Transcriptome changes associated with fat deposition in the <i>longissimus thoracis</i> of Korean cattle following castration

Na, Sang Weon; Park, Seung Ju; Hong, Soo Jong; Baik, Myunggi

doi:10.1111/jpn.13393

Cited by 9 publications

(3 citation statements)

References 48 publications

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“…Complement systems and coagulation cascades might play a vital role in post-trauma and subsequent inflammatory reactions as innate immunity elements [ 41 ]. A previous study observed greater IMF deposition in Korean cattle after castration, which might lead to alterations in the complement and coagulation cascade pathways, possibly owing to obesity and the subsequent inflammation [ 42 ]. Platelet activation is regulated by the complement system, and platelet activity is mostly linked to the start of coagulation cascades [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning

Yang,

Wang,

Wang

et al. 2023

Genes

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Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding.

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Section: Discussionmentioning

confidence: 99%

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning

Yang,

Wang,

Wang

et al. 2023

Genes

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“…Castration upregulated the transcriptomes involved in lipid metabolism, including adipogenesis, fatty-acid-synthesis/-esterification and fatty-acid-oxidation, tricarboxylic-acid-cycle, and oxidative-phosphorylation genes [ 79 ]. We also applied RNA-sequencing analysis to examine transcriptomic changes in Korean cattle bulls following castration and found that the transcriptomes involved in known pathways such as peroxisome proliferator-activated receptor signaling and retinol metabolism changed in the LM [ 80 ]. We also found that the transcriptomes of novel pathways such as the complement and coagulation cascades are changed.…”

Section: Mechanisms Of Intramuscular Adipose Tissue Depositionmentioning

confidence: 99%

— Invited Review — Factors affecting beef quality and nutrigenomics of intramuscular adipose tissue deposition

et al. 2023

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Beef quality is characterized by marbling (marbling degree and marbling fineness), physiochemical (shear force, meat color, fat color, texture, and maturity), and sensory (tenderness, flavor, juiciness, taste, odor, and appearance) traits. This paper summarizes and addresses beef-quality characteristics and the beef-grading systems in Korea, Japan, the USA, and Australia. This paper summarizes recent research progresses on the genetic and nutritional factors that affect beef quality. Intramuscular (i.m.) adipose tissue deposition or marbling is a major determinant of beef quality. This paper addresses the mechanisms of i.m. adipose tissue deposition focused on adipogenesis and lipogenesis. We also address selected signaling pathways associated with i.m. adipose tissue deposition. Nutrients contribute to the cellular response and phenotypes through gene expression and metabolism. This paper addresses control of gene expression through several nutrients (carbohydrates, fat/fatty acids, vitamins, etc.) for i.m. adipose tissue deposition. Several transcription factors responsible for gene expression via nutrients are addressed. We introduce the concept of genome-based precision feeding in Korean cattle.

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“…High-throughput RNA sequencing is a powerful tool for quantifying transcripts [ 7 ]. Several RNA sequencing studies have examined the molecular mechanisms of IMF deposition and identified differentially expressed genes (DEGs) between different IMF levels in the LT of cattle [ 8 , 9 ]. The molecular mechanisms responsible for marbling fineness are unknown.…”

Section: Introductionmentioning

confidence: 99%

Comparison of transcriptome between high- and low-marbling fineness in longissimus thoracis muscle of Korean cattle

Beak

Baik

2022

Anim Biosci

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Objective: This study compared differentially expressed genes (DEGs) between groups with high and low numbers of fine marbling particles (NFMP) in the longissimus thoracis muscle (LT) of Korean cattle to understand the molecular events associated with fine marbling particle formation. Methods:The size and distribution of marbling particles in the LT were assessed with a computer image analysis method. Based on the NFMP, 10 LT samples were selected and assigned to either high-(n = 5) or low-(n = 5) NFMP groups. Using RNA sequencing, LT transcriptomic profiles were compared between the high-and low-NFMP groups. DEGs were selected at P < 0.05 and |fold change| > 2 and subjected to functional annotation. Results:In total, 328 DEGs were identified, with 207 up-regulated and 121 down-regulated genes in the high-NFMP group. Pathway analysis of these DEGs revealed five significant (P < 0.05) Kyoto Encyclopedia of Genes and Genomes pathways; the significant terms included endocytosis (P = 0.023), protein processing in endoplasmic reticulum (P = 0.019), and adipocytokine signaling pathway (P = 0.024), which are thought to regulate adipocyte hypertrophy and hyperplasia. The expression of sirtuin4 (P < 0.001) and insulin receptor substrate 2 (P = 0.043), which are associated with glucose uptake and adipocyte differentiation, was higher in the high-NFMP group than in the low-NFMP group. Conclusion:Transcriptome differences between the high-and low-NFMP groups suggest that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT.

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Transcriptome changes associated with fat deposition in the longissimus thoracis of Korean cattle following castration

Abstract: Castration is a reliable method of increasing the intramuscular fat (IMF) content (marbling) of the longissimus thoracis (LT) muscle (Bong

Cited by 9 publications

References 48 publications

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning

— Invited Review — Factors affecting beef quality and nutrigenomics of intramuscular adipose tissue deposition

Comparison of transcriptome between high- and low-marbling fineness in longissimus thoracis muscle of Korean cattle

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