Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds

Abstract

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, F_ST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.

Keywords:

• Donkey
• evolution
• coat color
• physique
• genome comparison

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research was funded by the Shandong Province Science Major Project on Improved Agricultural Varieties, grant numbers 2013lz016 and 2017LZN022; Donkey Innovation Team of Shandong Modern Agricultural Industry Technology System, grant number SDAIT-27; Major Agricultural Application Technology Innovation Projects of Shandong Province, grant number SD2019 XM 008; Natural Science Foundation of Inner Mongolia Autonomous Region, grant number 2020MS03074; First-Class Disciplines Construction Project of Chifeng University, grant number CFXYYLXKB202102; and Innovation Research Team of Development and Utilization of Biological Resources in Eastern Inner Mongolia, grant number cfxykycxtd202008.