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

Transcriptomic analysis of yak longissimus dorsi muscle identifies genes associated with tenderness

Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers' buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the longissimus dorsi muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (WNT5A, ARID5B, SERPINE1 KLHL40, RUNX1, MAFF, RFX7 and ARID5A). Notably, SERPINE1 was involved in the significant enrichment pathways of 'complement and coagulation cascade pathway', 'HIF-1 signaling pathway' and 'AGE-RAGE signaling pathway in diabetic complications' which can regulate meat tenderness. This implies that SERPINE1 may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.

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

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.

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

Intramuscular fat (IMF) content, which is an important determinant of meat quality characteristics such as tenderness, juiciness and flavor, has long been a research hotspot. Chinese local pig breeds are famous for their excellent meat quality which is mainly reflected in the high IMF content, strong hydraulic system and et al. However, there are few analysis of meat quality by omics methods. In our study, we identified 12 different fatty acids, 6 different amino acids, 1,262 differentially expression genes (DEGs), 140 differentially abundant proteins (DAPs) and 169 differentially accumulated metabolites (DAMs) (p < 0.05) with metabolome, transcriptome, and proteome. It has been found that DEGs, DAPs and DAMs were enriched in the Wnt signaling pathway, PI3K-Akt signaling pathway, Rap1 signaling pathway, and Ras signaling pathway which were related to meat quality. Moreover, our Weighted genes co-expression network construction (WGCNA) showed RapGEF1 was the key gene related to IMF content and the RT-qPCR analysis was used to perform validation of the significant genes. In summary, our study provided both fundamental data and new insights to further uncover the secret of pig IMF content.

Temporal changes in muscle characteristics during growth in the goat

This study aimed to explore the temporal accumulative process of functional components and take insight into their dynamic regulatory metabolic pathways in the longissimus during growth in goats. Results showed that the intermuscular fat content, cross-sectional area and fast- to slow-switch fiber ratio of the longissimus were synchronously increased from d1 to d90. The dynamic profiles of functional components and transcriptomic pathways of the longissimus both exhibited two distinct phases during animal development. Expression of genes involved in de novo lipogenesis was increased from birth to weaning, leading to the accumulation of palmitic acid in the first phase. Accumulation of functional oleic acid, linoleic acid and linolenic acid in the second phase was dominatingly driven by enhancement in expression of genes related to fatty acid elongation and desaturation after weaning. A shift from serine to glycine production was observed after weaning, which was linked to the expression profile of genes involved in their interconversion. Our findings systematically reported the key window and pivotal targets of the functional components' accumulation process in the chevon.

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

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.

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

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.