Transcriptome, DNA Methylation And MicroRNA Expression Profiles In Grass-fed And Grain-fed Angus Cattle Rumen Tissue

Recently, most research has reported the effects of genetics on the growth and meat quality traits of beef cattle; however, rumen function under different feeding conditions on the beef quality was limitedly studied. In our present study, we firstly detected the growth rate and beef tenderness, showing that the growth rate of grass-fed and grain-fed animals was significantly different; meanwhile, we analyzed the biochemical profiles in the blood and muscle tissue, demonstrating notable distinction of certain biochemicals between the two groups. Rumen, as one of the key workshops to digest forage, constitutes a critical step to supply enough nutrients for animals’ growth and production. Therefore, we hypothesized that the distinct growth rate and beef quality under altered feeding regimens was due to the changed rumen function, which might be associated with the ruminal transcriptome, DNA methylation and microRNA expression. We chose the ruminal wall tissue of Angus cattle as our primary experiment material. High-throughput sequencing method was utilized to detect the transcriptome, methylome and microRNA expression profiles, in addition, we also performed the integrated genome-wide analysis of gene expression with microRNAs and DNA methylation with respect to explore the potential molecular mechanism of rumen function, which would provide valuable theory evidence for improving the economic traits, mainly including beef quality.The main results of our study were as follows:(1) The growth rate of grass-fed animals(0.73kg/day) was considerably lower than grain-fed cattle(1.07kg/day); the polyunsaturated fatty acids α-linolenic acid, EPA and DHA were significantly higher in grass-fed group. Generally, the beef quality of grass-fed animals was more preferable than grain-fed steers.(2) Through RNA-Seq, we totally detected 342 differentially expressed genes in the rumen tissue of grass-fed and grain-fed Angus cattle. We screened some genes which might influence the growth and beef quality, including F2RL1, MFAP5, SLC2A11, DSG1, RSPO3, PPARG, GATA6, FOXA1, BNIPL, GLRX, GSR and AGPAT2. Among the top ten differentially expressed genes, GALNT15, LOC512548 and MPZL2 were limitedly reported, modifying the expression of these genes may provide possibilities to improve the meat quality.(3) microRNA-Seq analysis revealed that bta-miR-122 was significantly highly expressed in grain-fed group, and bta-miR-655 was exclusively expressed in grain-fed group. We totally screened 145 targets for bta-miR-122, of which only OCLN and RBM47 were extremely distinctive between the two groups. For bta-miR-655, there were 749 targets, 14 of which were differentially expressed. Among the 14 targets, gene FAM84 A and EMP1 were related to gastric function; PCDH19 and DSG3 were the only two genes involved in the GO terms, they played a role in cell adhesion, and altering the pattern of cell adhesion might influence the beef quality.(4) Methylome analysis totally uncovered 217 differentially methylated regions(DMRs). Among them, 57 DMRs were found in the gene body region, corresponding to 52 different genes; only ADAMTS3 and ENPP3 were found differentially expressed between the two groups, the expression of ADAMTS3 showed negative correlation with its corresponding DMR, however, ENPP3 was positively associated with the corresponding DMR. Preliminary inference was made that DNA methylation could modulate beef quality through regulating the gene expression.Accordingly, through high-throughput sequencing, we performed the study on grass-fed and grain-fed Angus cattle rumen tissue surrounding the transcriptome, DNA methylation and microRNA expression; further, we carried out the integrated genome-wide analysis of gene expression with microRNAs and DNA methylation, providing evidence for understanding the molecular mechanism of rumen functioning.