Project description:The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.
Project description:Transcriptional profiling of bovine skeletal muscle comparing expression differences of a population of beef cattle selected for divergent response (shear force residuals) to post-mortem treatment (electrical stimulation)
Project description:Transcriptional profiling of bovine skeletal muscle comparing expression differences of a population of beef cattle selected for divergent response (shear force residuals) to post-mortem treatment (electrical stimulation) 4 condition experiment utilizing 47 total samples (originally 48, one sample could not be used). Samples were broken in to high/low groups based on residual WBSF following electrical stimulation (ES) and without electrical stimulation (NES). There are 4 groups based on residual WBSF: High-ES (12), Low-ES (11), High-NES (12), and Low-NES (12)
Project description:Beef constitutes one of the main food sources worldwide due to its high quality protein and other nutrients. Beef tenderness is one of the most important factors influencing the edible quality. To date, a large number of molecular studies have focused on the exploration of mechanisms to form beef tenderness. DNA methylation is the most studied epigenetic modification and research revealed that DNA methylation plays important roles in diverse process. However, the genome-wide DNA methylation regulation on beef quality and tenderness remains unknown. In this study, we reported the DNA methylome profiling related to divergent tenderness of beef. We found that more reads are harbored in the intron, exon and repeat elements of genes of beef. We identified the DMRs between tender and tough beef. And results showed that DNA methylation levels in different part of genome or divergent tenderness are significantly differed. Then we annotated the DMRs and identified the top pathways DMRs are involved in. Meanwhile, we also explored the relationship between DNA methylation and gene expression. This study describes the detail DNA methylome profiling related with beef quality and may provide new strategies for exploring the mechanism of beef quality.
Project description:Beef cow adipose tissue transcriptome Evaluation of the naturally occurring transcriptome variation among beef cows with divergent gain.
Project description:Steer liver transcriptome Evaluation of the naturally occurring transcriptome variation in liver among beef steers with divergent gain and feed intake phenotypes.
Project description:Steer spleen transcriptome Evaluation of the naturally occurring transcriptome variation in the spleen among beef steers with divergent gain and feed intake phenotypes.
Project description:Steer small intestine transcriptome Evaluation of the naturally occurring transcriptome variation among beef steers with divergent gain and feed intake phenotypes.