Project description:Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500. After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted with DAVID tool for categorization of DEGs. Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05). Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.
Project description:The aim of this study was to measure the effect of contrasting breed and dietary source on the skeletal muscle miRNA profile of beef cattle divergent for feed efficiency (RFI). Charolais (n=90) and Holstein-Fresian (N=77) steers) were offered two consecutive diets; namely a zero-grazed grass diet followed by a high concentrate diet. Dietary intakes were recorded for all steers throughout each dietary phase and residual feed intake values dertermined for each steer. At the end of each dietary phase the most efficient (Low-RFI; n=8) and least efficient (High-RFI; n=8) steers were selected across each breed for longissmus dorsi biopsy collection. RNA was isolated from all muscle tissue samples and subsequently used for small RNA sequencing. Ten miRNA were differentially expressed between the steers divergent for RFI across each diet and breed contrast. Biological pathway analyssi revealed enrichment of pathways related to both metabolic and growth processes.
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:RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Sixteen rumen papillae samples were sequenced by Cofactor Genomics (St.Louis, MO).
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:Growing ruminants maintained under dietary restriction for extended periods will exhibit compensatory growth when reverted to ad libitum feeding. This period of compensatory growth is associated with increased feed efficiency, lower basal energy requirements, and changes in circulating concentrations of metabolic hormones. To identify genetic mechanisms contributing to these physiological changes, 8 month-old steers were fed either ad libitum (control; n = 6) or 60-70% of intake of control animals (feed-restricted; n=6) for a period of 12 weeks. All steers were then fed ad libitum for the remaining 8 weeks of the experiment (realimentation period). Liver was biopsied from each animal at days -14, +1 and +14 relative to realimentation for RNA extraction and gene expression analysis by microarray hybridization. Steers were assigned randomly to one of two treatment groups, control or feed-restricted, and housed indoors in individual pens. Steers were acclimated to their pens for 5 d prior to starting the experimental treatments. Feed was offered once daily between 0630 and 0930 and orts from the previous day's feeding were collected and weighed to estimate actual intake. Control animals were fed ad libitum throughout the 20-wk experimental period. Feed-restricted steers were offered 60-70% of intake of control animals for 12 wks to target a limited rate of gain of approximately 0.5 kg/d. Restricted steers were then fed ad libitum for the remaining 8 wks of the experiment (realimentation period). During the first 3 d of realimentation, feed offered to both treatment groups was divided into two equal rations to gradually adjust restricted animals to full intake. Water was offered ad libitum throughout the experimental period. Approximately 200 mg of liver tissue was collected from each steer by needle biopsy using a Tru-Cut biopsy needle at -14, +1, +14 d relative to realimentation. Liver samples were immediately frozen in liquid nitrogen and stored at -80C until RNA isolation. Total RNA was isolated from 36 liver samples using TRIZOL Reagent (Invitrogen Corp., Carlsbad, CA). Samples were DNase-treated using the TURBO DNA-free kit (Ambion, Inc., Austin, TX) according to manufacturerâ??s instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Valencia, CA). Quality and concentration of RNA were assessed using a 2100 Bioanlayzer (Agilent Technologies, Palo Alto, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Probe labeling, hybridizations of probes to the oligo microarray, and array scanning were performed by the Roche NimbleGen Systems, Inc. Microarray Core Facility in Reykjavik, Iceland according to standard procedures (Madison, WI; http://www.nimblegen.com).
Project description:Steer small intestine transcriptome Evaluation of the naturally occurring transcriptome variation among beef steers with divergent gain and feed intake phenotypes.