Association of variants in FABP4, FASN, SCD, SREBP1 and TCAP genes with intramuscular fat, carcass traits and body size in Chinese Qinchuan cattle

Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle

Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of longissimus dorsi muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including ACAA2, ACADL, ACOX2, CPT1B, CPT2, LPL, SLC27A1, ACAT1, GK, ACOX3, and ACSM5, were screened as key candidate genes for IMF deposition. A "liver-muscle" regulatory network of IMF deposition was built to illustrate the tissues' interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle.

Erucic acid promotes intramuscular fat deposition through the PPARγ-FABP4/CD36 pathway

The regulation of intramuscular fat (IMF) accumulation plays a crucial role in determining meat quality in the beef industry. In humans, fat deposition in skeletal muscle is closely associated with insulin resistance and obesity. However, its underlying mechanisms are not fully elucidated. We previously identified erucic acid (EA) as a key metabolite that may affect IMF deposition of beef using omics strategies. By utilizing bovine intramuscular preadipocytes in vitro, the study demonstrates a dose-dependent increase in lipid storage induced by EA, along with mRNA expression levels of transporters FABP4 and CD36. At a mechanistic level, EA triggers ERK1/2 phosphorylation and enhances the expression of PPARγ, FABP4, and CD36, thereby facilitating the formation of lipid droplets within preadipocytes. In vivo experiments conducted in mice support these findings, indicating that EA stimulates fat accumulation in skeletal muscles and enhances the levels of FABP4 and CD36 proteins. These outcomes not only enhance our comprehension of the molecular mechanisms governing IMF deposition but also provide insights into potential strategies for enhancing meat quality and addressing metabolic disorders linked to fat accumulation in skeletal muscles. The findings of the study contribute to existing scholarly knowledge and lay the groundwork for future research endeavors aimed at improving meat quality and metabolic well-being.

FASN, SCD, and PLAG1 Gene Polymorphism and Association with Carcass Traits and Fatty Acid Profile in Hanwoo Cattle

Genetic polymorphisms have a great impact on enhancing quantitative traits in cattle. In this study, Fatty acid synthase (FASN) g. 16024 (A>G), Stearoyl-CoA desaturase (SCD) g. 10329 (C>T), and pleomorphic adenoma gene (PLAG1) g. 25003338 (C>G) genotypic and allelic polymorphisms were evaluated, along with their associations with fatty acid composition, adipogenic gene expression, and carcass characteristics (carcass weight, yield grade, backfat thickness, and marbling score) in Hanwoo steers. A total of 128 Hanwoo steers were selected for this study and the Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to identify polymorphism of these genes. The AG genotype and G allele in FASN g. 16024 (A>G), CT genotype and T allele in SCD g. 10329 (C>T), and GG genotype and G allele in PLAG1 g. 25003338 (C>G) showed higher frequency and positively correlated with carcass traits, yield, and quality grades. Fatty acid composition results indicate that C18:3n-6, C20:1, and C20:2n-6 were significantly higher in the AA genotype of FASN gene, C14:1 and C18:3n-6 in the CC genotype, and C16:1 in the TT genotype of SCD gene. C12:0, C14:0, C16:1, C18:0, and C20:0 were higher in the CC genotype of PLAG1 gene. Furthermore, RT-qPCR analysis of adipogenesis-related genes (AMP-activated protein kinase-α (AMPKα), Carnitine palmitoyl transferase-1β (CPT1), G-coupled protein receptor-43 (GPR43), and SCD) across different SNP genotypes suggests a systemic interaction between genetic factors and adipogenesis in beef cattle. This study emphasizes the significance of FASN g. 16024 (A>G), SCD g. 10329 (C>T), and PLAG1 g. 25003338 (C>G) SNPs for genetic selection to enhance beef quality and elucidate lipid metabolic pathways in Hanwoo cattle.

