Differential Gene Expression Analysis Of Breast And Leg Muscles Between Large Bone Chickens And AA+broiler Chickens Based On RNA Seq

ObjectiveIn order to learn the characteristics of m RNA differentially expressed genes of different breeds and different muscles,the breast and leg muscles of Dagu chicken and AA~+broiler were used to do RNA sequencing.To further analyze the genetic basis of meat quality differences between Dagu chickens and AA~+broilers,and lay the foundation for screening key genes that control muscle quality.MethodsAt the same time period in our research team’s research chicken farm,we raised Dagu chickens and AA~+broiler chickens roosters.Three roosters were slaughtered at the age of 24 weeks and 42 days respectively,and samples of chest and leg muscles were taken and frozen in liquid nitrogen.The Dagu chickens and AA~+broiler pectoral and leg muscles were taken for total RNA extraction and quality detection,and the c DNA library was constructed and sequenced;After the quality evaluation of the sequencing data,the reference sequences were compared,and variable splicing,SNP,In Del and new transcript prediction were analyzed.According to chicken breeds and muscle parts,this experiment was divided into four groups to screen and cluster the differently expressed genes,and to conduct GO enrichment analysis and KEGG enrichment analysis on the differentially expressed genes.Five differentially significant genes of oxidative phosphorylation were screened in Dagu chickens and AA~+broiler pectoral muscles and leg muscles for real-time quantitative PCR verification;Analyze the above test results using SPSS 26.0T test method.Results1.The clean bases of all samples in this experiment was 3.45 G,the error rate is 0.035%,the average GC content was 51.30%,the correlation coefficient of intra-group samples was>0.95,and there are a lot of variable shear,SNP and Index variations.The total number of muscle differential genes of Dagu Chicken vs AA~+broiler was 177,including 153 known genes and 22 new genes;After removing the chicken breed difference,the total number of leg muscle versus breast muscle difference genes was 253,including 221 known genes and 32 new genes.2.GO analysis found that compared with AA~+broilers,the highly expressed cell components of breast muscle and leg muscle of Dagu chicken were mitochondrial intimal components related to oxidative phosphorylation,the biological process was redox process and mitochondrial ATP synthesis coupled with electron transport,and the molecular function was oxidoreductase activity,while the highly expressed cell components of breast muscle and leg muscle of AA~+broilers were extracellular matrix(ECM),resulting in high expression of calcium ion binding Metallopeptidase activity,structural components of extracellular matrix and metalloendopeptidase activity.Compared with the leg muscle of the Dagu chicken,the breast muscle of the Dagu chicken was significantly enriched in the process of monobiological carbohydrate catabolism,glycolysis and carbohydrate catabolism.Compared with the leg muscles of AA~+broilers,the breast muscles of AA~+broilers were significantly enriched in the composition of myosin complex,carbohydrate metabolism process,hydrolase activity and function3.KEGG analysis found that oxidative phosphorylation,TCA cycle,myocardial contraction and other pathways in the pectoral and leg muscles of the Dagu chicken were significantly higher than those of the AA~+broiler,while the ECM receptor interaction and adhesion spots of the pectoral and leg muscles of the AA~+broiler were highly expressed.Compared with leg muscle of Dagu chicken,breast muscle of Dagu chicken was significantly enriched in glycolysis/gluconeogenesis and amino acid biosynthesis.The tight junction pathway of AA~+broiler leg muscle was significantly higher than that of chest muscle,and the pathway related to anabolism such as glycolysis/gluconeogenesis and amino acid biosynthesis of breast muscle were significantly higher than that of leg muscle.4.Through GO and KEGG methods,a total of 10 upregulated differentially expressed genes were screened for breast and leg muscles in both Dagu chickens and AA~+broilers,including UQCR11,COX5 A,UQCRFS1,COX7 C,MDH2,DLD,IDH3 B,NDUFV1,NDUFC2,and PTGES2.And real-time quantitative PCR was performed on 5 of the genes,and the results were consistent with the sequencing results.ConclusionsThe muscles of Dagu chicken and AA~+broiler have their special characteristics of high and low gene expression.The pectoral and leg muscles of the Dagu chicken have very high oxidative phosphorylation activity and carry out active aerobic metabolism,which was conducive to long-term exercise;However,AA~+broiler pectoral muscle and leg muscle are expressed in a large amount on the cell components,which are used for material synthesis and develop towards muscle deposition.Compared with leg muscle of Dagu chicken,the glycolysis/gluconeogenesis and amino acid biosynthesis of breast muscle of Dagu chicken are more active.The protein synthesis,starch and anaerobic sugar metabolism of AA~+broiler breast muscle were more vigorous than those of leg muscle.