MiRNA expression data from bulls with high and low intramusclar fat (IMF) content
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ABSTRACT:
ORGANISM(S): synthetic construct Bos taurus
PROVIDER: GSE147622 | GEO | 2020/03/28
REPOSITORIES: GEO
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Project description:Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.
2020-10-20 | GSE139102 | GEO
Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.
2022-04-30 | GSE171876 | GEO
Project description:The content of intramuscular fat (IMF) is closely related to meat quality traits. In this study, in order to explore the candidate genes related to IMF content, the longissimus dorsi muscle of Guangling donkey was measured for intramuscular fat content. According to its intramuscular fat content, it was divided into two groups, the low fat group (L , N=3) and high-fat group (H, n=3), using RNA-seq to identify differentially expressed genes (DGEs) on the longissimus dorsi muscle tissue of Guangling donkey with high and low intramuscular fat content to reveal the possibility Gene network and metabolic pathways that help increase intramuscular fat content. A total of 167 DEGs (|log2Fold Change|>=1 and FDR<0.05) were detected in the high (H) and low (L) groups of Guangling donkeys, of which 64 were up-regulated genes and 103 were down-regulated genes. The GO enrichment and KEGG pathway analysis showed that these differential genes were enriched in several biological processes and pathways related to adipocyte differentiation, lipid biosynthesis, and neutral lipid metabolism. These results will help to further explore the molecular mechanism of IMF deposition in donkeys and provide a theoretical basis for the molecular breeding of Guangling donkeys.
2021-09-01 | GSE156840 | GEO
Project description:Intramuscular fat (IMF) content in pork is an important element of consumer preference, and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate the differentially expressed genes (DEG) closely related with IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements and significant difference between extremely high (H, n=3) and low (L, n=3) IMF content groups was found (P < 0.0001). From multi-dimensional scaling analyses, it was observed that the relationships between H and L groups were similar to each other. Here, we identified a total of 134 genes that were differentially expressed between the groups (FDR < 0.05, and FC ≥ 2). Functional analyses with DEGs revealed that the lipid metabolism (SCD and FASN) was one of the significant biological processes related with IMF content determination. In addition, we also found that DEGs related with muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1, and COL15A1) were changed between individuals with the extreme IMF contents, interestingly. These results will aid in understanding the regulation of IMF contents in pigs.
2017-06-15 | GSE86086 | GEO
Project description:Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality. In the present study, we measured the IMF content for 265 crossed pigs of Duroc x Luchuan pigs, from which individuals with extremely high (6.03% ± 0.58%, n = 12) and low (1.67% ± 0.42%, n = 12) IMF contents were selected to identify differentially expressed genes (DEGs) related to IMF content in the longissimus dorsi. RNA sequencing for 24 samples in total identified 312 differentially expressed transcripts that were significantly enriched in triglyceride biosynthesis- and metabolism-related processes (p-value ≤ 0.05 and fold change ≥ 1.5). Functional enrichment analysis revealed that the PPAR signaling pathway was the most significantly enriched pathway (p-value = 0.024, represented by ADIPOQ, FABP3, FABP4, LPL, PLIN4 and SCD). When a more stringent condition was applied (gene-based q-value ≤ 0.2 and fold change ≥ 1.5), only 17 transcripts remained to be differentially expressed, including LEP, ATP6V1F, SDR16C5, TUSC5, MPZ, PRX, PTPN4, BEX1, MVB12B, ZFP62, P4HA2, IDH2, THOC7, KRT14, FCGRT, MYPN and LPL. Among these DEGs, TUSC5 was significantly upregulated in the group of high IMF contents (log2FC = 1.114, p-value = 3.02E-5) and was suspected as a strong new candidate gene affecting porcine IMF content since it was the target gene of PPAR-gamma. The present study provided new data and candidate genes for the genetic study of porcine IMF content.
2023-12-30 | GSE117414 | GEO
Project description:Background: Marketing products with added-value characteristics is a current trend in livestock production systems. Regarding meat, selection for intramuscular fat and muscular fatty acid composition is a way to improve the palatability and juiciness of meat while assuring a healthy fat content. This represents selecting animal with a different muscular metabolic profile with respect to the extended selection of lean animals. Results: The present study has analysed the muscular gene expression profiles of 68 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. Rather than upregulation of a single pathway, the main differences lied on the transcriptional levels of genes related with lipogenesis and lipolysis, revealing the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Most strikingly, several genes which enhanced fatty acid β-oxidation and favoured insulin signalling and glucose uptake were upregulated in the fattest animals, indicating that the events leading to peripheral insulin resistance in humans with increased levels of intramuscular fat and obesity do not take place in these pigs. Moreover, neither was detected the well-characterised low-grade inflammatory state observed in overweighed humans. Conclusion: As a whole, our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to fully understand how lipid deposition affects muscle physiology in pigs. 68 gluteus medius samples form 68 animals belonging to two groups of 34 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content
2010-03-07 | E-GEOD-19275 | biostudies-arrayexpress
Project description:Intramuscular (i.m.) fat content influencing consumer’s acceptability of pork is considered as a limiting factor for meat quality. To gain insight into the biological basis of individual variability in i.m. fat content, both gene expression profiling and proteomic investigation were associated in pig longissimus muscle (LM). Keywords: intramuscular fat, gene expression, pigs, proteomics, microarray, pork meat
2009-01-15 | GSE10759 | GEO
Project description:The Laiwu pig is famous for its excessively higher level of IMF content, however, the exact regulatory mechanism is still unknown. The intramuscular fat content (IMF) is an economically important traits in pigs, which is controlled by multiple genes and biological pathways. In the present study, we performed an integrated transcriptome-assisted label-free quantitative proteomic analysis of longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage. A total of 5074 unique proteins were identified and 191 were differentially abundant proteins (DAPs) (> 1.2-fold cutoff, p < 0.05), which were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. Proteins participating in the regulation of lipolysis in adipocytes and AMPK signaling pathway were identified. Six proteins were analyzed using parallel reaction monitoring (PRM) to confirm the reliability of the TMT proteomic analysis. Association networks of differentially abundant proteins revealed that these DAPs were mainly involved in ribosome biosynthesis in eukaryotic species. A comparasion between transcriptomic (mRNA) and proteomic data revealed seven differentially expressed genes corresponding to DAPs. This study, for the first time, provides some data for the elucidation of the molecular mechanism of IMF deposition in pigs.
2020-01-09 | PXD011718 | Pride
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays
2013-01-01 | E-GEOD-12927 | biostudies-arrayexpress
Project description:Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analysing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs in order to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 ± 0.09% in low IMF vs. 6.81 ± 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analysed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and in G-protein and ERK signalling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes comprised in the significant modules confirmed the results obtained for the DEGs, and the analysis with CytoHubba indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation.
2020-05-28 | GSE144780 | GEO