Abstract
Simple SummaryAfter a long period of artificial selection, the donkey now presents a variety of body types and production performance values. In this experiment, we performed selective signal scanning on the second-generation resequencing data of six different varieties. The regions and candidate genes related to artificial selection were identified to provide reference for future breeding.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.
Highlights
The donkey (Equus asinus) is an important livestock species used for farming that originates from about 5000 years ago
The research of selection signature plays an important role in 2animal breeding and population evolution
We utilized six genetically and phenotypically diverse domestic donkey breeds to systematically analyze the signatures of selection (Figure 1b; Table S1)
Summary
The donkey (Equus asinus) is an important livestock species used for farming that originates from about 5000 years ago. With the increasing use of modern agricultural machinery and efficient transportation, the value of the draft donkey has gradually declined, but the value of donkey meat and milk has gradually increased. Factors such as diverse ecological changes, human migration, and socio-economic impacts have influenced the phenotypic characteristics of donkeys; there are 157 registered donkey varieties. The research of selection signature plays an important role in animal. Animals 2019, 9, x FOR PEER REVIEW socio-economic impacts have influenced the phenotypic characteristics of donkeys; there are 157 of 12 varieties. The research of selection signature plays an important role in 2animal breeding and population evolution. As the cost of single nucleotide polymorphism arrays (e.g., SNV (single and nucleotide variant) chips) As andthe high-throughput sequencing continues toarrays decrease, breeding population evolution
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