Screening Of Candidate Genes Associated To Meat Quality Traits Of Yanbian Yellow Cattle By A Combination Of MiRNA And Functional Genes Transcriptome

The bovine genome expression profiles chip and miRNA genechip were used to analyze the different genes and miRNAs expressed in longissimus dorsi muscle tissue of bulls and steers of Yanbian Yellow Cattle in this study. The target genes of the differentially expressed miRNA.were predicted. By analyzing the correlation of the differentially expressed genes and miRNA, the gene-miRNA networks were constructed. The function genes and regulation pathways associated with meat quality traits were screened out. At last, the molecular mechanism of miRNA regulating steer meat quality traits were preliminarily clarified. The study provided a theory basis for the genetic mechanism of Yanbian Yellow Cattle meat quality traits and molecular breeding in beef cattle production. The results were as follows:(1)10bulls and10steers in Yanbian Yellow Cattle were selected for determining meat quality traits. The results showed that H2O, crude fat contents and the marbling grade of meat were significantly increased in steers(p<0.05). The lauric acid, myristic acid, palmitinic acid, monoenoic palmitinic acid, stearic acid, oleinic acid, linoleic acid, linolenic acid, total fatty acids, satisfied fatty acid, unsaturated fatty acid, monounsaturated fatty acid, and polyunsaturated fatty acid, backfat thickness of meat in steers was significantly higher than that in bulls(p<0.01). And the ratio of the stearic acid, linoleic acid, linolenic acid and polyunsaturated fatty acid in composition of fat acid in steers was significantly lower than that in bulls(p<0.01). The ratio of the lauric acid, myristic acid,-palmitinic acid, monoenoic palmitinic acid, oleinic acid and monounsaturated fatty acid in compositon of fat aced in steers was significantly higher than that in bulls(p<0.01). The ratio of satisfied fatty acid and unsaturated fatty acid in composition of fat-acid-was not-significant between steers and bulls （p>0.05), The crude protein and muscular apparatus area in steers were lower than that in bulls (p<0.05)., and shear value in steers were significantly lower than that in bulls (p<0.01).(2)3bulls and3steers in Yanbian Yellow Cattle were randomly selected to analyze the differential expressed genes in longissimus dorsi muscle by Affymetrix genechip. The screening results of differential expressed genes in longissimus dorsi muscle of bulls and steers showed that there were85differential expressed genes between bulls and steers, including30up-regulated genes and55down-regualted genes in steers. The GO analysis showed that32genes were involved in oxygen and reactive oxygen species metabolic process22genes were associated with apical part of cell, MHC class II protein complex and so on.39genes were relevant to lipid binding and vitamin binding and so on. The pathway analysis showed that27differentially expressed genes participated in57KEGG pathways.(3) The detection results of miRNA genechip of longissimus dorsi muscle from bulls and steers showed that3737miRNAs expressed in longissimus dorsi muscle of bulls and steers, among of which246miRNAs had been found in cattle and the other3491miRNAs were unknown. By analyzing the differential expression of known miRNAs in bulls and steers of Yanbian Yellow Cattle,32differentially expressed miRNAs were found, including25up-regulated miRNAs and7down-regulated miRNAs in steers. According to the negative regulation relationship of miRNA and target mRNA, this phenomenon was consistent with expression trend of differentially expressed genes after castration These miRNAs might be related to the difference of meat quality traits of bulls and steers and had about7181potential target genes.(4) Three miRNAs including bta-miR-2407, bta-miR-122and bta-miR-15a and8genes such as CRLF3, ABAT, USP15, SCN4B, ANGPTL4, ROCK2, DGAT2and FABP4were selected to validate the miRNA chip. The results showed that the expression of these selected miRNAs and genes were significantly different between bulls and steers (P<0.05).,FABP4, ANGPTL4and SCN4B were very significantly different (p<0.01). These were consistent with the results of miRNA genechip and bovine genome expression profiles chip. So the results of chips were reliable.(5) The results of the correlation of miRNA genechip and bovine genome expression profiles chip showed that26of32differentially expressed miRNAs in longissimus dorsi muscle from bulls and steers were related to21different target genes, Among of them,20miRNAs were up-regulated and6miRNAs were down-regulated. The20up-regulated miRNAs had12down-regulation target genes, and the6down-regulated miRNAs were related to9up-regulated target genes.(6) GO and Pathway of21different target genes were analyzed. GO analysis showed that the down-regulated target genes differentially expressed in steers belonged to81biology processes,35celelular components and33molecular functions respectively. The up-regulated target genes differentially expressed in steers belonged to77biology processes,33celelular components and44molecular functions. Pathway analysis showed that down-regulated target genes belonged to10Pathway classifications, and up-regulated target genes belonged to12Pathway classifications.(7) According to reports and the analysis of correlation of two kinds of chips, we preliminarily concluded that the miRNAs including bta-miR-2455, bta-miR-214, bta- miR-216b and bta-miR-671were down-regulated in muscle of the steers, the target genes of which including DGAT2, ANGPTL4, ROCK2and PLIN5were up-regualted in muscle of the steers. The miRNAs including bta-miR-122, bta-miR-1271, bta-miR-16a, bta-miR-200c, bta-miR-16b, bta-miR-29b, bta-miR-221, bta-miR-15a, bta-miR-199c, bta-miR-26b, bta-miR-31, bta-miR-224and bta-miR-27a-3p were up-regulated in muscle of the steers, and they inhibited the expression of the target genes (ABAT, ATP6V0D2, USP15, DDIT4and FPGT) in muscle of the steers. Moreover, those genes participated in the metabolism of carbohydrate, fat, protein and energy in muscle by mediating the WNT signaling pathway, PPAR signaling pathway, glycerolipid metabolism, butanoate metabolis, valine,leucine and isoleucine degradation, alanine,aspartate and glutamate metabolism, mTOR signaling pathway and β-alanine metabolism, etc.. This showed that these miRNAs were also closely related to meat quality traits of Yanbian Yellow Cattle. The9genes including DGAT2, ANGPTL4, ROCK2, PLIN5, ABAT, ATP6V0D2, USP15, DDIT4and FPGT might be the important candidate genes influenced meat quality traits of Yanbian Yellow Cattle.