Abstract
Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.
Highlights
Donkey (Equus asinus) is an important livestock animal in China because of its nourishment and medical value
We found that Gunsha donkey had the lowest nucleotide diversity, longest length, and largest number of runs of homozygosity
Gene annotation, functional enrichment, and differential expression analyses between large and small body donkey groups, we identified selective signals, including NCAPG and liganddependent nuclear receptor corepressor-like (LCORL), to be related to rapid growth and large body size
Summary
Ethics statementThis study was conducted to the guidelines of the Council of China and animal welfare requirements. We downloaded the latest donkey reference genome (PRJNA259598) from NCBI This genome was published in 2015 and is currently at the scaffold level [16]. We used the reference genome of a related horse species (PRJNA421018) to assemble the donkey scaffold at the chromosome level [17]. Using a Python script (Connect_Pseudo_Chromosome.py, Note S1), according to the comparison information in the paf file, the donkey's Scaffold was assembled to at the pseudo chromosome level, and the connection information of each scaffold was recorded. To obtain annotation information for the donkey's pseudo genome, we used a Python script (Pseudo_Chromosome_Annotation.py, Note S2) to convert the annotation information at the donkey scaffold level to the pseudogene which was assembled based on the donkey's scaffold connection information
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