be high, and the difference in genetic background is not obvious. Similar to the results of previous studies, we found that the Chinese donkey has two maternal sources and forms two branches, clade I and clade II. Among them, Clade II and Somali wild donkeys gather together, and this branch may have originated from Somali wild donkeys in Africa. As the Asian wild ass and Chinese donkey were present on different branches, it does not appear that the domestic donkey originated from the Asian wild ass.
By performing whole-genome selection scans, we analyzed the genetic basis of the divergence of different body sizes of donkey groups. The top two divergent genes on chromosome 3 between the large and small donkey groups were both strongly related to cell mitosis and bone development, including NCAPG and LCORL, which may play an important role in body growth. NCAPG is a subunit of the condensin 1 complex which is involved in chromosome condensation and interacts with a DNA methyltransferase linking methylation and chromatin condensation (37). LCORL encodes a transcription factor that is thought to function during spermatogenesis (38). These neighboring genes exhibit strong linkage. In previous studies of the functions of these two genes, the regions containing the genes were often described together in many species. The regions of NCAPG and LCORL have been identified as loci for adult human height in European (39–43), Japanese (44) and African/African American populations (45, 46). The region was also associated with the peak height velocity in infancy (47), birth weight (48) and birth length (49). In cattle, the two gene regions were associated with birth weight (50), weaning and yearling weight (51), increase in body frame size (52) and carcass weight (53). Further, this region was found to be associated with height in some horse breeds (26, 29, 54, 55) and has been identified as highly differentiated between dog breeds (38) and a selective sweep region in European domestic pigs (56).