| There are more than 400 breeds of domestic dog in the world,each breed has unique characteristic in physiology,behavior and morphology.Archaeological findings from ancient site around the world have indicated that the first livestock to be domesticated was dog.In recent years,more and more studies have reported the origin,genetic diversity and genomic regions associated with phenotypes in western dogs with high-density single nucleocide polymorphism(SNP)chips and whole-genome resequencing.However,the genetic structure,evolution relationship,and selected signature of Chinese indigenous dogs remain largely unknown.To investigate population structure,linkage disequilibrium(LD)extent and selection signature at the genome level in Chinese dogs,we performed a genomic survey in 16 diverse breeds from diferent geographic regions of China and and 3 Asian gray wolves using Canine 170 K SNP chips.The genotyping data of 456 western dogs was downloaded from LUPA database and also intergrated into alwaysis.Accumulating runs of homozygosity(ROH)in Chinese and Western breeds revealed that historical inbreeding reduced genetic variability in Western dogs.LD extent within each population was comparable between Chinese and Western dogs.The average LD at R2=0.3 of Chinese dogs was significantly than Western dogs(46.1Kb vs 117.4 Kb).We analyzed the population structure using Neighbor-Joining(NJ)tree among Chinese indigenous dogs,Western dogs and Asian gray wolves.Chinese dogs and Western dogs were divided into two branches and Asian gray wolf was clustered into the Chinese indigenous dog groups as expected for the NJ-tree results.Surprisingly,the Greenland sled dog was divided into Chinese high altitude dog group and almost overlaped with Tibetan mastiff.Finnish spitz was shown a closer relationship with Kazakhstan shepherd dog and Mongolian thin dog.The results indicated a path of Chinese dogs into Western dogs through Siberia and Central Asia.To provide the information for deciphering the genomic copy number variation of Chinese indigenous dogs,we used PennCNV software to analyze the genomic copy number variation of Chinese indigenous dogs.We randomly selected 8 CNVRs for validation by real-time quantitative PCR.And the genes and functional annotation were performed with BioMart and DAVID.As a result,we totally found 477 CNVs in 185 individuals,these CNVs randomly distributed on 38 autosomes.220 CNVRs were produced by combining 477 CNVs,including 115 deletions,74 duplications and 31 deletion/duplications.These CNVRs were equally 1.25%of dog whole-genome sequences.The average length of these CNVRs was 142.24 kb.Furthermore,except the CNVRs found in only one sample,we got 53 Chinese indigenous breed-specific CNVRs.We found 162 genes were located within the CNVRs.These genes were enriched in olfactory receptor activity,sensory perception of smell,sensory perception of chemical stimulus,sensory perception and neurological system process.To detect the selection signature of breed features,we performed di and Fst outlier tests for each Chinese breed and four groups with special characters(high altitude group,Southwestern mountainous,North China Plain,Northern pastoral and small body size group).We verified some selected genes identifed previously,such as HAS2 gene associated with wrinkle skin phenotype,EPAS1,HMOX2 genes related to the plateau adaptablity,IGF1 gene associated with body size.With the present study we also found some new selected gene regions,which were shown the strong selection signature,such as OTULIN,FAM105A for high altitude dog,NMNAT1 and RBP7 for Southwestern.mountainous,BICD2,IPPK,ECM2,ASPN,OMD,OGN for thin dog. |