Identification and Co-expression Analysis of Differentially Expressed LncRNAs and mRNAs Regulate Intramuscular Fat Deposition in Yaks at Two Developmental Stages

Intramuscular fat (IMF) content is a key indicator of yak meat quality. This study aimed to identify lncRNAs that regulate IMF deposition in yaks. Three male calf yaks (3 months) and three male adult yaks (3 years) were used in the current study. After slaughter, the tissue morphology of the longissimus dorsi (LD) muscle was assessed using a cry-sectioning technique and differentially expressed lncRNAs and mRNAs (DELs and DEMs) were identified using RNA-Seq technology. The diameter and volume of fat droplets were significantly larger and bigger, respectively, in adults than in calves (P < 0.001). A total of 37,790 genes and 16,400 lncRNAs that regulate fat deposition were identified. Among them, 2327 mRNAs and 474 lncRNAs were differentially expressed between calves and adult yaks. DEGs stearoyl-CoA desaturase (SCD), fatty acid synthase (FASN), fatty acid binding protein 4 (FABP4) and fibronectin 1 (FN1) and DELs MSTRG.15795.4 and MSTRG.35028.6 were screened. The enrichment and pathway analysis regulated by the DMEs and DELs were predicted. We found significantly enriched biological processes and pathways involved in fat deposition, including the biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, fatty acid elongation, and the mTOR signaling pathway. Co-expression network of the DELs and related genes, including MSTRG.10268.1-placenta associated 8 (PLAC8), MSTRG.16223.1-galectin 3 (LGALS3), MSTRG.34732.1-glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), MSTRG.11907.11-fibroblast growth factor 1 (FGF1), MSTRG.34342.1-lipase A, lysosomal acid type (LIPA), and MSTRG.1667.2-integrin subunit beta 2 (ITGB2) was constructed. RT-qPCR verified the sequence results. The molecular regulatory mechanisms of lncRNAs on intramuscular fat deposition in yak were further explored.

Effect of FABP4 Gene Polymorphisms on Fatty Acid Composition, Chemical Composition, and Carcass Traits in Sonid Sheep

Fatty acids (FAs) are a group of organic compounds that are regulated by polygenic and environmental factors and affect the taste, nutritional value, and quality of meat. Lamb meat is rich in FAs required by the human body, which has directed more attention to sheep research and meat production. The fatty acid-binding protein 4 (FABP4) gene is considered a candidate gene that can affect FA composition in livestock. Therefore, the aim of this study was to screen for genetic polymorphisms of FABP4 and confirm the association between these polymorphisms and FAs, chemical composition, and carcass traits in Sonid lambs. The results of the association study showed that g.57764667T>C, g.57764436T>G, g.57764242G>A, and g.57757988A>G were associated with the composition of certain long-chain FAs, and g.57764242G>A, g.57764436T>G, and g.57758026G>A were associated with free amino acid levels. In addition, g.57764667T>C and g.57757988A>G were associated with carcass weight and live weight in Sonid lambs. Therefore, the polymorphisms of the FABP4 gene are expected to be a genetic selection marker for superior traits in Sonid sheep breeding, which also provides new insights into how the ovine FABP4 gene affects traits of lamb quality.

Combined Multi-Omics Analysis Reveals the Potential Role of ACADS in Yak Intramuscular Fat Deposition

The Yak (Bos grunniens) is a special breed of livestock predominantly distributed in the Qinghai-Tibet Plateau of China. Intramuscular fat (IMF) content in beef cattle is a vital indicator of meat quality. In this study, RNA-Seq and Protein-Seq were respectively employed to sequence the transcriptome and proteome of the longissimus dorsi (LD) tissue from 4-year-old yaks with significant differences in IMF content under the same fattening conditions. Five overlapping genes (MYL3, ACADS, L2HGDH, IGFN1, and ENSBGRG00000000-926) were screened using combined analysis. Functional verification tests demonstrated that the key gene ACADS inhibited yak intramuscular preadipocyte (YIMA) differentiation and proliferation, promoted mitochondrial biogenesis gene expression, and increased the mitochondrial membrane potential (MMP). Furthermore, co-transfection experiments further demonstrated that interfering with ACADS reversed the effect of PPARα agonists in promoting lipid differentiation. In conclusion, ACADS potentially inhibits lipid deposition in YIAMs by regulating the PPARα signalling pathway. These findings offer insights into the molecular mechanisms underlying yak meat quality.

