Research

Transcriptomes analysis to reveal candidate biomarkers responsible for muscle cell

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Abstract

Muscle tissue are very essential for the growth traits. The previous studies reported that polyphenol resveratrol could enhance cellular and functional adaptations of skeletal muscle and recover the muscle mass. However, genome-wide transcriptomes studies on muscle tissue after polyphenol resveratrol treatment were scarce. In this study, six muscle cell samples of beef cattle were used to investigate the transcriptomes difference based on RNA sequencing (RNAseq). Three samples hadpolyphenol resveratrol treatment (25uM) in the solution for 4 days as case group and the other three samples were considered as control group without such treatment. The raw data of RNAseq were under qualify control by removing reads containing adapter, reads containing ploy-N and low quality reads. Then, the clean reads were mapped to the reference genome of Bos taurus (UMD_3.1.1/bosTau8) by Bowtie software. Differentially expression (DE) analysis was performed using R package DESeq and P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). DE genes were identified by adjusted P-value < 0.05 of FDR. Gene Ontology (GO) and pathway enrichment analysis were also conducted to achieve significant utilities of biological system (adjusted P-value < 0.05). Finally, our study filtered 3856 DE genes in which 1805 genes were up-regulated and 2051 genes were down-regulated. The GO andpathway results showed 378 and 4 significant GO terms and pathways, respectively. Three of most significant GO terms were extracellular region part (GO:0044421), anatomical structure morphogenesis (GO:0009653) and tissue development (GO:0009888) (adjusted P-value = 4.82e-12). Four significant pathways were focal adhesion (bta04510), ECM-receptor interaction (bta04512), axon guidance (bta04360) and proteoglycans in cancer (bta05205). The most significant up-regulatedgene CDKN1A (Cyclin-dependent kinase inhibitor) was enriched in nearly 20% (75/378) significant GO terms. CDKN1A was also enriched in the significant pathway of proteoglycans in cancer. Briefly, this study found a list of up/down-regulated DE genes for muscle tissue that could be potentially applied as biomarkers in the beef cattle breeding program of growth traits.