Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Abstract

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks

“…In these heatmaps, the DEmRNAs expression patterns at 0 d were significantly different from those at the other four stages. These results coincide with those of others, which found that the gene expression patterns of rumen at birth were completely different from those in youth and adulthood in Simmental beef cattle ( 34 ). We also found that the DEmRNAs expression patterns at 20 d and 60 d were similar, as well as at 15 m and in adulthood in four stomachs.…”

— Invited Review — Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality

“…There have been several reports on the relationship between rumen tissue gene expression and carcass traits. The transcriptome analysis of rumen tissue of Simmental cattle under different developmental stage revealed genes influencing carcass weight, stomach weight, marbling score, backfat thickness, ribeye area and lean meat weight [ 89 ]. It has become clear that host gene expression and epigenetic regulation could also influence the gut microbiota.…”

Blood Transcriptome Analysis of Beef Cow with Different Parity Revealed Candidate Genes and Gene Networks Regulating the Postpartum Diseases

“…For each stage-specific module, GO enrichment and KEGG pathway analyses were conducted using DAVID ( , accessed on 20 May 2022) and KOBAS ( , accessed on 20 May 2022). GO terms and pathways with a p -value ≤ 0.05 were defined as significantly enriched [ 24 ]. Genes in each stage-specific module were calculated separately by STRING ( , accessed on 20 May 2022) and Metascape ( , accessed on 20 May 2022), obtained the protein–protein interaction (PPI) network and imported into Cytoscape (v3.8.2, , accessed on 20 May 2022) [ 25 , 26 ].…”