Differential expression of extracellular matrix and integrin genes in the longissimus thoracis between bulls and steers and their association with intramuscular fat contents

Muscle tissue transcriptome of F1 Angus-Nellore bulls and steers feedlot finished: impacts on intramuscular fat deposition

BACKGROUND

Castration is a common practice in beef cattle production systems to manage breeding and enhance meat quality by promoting intramuscular fat (IMF) deposition, known as marbling. However, the molecular mechanisms that are influenced by castration in beef cattle are poorly understood. The aim of this study was to identify differentially expressed genes (DEGs) and metabolic pathways that regulate IMF deposition in crossbred cattle by RNA sequencing (RNA-Seq) of skeletal muscle tissue. Six hundred and forty F1 Angus-Nellore bulls and steers (n = 320/group) were submitted to feedlot finishing for 180 days. Sixty Longissimus thoracis muscle samples were collected randomly from each group in the hot carcass (at slaughter) and 48 h post-mortem (at deboning), at between 12th and 13th thoracic vertebrae. Three muscle samples of each group were randomly selected for RNA-Seq analysis, while the post-deboning meat samples were submitted to determination of IMF content.

RESULTS

Steers had a 2.7-fold greater IMF content than bulls (5.59 vs. 2.07%; P < 0.01). A total of 921 DEGs (FDR < 0.05) were identified in contrast between Bulls versus Steers; of these, 371 were up-regulated, and 550 were down-regulated. Functional transcriptome enrichment analysis revealed differences in biological processes and metabolic pathways related to adipogenesis and lipogenesis, such as insulin resistance, AMPK, cAMP, regulation of lipolysis in adipocytes, and PI3K-Akt signaling pathways. Candidate genes such as FOXO1, PPARG, PCK2, CALM1, LEP, ADIPOQ, FASN, FABP4, PLIN1, PIK3R3, ROCK2, ADCY5, and ADORA1 were regulated in steers, which explains the expressive difference in IMF content when compared to bulls.

CONCLUSIONS

The current findings suggest the importance of these pathways and genes for lipid metabolism in steers with greater IMF. Notably, this study reveals for the first time the involvement of the PI3K-Akt pathway and associated genes in regulating IMF deposition in F1 Angus-Nellore cattle. Castration influenced DEGs linked to energy metabolism and lipid biosynthesis, highlighting key molecular players responsible for IMF accumulation post-castration in beef cattle.

Effects of lidocaine-plus-meloxicam treatment on behavioral and physiological changes, and leukocyte heat shock protein 90 gene expression after surgical castration in Hanwoo bulls

This study examined the effects of surgical castration and lidocaine-plus-meloxicam treatment on growth, physiology, behaviors, and leukocyte heat shock protein 90 (HSP 90) gene expression in Hanwoo (Korean cattle) bulls. Twenty Hanwoo bulls (body weight 248.8 ± 28.5 kg, age 9.4 ± 1.04 months) were assigned to three treatments: surgical castration with lidocaine injection (5 mL in the scrotum) and oral meloxicam administration (1 mg/kg body weight; LM; n = 7); surgical castration with placebo injection (5 mL of 0.9% NaCl) and oral placebo administration (lactose, 1 mg/kg body weight; CAS; n = 7); and shame castration (SHAM; n = 6). Meloxicam and lactose were administered 3 h before castration, and lidocaine and NaCl were injected immediately before castration. Surgical castration was performed with a Newberry knife and a Henderson castration tool. Wight was measured the day before and 14 d after castration, and behavior was observed from 0.5 h to 4.5 h post-castration. Blood was collected at -1 d, 0.5 h, 6 h, 1 d, 3 d, 7 d, and 14 d after castration to measure plasma cortisol, haptoglobin, and leukocyte HSP 90 mRNA. Castration tended to decrease average daily gain (p = 0.06), but the LM treatment did not affect weight gain. Bulls in CAS showed higher cortisol concentration (p < 0.05) at 0.5 and 6 h after castration compared to SHAM, with no difference between CAS and LM. Castration increased haptoglobin concentration at 1 and 3 d after castration (p < 0.05) while LM bulls showed decreased haptoglobin concentration (p < 0.05) than CAS bulls at these times. HSP90 mRNA was increased at 6 h post-castration while LM did not reduce its expression, suggesting HSP90 may serve as an acute stress marker in castrated bulls. Castration increased (p < 0.05) frequencies of drinking, lying, walking, leg lifting, kicking, and stiff gait, while decreasing (p < 0.05) eating frequency. LM alleviated (p < 0.05) drinking, leg lifting, kicking, and stiff gait. Collectively, castration resulted in physiological changes, increased leukocyte HSP90 gene expression, and altered behaviors. These findings suggest that lidocaine-plus-meloxicam treatment partially mitigates pain and inflammation in the castrated bulls.

