Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations

Abstract

Donkeys (Equus asinus) are an important farm animal. After long-term natural and artificial selection, donkeys now exhibit a variety of body sizes and production performance values. In this study, six donkey breeds, representing different regions and phenotypes, were used for second-generation resequencing. The sequencing results revealed more than seven million single nucleotide variants (SNVs), with an average of more than four million SNVs per species. We combined two methods, Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values, to analyze the signatures of selection. We mapped 11 selected regions and identified genes associated with coat color, body size, motion capacity, and high-altitude adaptation. These candidate genes included staining (ASIP and KITLG), body type (ACSL4, BCOR, CDKL5, LCOR, NCAPG, and TBX3), exercise (GABPA), and adaptation to low-oxygen environments (GLDC and HBB). We also analyzed the SNVs of the breed-specific genes for their potential functions and found that there are three varieties in the conserved regions with breed-specific mutation sites. Our results provide data to support the establishment of the donkey SNV chip and reference information for the utilization of the genetic resources of Chinese domestic donkeys.

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next‐generation sequencing

“…These results suggest that the donkey populations in different areas may have been subjected to independent artificial selection on the traits of body sizes. However, the selected loci of the different populations at the genomic level may have common profiles, as common features are probably caused by common mechanisms leading to genetic convergence, which can also be observed among some livestock species, especially horses and donkeys (Zhou et al, 2020).…”

“…The genetic basis of body size variation in Chinese donkeys has been partially revealed, including the limited number of loci associated with TBX3 , LCORL , NCAPG , and FAM184B (Shen et al, 2021; Wang et al, 2021; Zhou et al, 2020). However, previous studies have been far from sufficient to illustrate the genetic basis of the trait.…”

Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids

“…We performed functional enrichment to the 346 genes using KOBAS ( http://kobas.cbi.pku.edu.cn/ ) to find vital KEGG pathways, and there were 11 pathways in the enrichment results ( Supplementary Table S12 ). “Melanogenesis” pathway is essential for color phenotype in animals, and KITLG gene in the pathway has been proved to be associated with the phenotype of horse ( Voß et al, 2020 ), donkey ( Wang et al, 2020 ; Zhou et al, 2020 ), human ( Yang et al, 2018 ) and dog ( Weich et al, 2020 ).…”

“…The KITLG gene is located on chromosome 2 of donkey, and KITLG have been proven to be involved in the formation of coat color in several species ( Anello et al, 2019 ; Voß et al, 2020 ; Weich et al, 2020 ; Wen et al, 2021 ; Wu et al, 2019 ; Yang et al, 2018 ). Furthermore, there have been some studies on donkey and horse ( Voß et al, 2020 ; Zhou et al, 2020 ). Therefore, our findings may provide new insights into the coat color formation of Asiatic wild ass and its Kulan hybrids.…”

“…A previous study indicated that several ROHs (Runs of homozygosity, ROH) exist in the KITLG region in horses ( Metzger et al, 2015 ). A genome-wide study of six donkey breeds in China revealed KITLG as a candidate gene for donkey color, and the formation mechanism of diluted gray pigmentation (Dun phenotype) in wild ass has been reported ( Wang et al, 2020 ; Zhou et al, 2020 ); however, there are few studies on the coat color of Asiatic wild ass.…”