Whole-genome Genetic Diversity And Selective Signals Analysis Of Southwest Donkeys In China

The long history of donkey breeding and diverse natural geographical environment have created rich donkey breed resources in China.At present,there are 24 local donkey breeds,which can be divided into north China plain donkey,the loess plateau donkey and the southwest plateau donkey based on their distributed regions in China.Southwest donkeys are distributed in Sichuan,Yunnan,and Tibet Autonomous Region,which are mostly highland,mountainous,and hilly areas.The mountainous environment,barren soil,and sparse vegetation have made the breeding conditions for local donkeys relatively rough,and only a small amount of supplementary feed can be obtained during pregnancy.As a result,three local small donkey breeds-Sichuan donkey,Yunnan donkey,and Tibet donkey-have gradually formed,which have the characteristics of being hardworking and having good adaptability to plateau environments.They are important donkey breed resources in China.However,there is currently no systematic research on the genetic diversity and environmental adaptability of Southwest Chinese donkeys.Therefore,this study collected 27 samples of Sichuan donkeys in Sichuan Province and conducted the whole genome re-sequence.At the same time,the whole genome data of 123 donkeys from 9 domestic donkey breeds from China（Tibetan Donkey and Yunnan Donkey in the Southwest Plateau,Guanzhong donkey in North China Plain,Gunsha donkey in the Loess Plateau）,Africa（Ethiopian donkey,Kenya donkey）,Europe（Spanishs donkey）,and Australia（Australian donkey）,and 4 wild donkey breeds from Africa and Asia were collected to analyze the population genetic structure,origin,evolution,and genetic diversity of donkey breeds in Southwest China from the level of autosomal,mitochondrial,and Y-chromosome genomes.In addition,this study also revealed the genomic characteristics of Sichuan donkey populations in terms of body size,cold resistance,hypoxia tolerance,and other traits related to environmental adaptability using genome wide selection signal analysis for the first time.The main results of this study are as follows:（1）Based on the autosomal genome SNP,it was found that the Southwest donkey population has fewer ROH fragments,low inbreeding coefficient,high nucleotide diversity and faster linkage disequilibrium decay rate,with rich genetic diversity and great potential for exploitation and utilization.（2）Through phylogenetic tree construction,principal component cluster analysis and ancestor component analysis of 13 breeds,the results showed that the ancestors of domestic donkeys were African wild donkeys,which was consistent with previous research results.The study also found that the nine domestic donkey breeds can be subdivided into three major groups:Chinese domestic donkey,tropical African domestic donkey,and southern European&Australian domestic donkey.The cluster relationship analysis of five Chinese domestic donkey breeds shows that the genetic relationship between Southwest plateau donkey and North China Plain donkey,Loess plateau donkey is relatively far away.In addition,among the Southwest donkey population,the Sichuan donkey has a relatively pure bloodline;The Tibetan donkey is closely related to the Sichuan donkey;Yunnan donkeys are closely related to Tibetan donkeys and Gunsha donkeys.（3）The maternal and paternal genetic maps of the mitochondrial genome of 113individuals and the Y chromosome of 65 male individuals were constructed respectively.The results showed that both the maternal and paternal origins of the domestic donkey were Equus africanus.The matriarchal origin of domestic donkeys can be divided into two matriarchal branches:the Nubian branch（Clade I）and the Somali branch（Clade II）,and the Somali branch（Clade II）is the dominant one in the Southwest donkey population.And there were 3 Y chromosome haplotype groups in 9 domestic donkey breeds,among which Hap2 subhaplotype was dominant,and Hap3 subhaplotype was unique in Tibet donkeys.Compared with foreign donkeys,the paternal genetic components of Chinese donkeys are more similar among different breeds.（4）In order to reveal the genetic mechanism of the adaptability of Sichuan donkeys to plateau environment,θπand CLR methods were used to search for the candidate regions of positive selection within the population of Sichuan donkeys.The results showed that genes related to innate immunity（BPIFB3,BPIFB2,BPIFB6）,lipid metabolism and thermogenesis regulation（NCOA2,PAM,SLC1A1）were strongly selected,which may be related to the adaptability of Sichuan donkeys to harsh and cold environment.At the same time,F_ST andθπ-ratio method were used to analyze the selective signals between Sichuan donkeys in high altitude region and Guanzhong donkeys in low altitude region.Genomic regions related to body size（LCORL,NCAPG,DCAF16,FAM184B）on chromosome 3 and hypoxic adaptation（DNAJB2,GLB1L,STK16,ANKZF1,ATG9A）on chromosome 19 were also strongly selected.The results indicated that the adaptability of Sichuan donkey to plateau environment was realized through the synergistic effect of complex gene network.In this study,the genetic diversity and origin evolution of donkey in Southwest China were systematically evaluated from the whole genome level,and the genes and pathways related to the adaptation of Sichuan donkey population to the plateau environment were excavated,which provided a theoretical basis for the scientific protection and genetic improvement of donkey breed resources in Southwest China.