Differential gene expression in neonatal calf muscle tissues from Hanwoo cows overfed during mid to late pregnancy period

Maternal nutrition significantly influences fetal development and postnatal outcomes. This study investigates the impact of maternal overfeeding during mid to late pregnancy on gene expression in the round and sirloin muscles of Hanwoo neonatal calves. Eight cows were assigned to either a control group receiving standard nutrition (100%) or a treated group receiving overnutrition (150%). After birth, tissue samples from the round and sirloin muscles of neonatal calves were collected and subjected to RNA sequencing to assess differentially expressed genes (DEGs). RNA sequencing identified 43 DEGs in round muscle and 15 in sirloin muscle, involving genes related to myogenesis, adipogenesis, and energy regulation. Key genes, including PPARGC1A, THBS1, CD44, JUND, CNN1, ENAH, and RUNX1, were predominantly downregulated. Gene ontology (GO) enrichment analyses revealed terms associated with muscle development, such as "biological regulation," "cellular process," and "response to stimulus." Protein-protein interaction networks highlighted complex interactions among DEGs. Random Forest analysis identified ARC, SLC1A5, and GNPTAB as influential genes for distinguishing between control and treated groups. Overall, maternal overnutrition during mid-to-late pregnancy results in the downregulation of genes involved in muscle development and energy metabolism in neonatal Hanwoo calves. These findings provide insights into the molecular effects of maternal nutrition on muscle development.

Gelatinase MMP Expression Is Correlated with Muscle Fiber Growth in Maiwa Yak Gluteus Maximus

Yak (Bos grunniens) is the only large mammal species in the Qinghai-Tibet Plateau. The most of the studies in yak remain confined for the main contributor of meat, which requires a good understanding of muscle growth. Matrix metalloproteinases-2 (MMP-2) and MMP-9 are widely expressed in mammal tissues they mainly degrade collagen in the extracellular matrix for muscle development. However, the influence of MMPs on yak muscle remains unclear. Hence, we assessed the expression of MMP-2, MMP-9, and related factors with ages in Maiwa yak for study the correlation between MMPs expression and yak muscle growth. The mRNA expression of MMP-2, MMP-9, MMP-14, and collagen III increased with age, except collagen I by quantitative real-time PCR. Moreover, muscle fiber diameter increased with age, whereas the density decreased, which showed that fiber grew thicker with age using hematoxylin-eosin staining. Interestingly, MMP and collagen expression significantly decreased with age using western blotting. Pearson correlation method showed that both mRNA and protein expression of MMP-14 and collagen were strongly correlated with muscle fiber growth, but MMP-2 protein and MMP-9 mRNA expression were moderately correlated with muscle fiber growth. Overall, the expression of MMPs and collagen significantly changed with age, which means that MMPs and their function related genes could correlate with Maiwa yak muscle fiber growth.

Characteristics of intramuscular collagen in calf-fed Nellore bulls and steers throughout the finishing phase

This study evaluated collagen solubility and gene expression of biomarkers for intramuscular collagen (IMCT) deposition and remodeling in the Longissimus muscle of bulls and steers through the finishing phase. Thirty-six Nellore calves were used (18 bulls and 18 steers), and six of each sexual condition were randomly assigned to be harvested at 0, 100, or 200 days on feed (DOF) to evaluate collagen characteristics in different time points throughout the finishing phase. Bulls showed a greater collagen solubility than steers (P = 0.03). The gene expression of fibrogenic markers (TGFβ1, COL1A1, and COL3A1) and IMCT remodeling mediators (MMPII, TIMPII, and LOX) were not affected by sexual condition or DOF (P > 0.05). Our data indicate that young Nellore bulls have a higher percentage of soluble intramuscular collagen, possibly due to higher collagen remodeling associated with a faster growth rate and muscle hypertrophy. Moreover, castration and DOF did not modify mRNA levels of fibrogenic and collagen remodeling markers.

