Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75981 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Seminole.Steers.May.2024.vcf.csi | Other | |||
| Seminole.Steers.May.2024.vcf.gz | Vcf |
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Project description:Background: Plasma microRNAs (miRNAs), which exist in exosomal (EX) and non-exosomal free circulating (FC) fractions, can be utilized as blood biomarkers. To identify early indicators of carcass traits, we performed comprehensive analysis of plasma miRNAs separately on EX and FC fractions in Japanese Black cattle at 20, 25, and 30 months of age. Results: We found a total of 1,071 miRNAs including 39 novel miRNA candidates, in which 345 and 358 miRNAs exhibited in measurable amounts in EX and FC fractions, respectively. Profiles of these miRNAs were similar at 20 and 25 months, but collectively different from those at 30 months. We identified 86 and 80 differentially existed miRNAs (DE-miRNAs) between 25 and 30 months in EX and FC fractions, respectively. Among the DE-miRNAs, we revealed significant correlations of bta-miR-150 (EX and FC), -30b-5p (EX), -423-3p (EX), and -222 (FC) with several carcass traits including marbling score. Interestingly, target genes of these DE-miRNAs were functionally enriched in KEGG pathways such as PI3-Akt and MAPK signaling pathways, suggesting their functional relevance to carcass quality and quantity traits. Conclusions: We clarified changes in plasma EX and FC miRNA profiles during the fattening period and identified several miRNAs having correlations with carcass traits. These results could support the utility of plasma miRNAs as potential early indicators of carcass traits in Japanese Black cattle.
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Project description:It has been proved that intramuscular fat (IMF) or marbling in beef improves palatability. Recently, consumers have considered not only the degree of marbling but also the size and distribution of marbling flecks for their health and appetizing looking of beef. Computer image analysis (CIA) systems have been developed to assess various characteristics of marbling particles (MPs) such as the number, size, and distribution (fineness or coarseness) objectively. Some CIA indexes about MPs indicating how MPs are distributed evenly had significant positive relationship with price which represents consumers’ interest. RNA-seq research about formation of fine MPs in the longissimus thoracis (LT) muscle tissue of cattle have not yet been tried in transcriptome level. This study was conducted to reveal the DEGs between groups which have high or low number of fine MPs in the Longissimus thoracis muscle of Korean beef cattle and to understand molecular events associated with marbling fineness.
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Project description:Vitamin A (VA) restriction for beef cattle improves meat marbling. However, its molecular mechanisms are not completely elucidated. We performed microarray analysis to clarify effect of VA restriction on longissimus thoracis muscle gene expressions in Japanese Black steers.
2017-10-03 | GSE94886 | GEO
Project description:Beef marbling is caused by intramuscular deposition, and it is an economically important trait in the beef industry. Vitamin A (VA) is an important feed supplement for cattle, but it can hinder marbling if provided in excess. In cattle, VA forms various derivatives such as all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9cRA). Therefore, we investigated the genes involved in bovine intramuscular adipogenesis after VA treatment with ATRA and 9cRA. Differential gene expression levels were validated by microarray analysis in a clonal bovine intramuscular preadipocyte (BIP) cell line derived from the intramuscular adipose tissue of Japanese Black cattle. BIP cells were harvested six days after adipogenic stimulation with either 1 μM ATRA, 1 μM 9cRA, or nonretinoic acids control. The ATRA- and 9cRA-treated cells exhibited reduced transcription of genes involved in the circulatory system and muscle development compared with the no retinoic acid (RA) treatment. In addition, the ATRA- and 9cRA-treated cells exhibited increased transcription of genes involved in the immune system, protein kinase B signaling, and responses to various stimuli. These results demonstrate the lower expression of muscle development in ATRA- and 9cRA-treated BIP cells during adipogenesis.
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Project description:Understanding age-associated transcriptome changes in longissimus thoracis (LT) muscle is important for determining beef quality and yield characteristics. We investigated age-related transcriptome changes in LT of Hanwoo (Korean cattle) steers. Six Hanwoo steers were used. LT samples were biopsied between the 11th and 12th ribs at 12, 18, and 24 months of age. Steers were slaughtered at 31 months of age and LT samples were collected. Transcriptomic profiles at different ages were measured by RNA sequencing (RNA-seq). A total of 13,753 transcriptomes were identified and a total of 2,522 differentially expressed genes were identified (false discovery rate < 0.05 and |fold change| > 2). In conclusion, transcriptomic age-related changes provide novel insights into understanding the molecular mechanisms responsible for age-related changes in beef quality and carcass weight in beef cattle.
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Project description:The goal was to identify beef marbling related genes
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Project description:Beef quality is the first deciding factor for consumers to consider before purchasing. The aim of this study was to evaluate the effects of suspension and aging time on beef quality. We compared the differences in pH, drip loss, cooking loss, color, shear force, myofibril fragmentation index (MFI) and electron microscope of three muscle tissues between Achilles tendon (AT) and neck-arm restraint (NR) suspensions during seven aging periods (day 0, 1, 2, 3, 7, 14 and 21) after slaughter using the carcasses of six Xinjiang brown cattle. We found that NR suspension could significantly increase water loss rate and MFI, as well as reduce shear force compared to AT suspension. The muscle fiber structure with NR suspension was more severely damaged. The proteomics of longissimus dorsi were checked for the post-mortem day 1, 7 and 14. We detected 50, 26, and 29 differential expressed proteins (DEPs) between NR and AT suspension at post-mortem day 1, 7 and 14, respectively. These proteins were involved in metabolic and muscle structure associated pathways, and contributed to a comprehensive understanding of suspension-dependent meat quality regulation by proteins in beef cattle. To conclude, NR suspension can accelerate the aging time of beef carcasses, which will reduce the cost of carcass suspension and bring more benefits in beef industry.
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