GWAS Association Analysis And Verification Of Candidate Genes For Milk Production In East Friesian-Hu Hybrid F2 Generation Sheep

Lactation traits are an important economic trait of dairy sheep.Genetic factor has an important effect on lactation traits.Studies have shown that the heritability of lactation traits of dairy sheep ranges from 0.18 to 0.30.Therefore,breeding an improved dairy sheep breed is a necessary condition for improving lactation traits.The dairy sheep industry started late in China and has not yet cultivated a found breed of dairy sheep.East Friesian sheep and Hu sheep hybridized the East-Hu crossbred sheep have excellent milk production performance and good adaptability.However,backward breeding technology has limited the breeding process and seriously restricted the development of dairy sheep industry in China.With the rapid development of high-throughput sequencing technology and the decrease in sequencing cost,Genome-wide association study has been widely used in livestock breeding.In this study,East Friesian-Hu hybrid F2 generation sheep were selected as test subject.Genome wide association study was used to screen the genomic SNPs and InDels loci of dairy sheep,and the correlation between the obtained variation loci and milk yield traits was analyzed to screen out the significant loci and candidate genes.The polymorphisms of SNPs and InDels loci in the population were detected by Sanger sequencing technology,and the correlation between different genotypes and milk yield was analyzed.false positive data was eliminated,and molecular markers and candidate genes related to milk yield traits were determined,to provide the basis for molecular breeding of dairy sheep.This study mainly obtained the following results:1.Genome wide association study of milk production traits in East Friesian-Hu hybrid F2 generation sheepA total of 47616147 SNPs and 3664834 InDels were obtained by 5× depth whole genome sequencing of 168 East Friesian-Hu hybrid F2 generation sheep,27750039 SNPs and 3477181 InDels were screened after quality control.The association analysis between the selected SNPs and the milk yield data of the first and second lactation periods obtained 1 and 14 significant SNPs.The association analysis between InDels loci and the milk yield data of the second lactation periods obtained 13 significant InDels.The analysis of SNPs showed that 73% of the SNPs were located in intergenic or in intronic regions,and 20% were located in non-coding RNA intronic regions and only 1 loucs were located in expressd regions.The analysis of InDels showed that 38.5% of the InDels were located in intronic regions,and 61.5% were located in intergenic regions.After KEGG pathway analysis,26.7% of the loci were found to be related to metabolic pathways,including ESPNL,ASB18,RRP1,AGPAT3,ZDHHC18,PIGV,AMER3,PIGV,SF1,ZDHHC18,FAM98 A,FHIT,TM7SF2 and other genes.These genes can be used as candidate genes for milk yield traits in dairy sheep.2.verification of candidate genes for milk production traits in East Friesian-Hu hybrid F2 generation sheepPopulation validation was performed between the SNPs loci and InDels loci was selected.The genotyping results showed that 2 of the 15 SNPs loci(Chr2: g.255903819C>T,g.255903820A>G)contained 3 genotypes,and the other 13 SNPs contained 2 genotypes each.The results of gene polymorphism analysis showed that 2 of the 15 SNPs were moderately polymorphic(0.25<PIC<0.5),and the other 13 were low polymorphic loci(PIC<0.25).In addition,all 15 SNPs were in Hardy-Weinberg equilibrium(P>0.05).The results of association analysis between lactation yield and SNPs showed that 11 SNPs were significantly associated with lactation yield(P< 0.05).The candidate genes mined at these loci included ASB18,RRP1,FHIT,SF1,TM7SF2,etc.InDel loci validation analysis showed that 13 InDels loci were all low polymorphism loci(PIC<0.25),all of which were in Hardy-Weinberg equilibrium.The results of linkage disequilibrium analysis showed that there was a strong linkage among the12 loci,and one of the loci was selected for association analysis with milk yield.The results showed that all the 12 linked InDels loci were significantly correlated with lactation yield(P<0.05).The candidate genes mined at these loci included SPATA17,ESRRG and GPATCH2.In summary,In this study,11 SNPs loci and 12 InDels loci were selected by GWAS,which affected the milk yield of East Friesian-Hu hybrid F2 generation sheep,and candidate genes that may affect milk yield traits,such as ESPNL,ASB18,RRP1,AGPAT3,ZDHHC18,PIGV,AMER3,TM7SF2 were initially mined after population validation.This study provides a basis for molecular breeding of East Friesian-Hu hybrid sheep.