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.

Keywords: ZHp; di; domesticated donkey; polymorphism; selection signatures.

Figure 1

Summary of six donkey breeds. (a) The six donkey breeds included in this study. (b) Geographic map indicating the distribution of the donkeys sampled in this study. Each point represents the location of sampling. The map was generated using the ‘ggmap’ package in R (version 3.5.2) (R Core Team 2018). (c) Principal components analysis (PCA) of six donkey breeds using the PC1 and PC2 components. DZ: Dezhou; GL: Guola; GZ: Guanzhong; KL: Kulun; QH: Qinghai; and XJ: Xinjiang. (d) A schematic representation of minor allelic frequency (MAF) plotted as a function of distance for each donkey population.

Figure 2

Overview of selective sweeps in the Dezhou and Xinjiang breeds plotted by Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values. (a) Dezhou donkey breed. (b) Xinjiang donkey. Functional genes are highlighted, and red and bold characters represent overlapping genes that were generated using the two methods. Absolute values of ZHp were used for plotting.

Figure 3

Overview of selective sweeps in the Qinghai, Guola, and Kulun donkeys plotted by ZHp and di values. (a) Qinghai breed. (b) Guola breed. (c) Kulun breed.

Figure 4

The conservation analyses identified candidate functional mutations that are specific to donkey breeds. Breed-specific SNVs within or close to the key selected genes. (a) GLDC, (b) ASIP, (c) CDKL5, and (d) ACSL4 were screened, and the SNVs localized to evolutionary conserved sites were retained. The locations and positions of the candidate SNVs are indicated.