The Study On Selection Signals Of Five Chinese Donkey Breeds Based On Whole Genome Resequencing

Donkeys(Equus asinus)are key members of the livestock,domesticated for farming,transportation and food supply,thereby enhancing the development of human civilization.In recent years,with the development of the health industry represented by donkey-hide gelatin,the price of donkey skin keeps going up.At the same time,the nutritional value of donkey meat and donkey milk is gradually accepted and recognized by consumers.The benefits of donkey breeding are increasing year by year.However,because the donkey industry has been neglected for a long time in China,there are no specialized breeds for skin,meat and milk.In the meantime,the research about genetic basis of donkey economic traits is lacking.In this study,we used the high-throughput sequencing technologies and bioinformatics analysis to detect selection signatures of the six selected donkey breeds.The candidate genes included body size genes,coloration genes and so on.The results showed as follows.(1)The reserch objects were six Chinese domesticated donkey breeds,representing morphologically or geographically specific populations: 9 Dezhou donkeys,10 Guola donkeys,10 Guanzhong donkeys,10 Kulun donkeys,9 Qinghai donkeys,and 9 Xinjiang donkeys.These donkeys are no blood relationship between them.And then our generated total clean data had 201 Gb and the sequencing depth was 10-fold coverage for each breed with the six donkey breeds mixed pool whole genome re-sequencing data,Comparing with the reference genome(Equus asinus ASM130575v1),we discovered more than seven million single nucleotide polymorphisms(SNPs),and approximately four million SNPs for each breed.Principal components analysis(PCA)was performed to examine the genetic separation of six donkey breeds.Two large donkey breeds(Guanzhong and Hetian Gray)were clustered together,and were closely related to Kulun.The other three donkey breeds are far away from Guanzhong,Hetian Gray and Kulun.At the same time,they are far away from each other.The results of the PCA were consistent with the analysis of breeding history and phenotypic traits of these six Chinese indigenous breeds.The cluster results also were in agreement with the findings of a previous study on the genetic diversity of donkey breeds in China;(2)There are two selective sweep methods,which are di test based on difference of population and Zhp test based on heterozygosity.Then we analyzed the six donkey breeds' selection signatures with these methods.We calculated Hp values,ZHp values,Fst values and di values of each window with 50 kb size windows and 10 kb sliding step.By combining two approaches,ZHp and di values,we identified 11 genomic regions that may have contributed to the phenotypes in coat color patterns,body size,motion,as well as high altitude adaptation in donkey populations.Candidate genes underlying strong selection signatures including coloration(ASIP and KITLG),body size(ACSL4,BCOR,CDKL5,LCOR,NCAPG,and TBX3),motion(GABPA),and hypoxia adaptation(GLDC and HBB)were identified;(3)We also identified candidate functional SNPs within selected genes that may be important for each trait.Breed-specific SNPs among four genes(GLDC,ASIP,CDKL5,and ACSL4)were localized to evolutionary conserved regions in mammals,suggesting that these SNPs might be functional.There are rarely detection of selection signatures studies in Chinese donkeys at a genome-wide scale.Our results demonstrated the potential of using 6 Chinese donkey breeds' mixed pool sequence data in identifying genomic regions that have selection signals.We identified 11 genomic regions that may have contributed to the donkey phenotypes,and also identified candidate functional SNPs within 4 selected genes that may be important for each trait.These SNPs will lay a foundation for the further development of donkey molecular breeding markers.