Construction Of Cattle,Goat And Sheep CNVR Database And Functional Research Of MUC6 CNVR Related To Goat Immunity

Copy number variation(CNV)is one of the important mutations in the genome,involving an increase or decrease in copy number.Copy number variation plays an important role in the life activities of species and is an important part of the evolution of species.Important ruminant livestock such as cattle,goat and sheep,along with the development of human civilization,have played an important part in human production and life.The study of copy number variation in the genomes of these typical species laid a theoretical foundation for the protection of ruminant genetic resources and the development and utilization of excellent traits.Species are accompanied by changes in their adaptation to the environment during the complex evolutionary process,and the adaptation of the ruminant to the environment in terms of copy number variation remains to be explored.The sharing of a certain number of copy number variations among species,and the occurrence and preservation of evolutionary processes are very interesting scientific issues.The important role of copy number variation in function is beyond doubt.In this study,a 246 bp copy number variation region(CNVR)located in the goat MUC6 gene was found.It is speculated that it may be related to changes in immune function during the early domestication of goat.Exploring the function of this CNVR provides a strong evidence for understanding the important role of copy number variation in organisms.This study involved a total of 866 NGS resequencing data,as follows:(1)233 cattle,including 140 Bos taurus,82 B.indicus,11 hybrid cattle(B.taurus × B.indicus hybird);(2)241 goat and wild relatives,including 210 Capra hircus,and 24 C.aegagrus,7 C.ibex;(3)412 sheep and wild relatives,including 387 Ovis aries,17 O.musimon,3 O.ammon,3 O.canadensis and 2 O.dalli.Besides,single molecule sequencing data of a crossbred cattle,a goat,and a sheep.At the same time,we also downloaded two haploid genomes including a taurus cattle and a indicus cattle.We used population genetics and comparative genomics methods,combined with epidemiological and artificial infection test to analysis the above resequencing data and genome data.The results were described as below:1.Genomics analysis of multiple type of data,and verification of CNVplex and q PCR,we obtained high-quality whole genome copy number variation database for cattle,goat,and sheep,and obtained screening criteria for the copy number variation database.The populations of the three sets are rich in genetic diversity,which is consistent with the results of previous studies in SNP.At the same time,unique copy number variations were found in many breeds.This study also found that CNVR tends to enrich in exon regions(p<0.00001)compared to random distribution,and the proportion of exon CNVR is nearly 50%.2.Through population differentiation analysis,this study found a total of 830 CNVR sites that are highly differentiated between populations(VST?0.5).Gene annotation and enrichment analysis revealed that these loci are related to many important life processes,such as species metabolism.We found 11,26,16 significant CNVR sites in cattle,goat and sheep,respectively,by genome-wide association analysis with climate factors.These sites all showed the adaptive changes of ruminants to the environment under selection.3.This study compared the difference between species-shared CNVRs and species-shared single nucleotide polymorphisms(SNPs).We found that the proportion of species-shared CNVR were much higher than the species-shared SNPs(p<0.00001).Shared SNPs seem to be less affected by species divergence times and are more easily retained.Computational simulation studies showed that the proportion of species-shared CNVR was much higher than random(p<0.01),further research into the species-shared CNVR revealed that CNVR hotspots have little effect on them,and the formation and retention of species-shared CNVR are more likely to be affected by balancing selection and convergence evolution.4.Based on epidemiological investigation and artificial infection test,this study investigated the function of an important CNVR located in goat MUC6 gene.The epidemiological investigation concluded that the higher frequency MUC6 D haplotype in domestic goat was compared with MUC6 B haplotypes with higher frequency in wild ancestors have higher resistance to gastrointestinal parasites.In addition,artificial infection tests were not successful.It is speculated that the cause of the failure may be related to a complex process by many factors such as goat self-healing,environment,and parasite body vigor.But overall,this study demonstrated the immune resistance of important CNVR in the MUC6 functional region to gastrointestinal parasites in goat.It is speculated that it played an important role in the early domestication of goat,but the specific molecular mechanism needs further development.This study provides a database of CNVR data for ruminants such as cattle,goat,and sheep.Through population genetics and comparative genomics,which is helpful to guide genetic breeding and find the adaptive evolutionary mechanism of species to the environment.Besides,epidemiology surveys and other methods have verified important CNVR,revealing that the CNVR in MUC6 gene may have an immune effect on gastrointestinal parasites in the early stages of domestication of goat.It provides theoretical and technical basis for the disease resistance breeding of goat,and at the same time contributes to promoting the healthy and rapid development of the domestic goat industry.