Analysis On Genetic Structure And Body Size Selection Signature Of Chinese Domestic Donkey Population Based On Whole Genome Sequencing

Before entering the age of mechanization and electrification,the domestic donkey,as an important draft and livestock with medicinal value in Chinese society,was widely used in many aspects of social life.The domestic donkey is widely distributed in different areas of China.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant.The phenotype of domestic donkey breeds can be divided into large,medium and small donkeys according to their size.However,the genetic mechanism of population structure and phenotypic differences among cultivars remains unclear.In this study,we clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 domestic breeds and the 11 wild donkeys downloaded from the NCBI databases.This study revealed the unique genetic variation of the autosomal and mitochondrial genomes of Chinese domestic donkey in the genome-wide level,and discussed their origin,evolution and genetic diversity.In order to provide a theoretical basis for the conservation and development of Chinese domestic donkeys,we analyzed the genetic characteristics of the body size differences of Chinese domestic donkeys by scanning the selection signals between large donkeys and small donkeys.The main findings are as follows:(1)This study analyzed the genetic diversity of 12 domestic donkey breeds in China.Compared with other breeds,Gunsha donkey had lower nucleotide diversity and longer runs of homozygosity(ROH)length,which might be due to strong artificial selection and recent excessive inbreeding of the Gunsha donkey.(2)Based on the autosomal and mitochondrial genome data,it was found that the ancestral origin of Chinese donkey was relatively single.The population structure of Chinese donkey had obvious geographical distribution characteristics,which could be divided into three types: including those from North China Plain(Guanzhong,Taihang,Dezhou,Huaibei Grey,Biyang,Qingyang),Loess Plateau(Gunsha,Jiami),and Southwest China Plateau(Qinghai,Guola,Xinjiang,Tibetan).Mitochondrial results showed that the Chinese domestic donkey consisted of two maternal lines of origin,namely Clade Ⅰ and Clade Ⅱ.Asian wild ass and Chinese domestic donkey appeared in different branches.Thus,the origination of the Chinese domestic donkey population from the Asian wild ass was unlikely.(3)In the selective sweep,gene annotation,functional enrichment,and differential expression analyses between large and small donkey groups,we identified selective signals on chromosome 3,including NCAPG and LCORL,which are related to rapid growth and large body size.There were 11 and 5 missense mutation loci,respectively,which together constituted genotypes that could distinguish large donkeys from small donkeys.Our findings elucidated the evolutionary history and formation of different donkey breeds,provided theoretical insights into the genetic mechanism underlying breed characteristics and laid the foundation for molecular breeding programs of donkey.