Exploring The Genetic Mechanism Of Meat Quality Traits In Chinese Simmental Beef Cattle Based On Multi-Omics Data Analysis

Genetic improvement of meat quality traits has always been an important work in the beef cattle breeding industry.However,meat quality traits are complex economic traits with many genes involved in their regulation process.In addition,meat quality traits are limited by too many measurements,difficulty in collection and high cost of measurement,thus the research of genetic regulation mechanism of meat quality traits in beef cattle is not deep enough currently.This study aims to identify and analyze the candidate genes,small molecular metabolites,and metabolic pathways that associated with meat quality traits in Chinese Simmental beef cattle by integrating genomics,transcriptomics,and metabolomic data in conjunction with statistical genetics,bioinformatics,and multivariate statistical analysis methods.The main results are as follows:1.Genetic parameter estimation for meat quality traits including marbling score(MS),water holding capacity(WHC),and shear force(SF)were firstly performed with use of 770 K SNP data and phenotypic data of 1478 individuals which from Chinese Simmental beef cattle population.The results showed that MS,WHC and SF were moderate or low heritability traits which with different genetic correlation among them.Then,the GWAS for MS,WHC and SF were conducted by single-trait and multi-trait strategies respectively.The results showed that:(1)Multi-trait GWAS performs better than single-trait GWAS in identifying the significant SNPs.(2)A total of 15 candidate genes associated with the target traits were identified.Meanwhile,seven candidate genes,including RGS5,S100A10,CAST,ANGPTL4,FER1L6,FABP4,and MYPN were identified by the two GWAS strategies,which could be regarded as key candidate genes affecting meat quality traits in beef cattle.2.Based on the RNA-seq data of longissimus dorsi,and phenotypic data of intramuscular fat content(IMF),WHC,SF that obtained from 76 experimental cattle which with same genetic background and feeding conditions,the weighted gene co-expression network analysis(WGCNA)of the three meat quality traits was carried out.The results showed that two gene modules were significantly associated with WHC and SF,and 27 hub genes in the two significant gene modules were identified.Given the significant effect of fat deposition for the meat quality traits,differential expression gene(DEG)analysis of 12 individuals with extreme high and low IMF were further performed.Then a total of 556 DEGs were identified,of which 513 genes were up-regulated and 43 genes were down-regulated in the high IMF individual group.GO annotation and KEGG functional enrichment analysis of DEGs revealed a series of biological processes and metabolic pathways involved in fat deposition,and 20 important candidate genes associated with lipid and energy metabolism were identified.Furthermore,four genes,including ANGPTL4,FABP4,GNA11 and CAST,identified in the GWAS above were also identified in our transcriptome study,which verified their regulatory effect of the meat quality traits in the gene expression level.3.Using the non-targeted metabolite data of longissimus dorsi,and phenotypic data of IMF,WHC,and SF from the 76 individuals described above,the significant difference metabolites of IMF,WHC,and SF were screened by MRA and OPLS-DA method.Then a total of 94,34,and 56 important metabolites associated with IMF,WHC,and SF were identified respectively,which including nine key metabolites(L-carnitine,CIS aconitic acid,furoic acid,citric acid,itaconic acid,adenine,reduced glutathione,linolenic acid,and lactic acid).Meanwhile,metabolic pathway enrichment analysis was carried out for the important metabolites of the three traits.Then,a total of 22,15,and 13 metabolic pathways were enriched for IMF,WHC,and SF respectively,which including five intersect metabolic pathways(TCA cycle,Glycolysis/Gluconeogenesis,Glyoxylate and dicarboxylate metabolism,Pyruvate metabolism,and Purine metabolism).It was speculated that they were involved in the genetic regulation of the meat quality traits in beef cattle.In conclusion,our research identified a series of candidate genes,metabolic pathways,and small molecule metabolites associated with meat quality traits in Chinese Simmental beef cattle by multi-omics analysis.The findings provide important theoretical basis for revealing the genetic regulation mechanism of beef meat quality traits and provide data support for high quality beef cattle breeding which based on molecular breeding strategy in the future.