A Meta-analysis Of Genome-Wide Association Studies For Average Daily Gain And Lean Meat Percentage In Two Duroc Pig Populations

Average daily gain(ADG)and lean meat percentage(LMP)are the main factors that influence the production cost and income of farms,and they are usually considered to be the main economic traits of pigs.Thus,increasing ADG and LMP have always been the main goal of breeders.Nevertheless,the genetic architecture of the pig ADG and LMP remains elusive,lacking of precisely the method of the molecular breeding.With the completion of sequencing of the pig genome and the development of high density single nucleotide polymorphism(SNP)chips,genome-wide association study(GWAS)was performed for pigs has become a reality.However,GWAS requires a large sample size to detect the true SNP associated with complex traits.Given the huge workload of GWAS and the high cost of experimentation,which lead to a single GWAS sample size meet the sample size of the test requirement may be difficult.Meta-analysis can expand the sample size by combining multiple independent study data to increase the power and reducing false-positive findings.Thus,meta-analysis is an effective method to solve the problem of insufficient sample size in GWAS.In this study,we conducted a genome-wide association study(GWAS)for ADG and LMP on 3917 S21 Duroc pigs(American origin)and 2127 S22 Duroc pigs(Canadian origin),to reveal novel major loci and candidate genes that were associated with ADG and LMP in pigs.The results are as follows:(1)In S21 and S22 Duroc pigs,the heritability of ADG and LMP ranged from 0.36 to 0.42,the two traits are little higher than moderate heritability;the phenotypic variation coefficients of the ADG and LMP traits are greater than 2.5% in the two pig populations.The results showed that ADG and LMP have a certain genetic improvement space.(2)We detected 12 SNPs were associated with ADG and LMP in S21 Duroc pig population,including six suggestive SNPs were associated with ADG,three suggestive and three genome-wide SNPs were associated with LMP.In addition,two SNPs have not been included in any previously reported QTLs that were associated with ADG and/nor LMP.Among them,one SNP on Sus scrofa chromosome(SSC)6 was associated with ADG and LMP,but the nearest Olfr1328 gene function of this locus is unknown;the remaining SNP on SSC12 was associated with LMP,and the nearest TOB1 gene of this may be involved in skeletal muscle development.(3)Ten and 12 suggestive SNPs were identified to be associated with ADG and LMP in S22 Duroc pig population,respectively.Interestingly,these 12 SNPs that were associated with LMP have not been included in any previously reported QTLs that were associated with LMP.Among them,nine SNPs were located in a 651 kb haplotype block on SSC16,SNX18 is a strong candidate gene in this region and involved in cell mitosis;the remaining three SNPs on SSC1,their the nearest gene TLE3 is associated with adipogenesis.(4)In meta-analysis,we detected eight genome-wide and 16 suggestive SNPs were associated with ADG,three genome-wide and 9 suggestive SNPs were associated with LMP.Moreover,meta-analysis identified 12 SNPs that were associated with LMP,of which eight SNPs have not been included in any previously reported QTLs that were associated with LMP.Among them,the candidate gene of one SNP on SSC1 is GLRX,this gene is associated with dyslipidemia;the remaining seven SNPs on SSC16 were shared by S22 Duroc pig population and meta-analysis.Compared with single-population GWAS results,meta-analysis detected several additional SNPs,including 17 and 3 SNPs were associated ADG and LMP,respectively.As expected,the meta-analysis can significantly enhance the call rate of QTL.(5)Base on the identified tag SNPs position,we find the genes that were within or near the identified tag SNPs by the Ensembl website.A total of 23 and 12 candidate genes were identified to be associated with ADG and LMP,respectively.Further gene set enrichment analysis for these candidate genes,the results indicated that these candidate genes that are associated with ADG are involved in urate metabolic process,regulation of transcription and DNA-templated;these candidate genes that are associated with LMP are involved in Ras signaling pathway,MAPK signaling pathway,and small GTPase mediated signal transduction.We performed GWAS and meta-analysis for ADG and LMP,involving 6044 Duroc pigs from S21 and S22 Duroc pig populations.In this study,a total of 15 SNPs were reported for the first time.Among them,14 SNPs were associated with LMP,the nearest genes of these loci are SNX18,GLRX,TLE3,and TOB1;the other one SNP may have pleiotropic effects on the ADG and LMP traits,the Olfr1328 candidate gene was identified by this locus position.Our results provide new insight into the genetic architecture of ADG and LMP in pigs,and will be useful for marker assisted selection and molecular breeding of ADG and LMP in breeding programs.