Effects of dietary glycerol supplementation on meat quality, palatability, and lipid metabolism gene expression in the longissimus thoracis of Hanwoo steers

This study tested the hypothesis that dietary glycerol supplementation (GS) would affect growth of Hanwoo steers, beef marbling and palatability, and gene expression for lipid uptake and transport and lipogenesis in the longissimus thoracis (LT). Diets with or without 45.2 g daily glycerol supplementation/kg dry matter concentrate were tested in fourteen Hanwoo steers during a 16-week feeding trial. GS did not affect (P ≥ 0.40) the average daily gain or the gain-to-feed ratio. GS increased the LT marbling score (P = 0.01). GS enhanced (P ≤ 0.01) the sensory traits, including the flavor and overall acceptance of the LT. GS tended (0.05 < P ≤ 0.10) to upregulate mRNA levels of fatty acid translocase, lipoprotein lipase, and fatty acid binding protein 4 genes in the LT. These tendencies of upregulated expression of fatty acid uptake and cytosolic transport genes may, in part, contribute to the increased marbling by GS. The increased marbling degree caused by GS may improve palatability including the flavor and overall acceptance of the LT.

Effects of genomic estimated breeding value and dietary energy to protein ratio on growth performance, carcass trait, and lipogenic gene expression in Hanwoo steer

"Genome-based precision feeding" is a concept that involves the application of customised diets to different genetic groups of cattle. We investigated the effects of the genomic estimated breeding value (gEBV) and dietary energy to protein ratio (DEP) on growth performance, carcass traits, and lipogenic gene expression in Hanwoo (Korean cattle) steers. Forty-four Hanwoo steers (BW = 636 kg, age = 26.9 months) were genotyped using the Illumina Bovine 50 K BeadChip. The gEBV was calculated using genomic best linear unbiased prediction. Animals were separated into high gEBV of marbling score or low-gMS groups based on the upper and lower 50% groupings of the reference population, respectively. Animals were assigned to one of four groups in a 2 × 2 factorial arrangement: high gMS/high DEP (0.084 MJ/g), high gMS/low DEP (0.079 MJ/g), low gMS/high DEP, and low gMS/low DEP. Steers were fed concentrate with a high or low DEP for 31 weeks. The BW tended to be higher (0.05 < P < 0.1) in the high-gMS groups compared to the low-gMS groups at 0, 4, 8, 12, and 20 weeks. The average daily gain (ADG) tended to be lower (P = 0.08) in the high-gMS group than in the low-gMS group. Final BW and measured carcass weight (CW) were positively correlated with the gEBV of carcass weight (gCW). The DEP did not affect ADG. Neither the gMS nor the DEP affected the MS and beef quality grade. The intramuscular fat (IMF) content in the longissimus thoracis (LT) tended to be higher (P = 0.08) in the high-gMS groups than in the low-gMS groups. The mRNA levels of lipogenic acetyl-CoA carboxylase and fatty acid binding protein 4 genes in the LT were higher (P < 0.05) in the high-gMS group than in the low-gMS group. Overall, the IMF content tended to be affected by the gMS, and the genetic potential (i.e., gMS) was associated with the functional activity of lipogenic gene expression. The gCW was associated with the measured BW and CW. The results demonstrated that the gMS and the gCW may be used as early prediction indexes for meat quality and growth potential of beef cattle.

- 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.

Main regulatory factors of marbling level in beef cattle

The content of intramuscular fat (IMF), that determines marbling levels is considered as one of the vital factors influencing beef sensory quality including tenderness, juiciness, flavour and colour. The IMF formation in cattle commences around six months after conception, and continuously grows throughout the life of the animal. The accumulation of marbling is remarkably affected by genetic, sexual, nutritional and management factors. In this review, the adipogenesis and lipogenesis process regulated by various factors and genes during fetal and growing stages is briefly presented. We also discuss the findings of recent studies on the effects of breed, gene, heritability and gender on the marbling accumulation. Various research reported that feeding during pregnancy, concentrate to roughage ratios and the supplementation or restriction of vitamin A, C, and D are crucial nutritional factors affecting the formation and development of IMF. Castration and early weaning combined with high energy feeding are effective management strategies for improving the accumulation of IMF. Furthermore, age and weight at slaughter are also reviewed because they have significant effects on marbling levels. The combination of several factors could positively affect the improvement of the IMF deposition. Therefore, advanced strategies that simultaneously apply genetic, sexual, nutritional and management factors to achieve desired IMF content without detrimental impacts on feed efficiency in high-marbling beef production are essential.

