| Pork quality is a complex trait containing multiple indicators.Despite some progress that has been made in the genetic dissection of pork quality traits based on traditional quantitative trait loci(QTL)mapping and genome wide association study(GWAS)analysis,there are still many causal genes and functional mutations in QTL regions that have not been identified.Compared with GWAS,expression quantitative trait loci(eQTL)analysis can highlight regulatory mutations and then build the SNP-gene-trait bridge.Based on this,eQTL analysis was performed on the longissimus dorsi of 189 Duroc and Luchuan crossbred individuals,and the correlation analysis between genes and traits and GWAS analysis were combined to deeply explore the functional genes or mutations affecting pork quality traits.Furthermore,the present study combined six molecular quantitative trait loci,(MolQTL)analyses to investigate the formation mechanism of cis-eQTL and to identify functional mutations of the corresponding genes.The main results of this research obtained are as follows:(1)Based on RNAseq and DNA chip data,2,098 cis-eQTL genes(FDR ≤ 0.05),863trans-eQTL genes(FDR ≤ 0.05),and 2,253 ASE genes were identified in this study.In addition,we identified 33 IMF-correlated genes which had both eQTL and ASE signals,and 63 genes with both eQTL and ASE signals that have been reported previously to be associated with meat quality or economic traits.(2)By the Correlation analysis with IMF and gene expression levels,we identified212 genes significantly associated with IMF(FDR ≤ 0.01),and these genes could be significantly enriched in AMPK/PPAR,energy metabolism,and lipid metabolism signaling pathways.Integrating analysis of eQTL,GWAS,and trait correlated expression analysis,we identified four GWAS candidate gene,namely EMG1,PCTP,and,AGT.(3)Six type MolQTL analyses based on resequencing and RNAseq data identified3,173 cis-eQTL genes(BBFDR ≤ 0.05),1,972 ASE genes(FDR ≤ 0.01),2,440 TreQTL genes(BBFDR ≤ 0.05),210 s QTL genes(BBFDR ≤ 0.05),281 APAQTL genes(BBFDR≤ 0.05),and 559 CNV-eQTL genes(BBFDR ≤ 0.05).(4)In this study,we proposed a method to evaluate effective ASE-SNPs and identified2,096 effective ASE-SNPs involving 767 genes.Among them,444 effective ASE-SNPs were also cis-eQTL signatures,and 95.05% of the effective ASE-SNPs had the same regulatory direction in ASE and cis-eQTL analysis.In addition,this study demonstrated that the effective ASE-SNP(rs326817713)and its linked mutation rs339011837 are both the functional mutation of lipid metabolism-related gene NAXE,and SSC12:13,473,811-13,474,615 is a functional region of CACNG1,a functional candidate gene for muscle fiber traits.(5)By co-localization analysis,we identified 13 s QTL-eQTL co-localization genes and 9 APAQTL-eQTL co-localization genes.Among them,we revealed that the splicing mutation(rs325100969)could affect the promoter activity of ZFAND2 B,and rs344004299 was a functional mutation of APAQTL and eQTL of PNPO.(6)By the overlap analysis of CNV-eQTL and eQTL,we identified 559 common genes.Among them,the CNV-eQTL of 13 genes intersected with exons of the genes.Furthermore,we revealed the fragment duplications on the SSC7:97,256,620-97,265,072 and SSCX:6,862,262-7,006,814 were responsible for cis-eQTL signals of COQ6 and WWC3,respectively.(7)Integrating the six MolQTL analyses,42.83% of eQTL target genes were explained in our study..In summary,this study has built a platform for integrating analysis of eQTL,GWAS,and trait correlated expression analysis.The results provide some new candidate gene materials and functional mutation clues for genetic analysis of meat quality traits in pigs,and also provides an important foundation for subsequent in-depth genetic research on meat quality traits.In addition,the integration of six MolQTL analyses provided new ideas for resolving the eQTL genetic regulatory mechanism and mining gene functional mutations,and six functional mutations of candidate genes related to meat quality were identified. |
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