Functional genomic analysis of variation on beef tenderness induced by acute stress in angus cattle.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhao C
PROVIDER: S-EPMC3332163 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
Functional genomic analysis of variation on beef tenderness induced by acute stress in angus cattle.
Zhao Chunping C Tian Fei F Yu Ying Y Luo Juan J Mitra Apratim A Zhan Fei F Hou Yali Y Liu George G Zan Linsen L Updike M Scott MS Song Jiuzhou J
Comparative and functional genomics 20120412
Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Microarray analysis and qPCR identified a variety of genes that were differentially expressed. Pathway analysis show ...[more]
Similar Datasets
Project description:miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3' untranslated regions. Research has found that miRNAs involved in the regulation of many metabolic processes. Here we uncovered that the beef quality of Angus cattle sharply diversified after acute stress. By performing miRNA microarray analysis, 13 miRNAs were significantly differentially expressed in stressed group compared to control group. Using a bioinformatics method, 135 protein-coding genes were predicted as the targets of significant differentially expressed miRNAs. Gene Ontology (GO) term and Ingenuity Pathway Analysis (IPA) mined that these target genes involved in some important pathways, which may have impact on meat quality and beef tenderness.
| S-EPMC3436641 | biostudies-literature
Project description:Beef is an essential food source in the world. Beef quality, especially tenderness, has a significant impact on consumer satisfaction and industry profit. Many types of research to date have focused on the exploration of physiological and developmental mechanisms of beef tenderness. Still, the role and impact of DNA methylation status on beef tenderness have yet to be elucidated. In this study, we exhaustively analyzed the DNA methylation status in divergent tenderness observed in Angus beef. We characterized the methylation profiles related to beef tenderness and explored methylation distributions on the whole genome. As a result, differentially methylated regions (DMRs) associated with tenderness and toughness of beef were identified. Importantly, we annotated these DMRs on the bovine genome and explored bio-pathways of underlying genes and methylation biomarkers in beef quality. Specifically, we observed that the ATP binding cassette subfamily and myosin-related genes were highly methylated gene sets, and generation of neurons, regulation of GTPase activity, ion transport and anion transport, etc., were the significant pathways related with beef tenderness. Moreover, we explored the relationship between DNA methylation and gene expression in DMRs. Some methylated genes were identified as candidate biomarkers for beef tenderness. These results provide not only novel epigenetic information associated with beef quality but offer more significant insights into meat science, which will further help us explore the mechanism of muscle biology.
| S-EPMC7479246 | biostudies-literature
Project description:Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues-connective tissue, skeletal and muscular system and functional tissues-; while in tough group those genes engaged in cell death, lipid metabolism and small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness.
| S-EPMC4473007 | biostudies-literature
Project description:Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues–connective tissue, skeletal and muscular system and functional tissues–; while in tough group those genes engaged in cell death, lipid metabolism and small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness.
2015-03-31 | GSE61936 | GEO
Project description:Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues–connective tissue, skeletal and muscular system and functional tissues–; while in tough group those genes engaged in cell death, lipid metabolism and small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness. Nineteen purebred Angus steers were obtained from the Wye Farm. At approximately 12 months of age, the animals were serially harvested. Immediately after harvest, samples of longissimus dorsi (LD) from the right side of the carcass were obtained and placed in RNAlater solution at -80°C. The carcass were stored at 4°C for a total of 14 days. After this period, steaks were obtained from the LD at the level of the 12th intercostal space and then frozen. For measurement of the WBSF, steaks were thawed at room temperature to an internal temperature of 4°C. Then, the steaks were cooked to a core temperature of 70°C using a George Foreman Lean Mean Fat Grilling Machine. The cooked steaks were then cooled down to room temperature. Using a sharp cylinder, especially designed for muscle, six cores (1.27 cm in diameter) were sampled parallel to the muscle fiber orientation. The Warner-Bratzler shear forces (WBSF) of the cores were obtained. The average WBSF of the six cores was calculated and used as the WBSF for the samples. From these 19 steers, 4 with the lowest WBSF values (6.77±0.56 kg) were identified as tender and 5 samples with the largest WBSF values (19.93±0.39 kg) labeled as tough. Then both groups underwent further analysis..
2015-03-31 | E-GEOD-61936 | biostudies-arrayexpress
Project description: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.
| S-EPMC4475051 | biostudies-literature
Project description:Rumen fluid from Angus beef cattle Raw sequence reads
| PRJNA758503 | ENA
Project description:BackgroundThe small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate bacterial composition and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the influence of diets on jejunal bacterial communities and examined its relationships with bile acids. Here, we examined the impact of grain- and grass-based diets on jejunal and fecal bacterial communities' composition and investigated possible association of bacterial features with bile acids.ResultsWe demonstrated that the influences of diets on intestinal bacteria can be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was documented in feces of grass-fed cattle comparing to grain-fed cattle. Top 20 important genera identified with random forest analysis on fecal bacterial community can be good candidates for microbial biomarkers. Moreover, the jejunal bacteria of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and bacteria signatures predictive of bile acids were identified, indicative of the potential association of bacterial features with bile acids.ConclusionsThe findings from this study provided novel insights into the relationships between jejunal bacteria and bile acids under different diets in Angus beef cattle. Our results should help us gain a better understanding of potential health benefits of grass-fed beef.
| S-EPMC7807434 | biostudies-literature
Project description:Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer's palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.
| S-EPMC6182065 | biostudies-literature
Project description:Most tall fescue [Lolium arundinaceum (Schreb.) Darbysh] in the Southeastern United States contains an endophyte that causes fescue toxicosis (FT) in grazing animals, a serious disease that causes approximately $1 billion in economic losses to the animal industries in the United States. Recently, a genetic test called T-Snip (AgBotanica, LCC, Columbia, MO), was developed with the objective of identifying animals with genetic variation for FT tolerance. The aim of this study was to validate the use of this genetic test in mature, pregnant cows. Over 13 wk, weekly phenotypic data, including body weight, rectal temperatures, hair coat scores, hair shedding scores, and body condition scores, were collected on 148 pregnant purebred Angus cows at 2 locations in NC where infected fescue was the primary source of feed. Birth weights (cBW) and 205-d adjusted weaning weights (adjWW) from these cow's calves were recorded. All cows were genotyped for T-Snip. At the end of the trial, each phenotypic trait was calculated as the slope of the linear regression of performance on weeks. The effect of T-Snip rating genotypes (4 levels) on slope traits was tested using a linear model also including the fixed-effects of location, parity, and the initial measurement for each trait (covariate). For cBW and adjWW, the model also included the sex of the calf and the month of birth as categorical effects. Associations of T-Snip genotypes were observed for body weight gain (aBWd) of pregnant cows (P = 0.15; interaction with location), change in body condition score (aBCSd; P = 0.13), and adjWW (P = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location (P = 0.017 and 0.047, respectively), which was the location with higher endophyte infection rate. For all associations, the direction of the T-Snip genotypes was the same and as expected: the greater the genotype score, the better performance. No associations were found for the other traits (P > 0.10). These results indicate that the T-Snip test may be predictive of cow performance (aBWd, aBCSd, and adjWW) in an endophyte-infected tall fescue environment.
| S-EPMC7724970 | biostudies-literature