Screening Of Differentially Expressed Genes Related To Beef Quality In Angus And Functional Analysis Of PPARD Gene

Black Angus is a special breed of beef cattle,which is introduced into China because of its strong adaptability,high meat yield,strong reproductive performance,fast growth rate,high feed utilization rate and good meat quality.Peroxisome proliferator activated receptor PPARD is a kind of ligand activated nuclear transcription factor,which has many biological functions in vivo,and plays an important role in the growth and development of the body,lipid metabolism,fatty acid production,adipocyte differentiation,immune and cell cycle control.In order to study the quality traits of Black Angus beef and the structure and function of the key regulatory gene encoding protein in Ningxia,three 24-month-old Black Angus cattle and Simmental cattle were used respectively After transcriptome sequencing of all samples collected by hiseqtm technology,bioinformatics method and relevant software were used to classify and analyze the sequencing results,and differential expression genes related to meat quality traits were screened out;in order to further study the differential expression gene PPARD gene,real-time fluorescence quantitative analysis was used PCR(QRT-PCR)was used to detect and analyze the mRNA expression of PPARD gene in 13 tissues of Angus cattle,including heart,liver,spleen,lung,kidney,rumen,reticulum,omasum,abomasum,large intestine,small intestine,longissimus dorsi and subcutaneous fat The CDs of PPARD gene was analyzed by Bioinformatics The physical and chemical properties,signal peptide,transmembrane domain,hydrophilicity/hydrophobicity,secondary structure and phosphorylation sites were predicted1.Through the quality evaluation,reference sequence comparison,gene expression level analysis of the transcriptome data,and intra group analysis and comparison of the duplicate data,the final result reflected in FPKM is the average value of all the duplicate data.The distribution and expression of different genes were inferred by volcanic map,and then classified by cluster analysis,go enrichment analysis,KEGG enrichment analysis,R language and other methods.Finally,the differential expression genes regulating meat quality were screened.There were 409 differentially expressed genes between Black Angus and Simmental,among which 115 were up-regulated and 294 were down regulated.Through further analysis of the up-regulated genes PPARD,a differential expression gene related to the differential expression of meat quality traits,was finally screened out.Further analysis showed that PPARD expression was significantly higher in Black Angus than in Simmental(P<0.01).The results of Q-PCR were consistent with those of transcriptome.These results showed that PPARD expression was higher in Black Angus than in Simmental.2.Through Q-PCR analysis,PPARD mRNA was expressed in 13 tissues of Black Angus and Simmental cattle.The expression of PPARD mRNA in abomasum and longissimus dorsi of Black Angus cattle was significantly higher than that of Simmental cattle(P<0.001);the expression level of PPARD gene in the abomasum of Black Angus cattle was significantly higher than that in other tissues(P<0.001),which was 42.36±13.256,and the lowest in liver.The expression level in Simmental subbovine fat was significantly higher than that in other tissues(P<0.001),and the lowest in longissimus dorsi(0.27±0.212).Cloning and bioinformatics analysis of PPARD gene of Black Angus cattle showed that the CDs region of PPARD gene of Angus cattle was 1326bp.An open reading frame with a total length of 1326bp was obtained from the PPARD gene of Angus cattle,and 442 amino acids were encoded.The theoretical isoelectric point was 6.91,which was alkaline.The atomic composition of PPARD gene protein of Angus cattle is C2206H3490N608O647S28,the molecular weight is 49779.34,the total number of atoms is 6973,the estimated half-life is 30 hours,and the instability index is 48.13(>40).Angus bovine PPARD gene protein has a strong hydrophilic region,which is a water-soluble protein.There is no transmembrane domain in the PPARD gene protein of Angus cattle.Angus bovine PPARD protein may participate in transcription regulation and DNA templating in the cytoplasmic internal biological process,and bind to zincion,nuclear receptor activity,DNA binding and DNA binding transcription factor activity in molecular function.The PPARD protein of Angus cattle may have no signal peptide,and it is a non secretory protein.There are 16 serine phosphorylation sites,13 threonine phosphorylation sites and 9 tyrosine phosphorylation sites in Angus cattle PPARD gene protein.Through coexpression analysis,we found that Angus PPARD gene coexpressed genes including PDHB,DLAT,DLD,LOC517402 and PDHA1 genes.In other organisms,PPARD is associated with RXRA,MED1,PDHB,LOC517402,DLD,PDHA1 and DLAT and PDHA2 were coexpressed.The genetic distance between Angus cattle PPARD gene and cattle was the closest,and the genetic distance with Rattus norvegicus was the farthest.The results of transcriptome sequencing showed that PPARD was significantly higher in most tissues than that of Simmental(P<0.01),which indicated that PPARD had a certain regulatory effect on beef quality,and the research results provided a theoretical basis for the selection of Angus cattle in Ningxia.