Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig

Yu, Taiyong; Tian, Xuekai; Li, Dong; He, Yulin; Yang, Peiyu; Cheng, Ya; Zhao, Xin; Sun, Jingjing; Yang, Gongshe

doi:10.1016/j.foodres.2023.112550

Cited by 11 publications

(7 citation statements)

References 49 publications

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“…This suggests that the proportion of unsaturated fatty acids may be an important factor affecting IMF contents. Additionally, creatine, lysine, and glutamine were the three amino acids with the highest concentrations in both group Q and group J. Creatine, an amino acid derivative, is ubiquitous in meat and is one of the most important ingredients in meat, affecting its flavor and physiological function . Creatine improved the growth performance and meat quality of fattened pigs by delaying glycolysis .…”

Section: Discussionmentioning

confidence: 96%

“…Additionally, creatine, lysine, and glutamine were the three amino acids with the highest concentrations in both group Q and group J. Creatine, an amino acid derivative, is ubiquitous in meat and is one of the most important ingredients in meat, affecting its flavor and physiological function. 17 Creatine improved the growth performance and meat quality of fattened pigs by delaying glycolysis. 18 Lysine is a restricted amino acid, and supplementation with lysine had no significant effect on the production and slaughter performance of fat pigs and could improve meat quality and flavor.…”

Section: ■ Discussionmentioning

confidence: 99%

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Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

Yu,

Guo

et al. 2024

J. Agric. Food Chem.

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The intramuscular fat (IMF) content of beef determined the meat quality, and the market value of beef varies with different breeds. To provide some new approaches for improving meat quality and cattle breed improvement, 24-month-old Qinchuan cattle (Q, n = 6), Nanyang cattle (N, n = 6), and Japanese black cattle (J, n = 6) were selected. IMF content of the J group (16.92 ± 1.08%) is remarkably higher than that of indigenous Chinese cattle (Q, 13.38 ± 1.08%, and N, 12.35 ± 1.22%). Monounsaturated fatty acids and polyunsaturated fatty acids in the J group are higher than the Q and creatine, lysine, and glutamine are the three most abundant amino acids in beef, which contribute to the flavor formation. Similarly, IMF content-related genes were enriched in four vital KEGG pathways, including fatty acid metabolism, biosynthesis of unsaturated fatty acids, fatty acid elongation, and insulin resistance. Moreover, weighted genes coexpression network analysis (WGCNA) revealed that ITGB1 is the critical gene associated with the IMF content. This study compares transcriptome and metabolome of local and high-IMF cattle breeds, providing data for native cattle breeding and improvement of beef quality.

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Section: Discussionmentioning

confidence: 96%

Section: ■ Discussionmentioning

confidence: 99%

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

Yu,

Guo

et al. 2024

J. Agric. Food Chem.

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“…The coDASG_DEGs in adipose tissue were mainly enriched in pathways related to adipose deposition, immune inflammation, and insulin resistance. Previous researchers have shown that pathways such as the Ras signaling pathway, FoxO signaling pathway, PI3K-Akt signaling pathway, insulin resistance, MAPK signaling pathway, and AMPK signaling pathway play essential regulatory roles in adipose deposition [ 31 , 32 , 33 , 34 , 35 ]. Inflammation response and the immune system are closely related to adipose deposition, as they can influence the function, metabolism, and differentiation of adipocytes, thereby affecting adipose deposition [ 36 , 37 , 38 ].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

Liu,

Wang,

Liu

et al. 2024

IJMS

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Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21–76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.

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“…Nowadays, multi-omics linkage techniques are widely used in the muscle tissues of sheep, cattle, and pig to uncover the molecular mechanisms associated with muscle metabolism [9], which has the advantage of providing comprehensive biological information and promoting a deeper understanding of biological systems, but has the disadvantages of complexity in data processing and analysis, high cost and technology requirements, and limitations in sample quantity and quality [10]. Studies have shown that transcriptomics and metabolomics are powerful tools for studying meat quality traits [11].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Longissimus Thoracis et Lumborum Muscle Quality of Chaka and Tibetan Sheep and the Analysis of Possible Mechanisms Regulating Meat Quality

Liu

Wang

et al. 2023

Animals

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This study aimed to comprehensively evaluate the characteristics in the longissimus thoracis et lumborum (LTL) muscle of Chaka (CK) sheep and Tibetan (TB) sheep, and transcriptomics–metabolomics association analysis was used to find the possible genes, differential metabolites, and significant differential metabolic pathways that lead to meat quality differences. Based on the researched results, the nutritional quality of meat, including the contents of ether extract (11.95% vs. 10.56%), unsaturated fatty acid (51.20% vs. 47.69%), and polyunsaturated fatty acid (5.71% vs. 3.97%), were better in TB sheep than in CK sheep, while the CK sheep has better muscle fiber characteristics, such as the total number (62 vs. 45) and muscle fiber density (1426.54 mm2 vs. 1158.77 mm2) and flavor. Omics research has shown that the key differential metabolites and metabolic pathways were dominated by amino acid metabolism, particularly the glutathione metabolism, taurine and hypotaurine metabolism, and lipid metabolism-related pathways, such as glycerophospholipid metabolism and the sphingolipid signaling pathway. The intermediate metabolite sn-Glycerol 3-phosphoethanolamine played a key role in determining sheep meat quality, which was regulated by GPAT2, PLPP2, AGPAT1, PNPLA2, and GPAT4 and correlated with meat color, texture, and flavor. Overall, these results will provide effective information and more evidence to support further exploration of valuable biomarkers of meat quality.

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Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig

Cited by 11 publications

References 49 publications

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

Evaluation of the Longissimus Thoracis et Lumborum Muscle Quality of Chaka and Tibetan Sheep and the Analysis of Possible Mechanisms Regulating Meat Quality

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