Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait

Muniz, Maria Malane Magalhães; Fonseca, Larissa Fernanda Simielli; Magalhães, Ana Fabrícia Braga; Silva, Danielly Beraldo dos Santos; Cánovas, Ángela; Lam, Stephanie; Ferro, Jesus Aparecido; Baldi, Fernando; Chardulo, Artur Loyola; Albuquerque, Lúcia Galvão de

doi:10.1007/s10142-020-00738-9

Cited by 13 publications

(8 citation statements)

References 72 publications

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“…Furthermore, both LPL and FABP3 are enriched in the PPAR signaling pathway, which is known to be a key regulatory pathway in adipogenesis ( Lehrke and Lazar, 2005 ). In addition to this, we also found up-regulated genes including MYL2 , MYL6 and TNNC1 , which have been shown to correlate with meat quality ( PilNam et al, 2008 ; Pierzchala et al, 2014 ; Muniz et al, 2020 ). In this experiment, FABP3 and LPL were significantly up-regulated in the muscle tissue of the DP, this is consistent with the actual situation, as fat deposition of DP is early ( Brand et al, 2017 ).…”

Section: Discussionsupporting

confidence: 65%

Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Peng

Liu

et al. 2022

Front. Genet.

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It is well known that Dorper (DP) is a full-bodied, fast-growing and high dressing percentage breed, while the production performance of Small-tailed Han sheep (STH) is not so excellent, in contrast to DP. Therefore, in this study, a comparative transcriptomic analysis of liver and muscle tissues from DP and STH breeds was carried out to find differentially expressed genes (DEGs) that affect their growth and meat quality traits. The results showed that the total number of DEGs was 2,188 in the two tissues. There were 950, 160 up-regulated and 1,007, 71 down-regulated genes in the liver and muscle, respectively. Several DEGs such as TGFB1, TGFB3, FABP3, LPL may be associated with growth and development in DP. Also, several GO terms were found to be associated with muscle growth and development, such as developmental growth (GO:0048589), and myofibril (GO:0030016). Further validation of eight genes (6 up-regulated, and 2 down-regulated) was performed using quantitative RT-PCR. These findings will provide valuable information for studying growth and development as well as meat quality traits in sheep.

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Section: Discussionsupporting

confidence: 65%

Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Peng

Liu

et al. 2022

Front. Genet.

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“…pH, proteolysis, and tenderization), and how those processes influence economically important meat quality characteristics like meat colour and tenderness [2,[6][7][8]. Recent studies on muscle transcriptome profiles from cattle and pigs have identified genes influencing meat quality traits such as tenderness and marbling in beef and pork [9][10][11][12]. The potential for drawing valid inferences between gene biomarkers and meat quality traits at the abattoir could, however, be improved through a better understanding of RNA viability post-mortem and expression of specific biomarker genes.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem

et al. 2021

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Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from longissimus thoracis (LT) sampled from British Continental crossbred heifer carcasses (n = 7) stored at 4°C in an abattoir drip cooler at 5 time points post-mortem, i.e., 45 min (0 h), 6 h, 24 h, 48 h, and 72 h. Following RNA-Sequencing, processed reads were aligned to the ARS-UCD1.2 bovine genome assembly. Subsequent differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend for increasing counts of both upregulated and downregulated genes over time. Gene ontology and biological pathway term enrichment analyses on sets of DE genes revealed several processes and their timelines of activation/deactivation that accompanied or were involved with muscle transformation to meat. Although the quality of RNA in refrigerated LT remained high for several days post-mortem, the expression levels of several known biomarker genes for meat quality began to change from 24 h onwards. Therefore, to ensure accuracy of predictions on meat quality traits based on the expression levels of those biomarker genes in refrigerated beef muscle tissue, it is crucial that those expression measurements be made on RNA sampled within 24 h post-mortem. The present study also highlighted the need for more research on the roles of mitochondrial genes and non-coding genes in orchestrating muscle tissue processes after death, and how pre-mortem immune status might influence post-mortem meat quality.

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“…Most studies on the evaluation of different genes (LEP, HSP90AA1, FABP4, GH1, HSPB1, MYF5, MYF5, DNAJA1, DGAT1, HRSP12, ADAMTS4, etc., mainly CAPN, CAST and their isoforms) and their SNPs as markers for tenderness traits were performed until about 2010 (e.g., [ 45 , 46 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 ]), but later, related papers were also published on cattle of different breeds and in other geographic locations [ 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 ]. The new research groups are especially focused on the use and improvement of genomic selection [ 32 , 44 , 77 , 78 , 79 , 80 , 81 ] and also on the use of RNA sequencing technology to identify the mechanisms involved in gene expression for beef tenderness [ 82 , 83 , 84 ].…”

Section: Resultsmentioning

confidence: 99%

Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness

Gonzales-Malca¹,

Tirado-Kulieva²,

Abanto-López³

et al. 2022

Animals

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Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness.

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Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait

Cited by 13 publications

References 72 publications

Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep

Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem

Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness

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