Selection of candidate genes for differences in fat metabolism between cattle subcutaneous and perirenal adipose tissue based on RNA-seq

The site of fat deposition plays an important role in meat quality and body health. Biologically, the perirenal visceral fat (PF) and back subcutaneous fat (BF) are distinct. Angus and Simmental cattle (Bos taurus) were used as models. HE staining, triglyceride assay kit and RNA-seq were used to analyze the differences in tissue morphology and lipid accumulation, co-genes, and differentially expressed genes (DEGs) between the two tissues. According to the findings, BF has a smaller cell area and greater lipid deposition ability than PF. RNA-seq generated approximately 10.99 Gb of data in each library, and 23,472 genes were identified. The genes FABP4, ADIRF, and SCD that are related to adipose deposition were highly expressed in four tissues. There were 1678 DEGs and 1955 DEGs between BF and PF in Angus and Simmental cattle respectively. Gene Ontology function analysis identified several DEGs involved in metabolism. KEGG pathway analysis showed that four pathways related to fat metabolism were enriched. In the BF, seven genes (COL1A1, COL1A2, COL3A1, COL2A1, RXRA, C1QTNF7, and MOGAT2) were up-regulated. Five genes (ADRB3, ABHD5, CPT1B, CD36, LPIN1) were down-regulated. This study identified candidate genes that led to differences in fat metabolism, which could be useful in cattle breeding.

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.

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

The castration of bulls increases the intramuscular fat (IMF) content in skeletal muscle. However, the biological processes of IMF accumulation in skeletal muscle after castration are not completely understood at the molecular level. This study examined the global transcriptomic changes in the longissimus thoracis muscle (LT) of bulls following castration using RNA sequencing (RNA-Seq) and identified new genes or pathways associated with beef quality. Ten bulls and 10 steers castrated at 6 months of age were slaughtered at 26 and 32 months of age respectively. For transcriptome analysis, six LT samples from three bulls and three steers were selected based on age, carcass weight, carcass quantity and beef quality grades. Using RNA-Seq, transcriptomic profiles of the LT were compared between bulls and steers. In all, 640 of the 18,027 genes identified through RNA-Seq were differentially expressed genes (DEGs) between bulls and steers. Pathway analysis of these 640 DEGs showed significant (p < .05) changes in seven Kyoto Encyclopedia of Genes and Genomes pathways, and the most significant terms were complement and coagulation cascade pathways. The transcriptomic expression patterns of 10 genes in the complement and coagulation cascades were validated using all animals through quantitative real-time polymerase chain reaction analysis. In conclusion, transcriptome changes associated with the complement and coagulation cascade pathways provide novel insights into understanding molecular mechanisms responsible for IMF accumulation following castration in beef cattle.

A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

Up-regulation of bone morphogenetic protein and its signaling molecules following castration of bulls and their association with intramuscular fat content in Korean cattle

We evaluated whether castration affects bone morphogenetic protein 2 (BMP2) level and the expression of its signaling molecules in Korean cattle bulls. We also checked whether castration affects the expression of muscle fiber type and oxidative and glycolytic enzyme genes. Enzyme-linked immunosorbent assays revealed that steers had higher plasma BMP2 and leptin concentrations than bulls. Quantitative real-time PCR showed that steers had higher mRNA levels of the lysyl oxidase gene, a downstream target of the BMP signaling pathway, in the longissimus thoracis (LT) muscle. Steers had higher adipogenic peroxisome proliferator-activated receptor gamma and lipogenic fatty acid binding protein 4 mRNA levels in the LT than bulls. Steers had lower mRNA levels for several muscle fiber type 1 genes and fiber type 2A myosin heavy chain 2 gene than bulls. Steers had higher mRNA levels of the glycolytic enzyme phosphoglycerate kinase 1 gene than bulls. Transcript levels of oxidative enzyme genes did not differ between bulls and steers. Regression analysis revealed a positive association between plasma BMP2 levels and intramuscular fat (IMF) content in the steer group. These findings suggest that upregulation of the BMP signaling pathway in response to castration induces increased adipogenic gene expression, contributing to the increased IMF deposition observed in castrated animals.