Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle

Abstract

Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.

Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmental stage specific gene expression

“…KRT36, for 627 example, showed a more than 4-fold increase in expression between one and 8 weeks of age 628 (Table 3). KRT36 has been shown to exhibit significant transcriptional responses to changes 629 in diet in dairy cattle (Li et al 2015) and the change in diet between one and 8 weeks of age 630 is likely to be driving at least a proportion of the observed expression patterns. 631…”

Large-scale gene co-expression network as a source of functional annotation for cattle genes

“…Gene co-expression analysis provides a framework to study gene function in the context of interactions derived from multiple data sources and integrated into a global interactome. With emphasis on cattle the application of RNA-sequencing has paved the way for transcriptome analysis of cattle in recent years in various experimental conditions [24–26]. For the purpose of genome-wide co-expression analyses, a comprehensive catalogue of experimental conditions from RNA-seq studies is still incomplete.…”

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus Cattle rumen tissue

“…After identification of the differentially expressed miRNAs, the target genes for those miRNAs were predicted using TargetScan, which were then utilized for the integrated analysis with transcriptome analysis results published in 2015 31 .…”

“…Finally, the DMRs were annotated based on specific genomic features. In addition, we integrated the results of DMRs and transcriptome which has been published in 201531 , and compared the methylation abundance of the DMRs and the expression level of their corresponding genes, from which we hypothesized the relationship between the methylation abundance of the DMRs and the expression level of their corresponding genes.…”