Identification of FASN Gene Polymorphisms, Expression and Their Relationship with Body Size Traits in Guizhou White Goat (Capra hircus) with Different Genders

To investigate the nucleotide variation sites (SNPs) and expression differences of the fatty acid synthase gene (FASN) in Guizhou white goats, the relationship between the variation and body size traits was investigated. In this study, DNA was extracted from the blood of 100 samples of white goats from different regions in Guizhou province, China, and the variation sites were screened using pooled sequencing by mixing DNA samples, and 242 blood samples with body size traits were used for association analysis. The allele frequency, genotype frequency, homozygosity, heterozygosity and effective gene number were calculated by using PopGene 32.0 software, the population polymorphism information content was calculated by using PIC software (Version 0.6), and the state of genetic balance of the genes was analyzed by using the chi-square test. The mRNA of FASN gene expression levels in male and female goats were investigated by using real-time fluorescence quantitative PCR (RT-qPCR). The general linear mixed model of MINTAB software (Version 16.0) was used to analyze the association between FASN gene nucleotide mutation sites and body size traits. The results showed that there was one nucleotide mutation site g.141 C/T in the target fragment of FASN gene amplification, and revealed two alleles, C and T, and three genotypes CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.4308, 0.4205 and 0.1487, respectively. The allele frequencies for C and T were 0.6410 and 0.3590, respectively. The genetic homozygosity (Ho) was higher than the heterozygosity (He). The χ2 test showed that the mutation site was in the Hardy-Weinberg equilibrium state (p > 0.05). The RT-qPCR results showed that the FASN gene had different expression levels in the longissimus dorsi muscle of male and female goats, and its expression was significantly higher in male goats than in female goats. The association analysis results showed that the mutation of the FASN gene had different effects on body size traits of male and female goats, and the presence of the populations of the T allele and the TT genotype recorded higher body size traits (body weight, heart girth and wither height) in female populations. Therefore, the site of the FASN gene can be used as a candidate marker for the early selection of growth traits in Guizhou white goats.

The role of lncFABP4 in modulating adipogenic differentiation in buffalo intramuscular preadipocytes

Intramuscular fat (IMF) is a crucial determinant of meat quality and is influenced by various regulatory factors. Despite the growing recognition of the important role of long noncoding RNAs (lncRNAs) in IMF deposition, the mechanisms underlying buffalo IMF deposition remain poorly understood. In this study, we identified and characterized a lncRNA, lncFABP4, which is transcribed from the antisense strand of fatty acid-binding protein 4 (FABP4). lncFABP4 inhibited cell proliferation in buffalo intramuscular preadipocytes. Moreover, lncFABP4 significantly increased intramuscular preadipocyte differentiation, as indicated by an increase in the expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARG), CCAAT enhancer binding protein alpha (C/EBPα), and FABP4. Mechanistically, lncFABP4 was found to have the potential to regulate downstream gene expression by participating in protein-protein interaction pathways. These findings contribute to further understanding of the intricate mechanisms through which lncRNAs modulate intramuscular adipogenesis in buffaloes.

A Comparative Study on the Carcass and Meat Chemical Composition, and Lipid-Metabolism-Related Gene Expression in Korean Hanwoo and Brindle Chikso Cattle

The objective of this study was to elucidate the effect of cattle breed on carcass and meat chemical composition, fatty acid profiles, and lipid-metabolism-related genes. For this study, same-age Hanwoo and Chikso steers (n = 6 per breed) reared under identical conditions were used. Immediately after slaughter, muscle tissues were collected for analysis of mRNA expression. At 24 h post-mortem, the carcasses were assessed for carcass traits (marbling score, meat yield, etc.), and meat quality and fatty acid profiles in the longissimus lumborum (LL) and semimembranosus (SM) muscles. The results showed that no differences in the slaughter weight, dressing rate, back-fat thickness, trimmed fat, and total meat yield occurred between the two breeds (p > 0.05). However, Hanwoo cattle had a higher marbling score, intramuscular fat (IMF) content, and expression level of lipid-metabolism-related genes such as lipoprotein lipase, peroxisome proliferator-activated receptor gamma, and fatty acid binding protein 4, compared with Chikso (p < 0.05). Contrastingly, Chikso had a higher total unsaturated fatty acid content and expression level of stearoyl CoA desaturase 1 (p < 0.05). It may be said that the difference in the expression levels of lipid-metabolism-related genes could be the molecular factors underlying IMF deposition and fatty acid profile differences in the beef from the two breeds.

Effects of the Expressions and Variants of the CAST Gene on the Fatty Acid Composition of the Longissimus Thoracis Muscle of Grazing Sonid Sheep

Fatty acid (FA) composition has an important impact on the nutrition and flavor of meat, and on consumer health, and is receiving more attention in the sheep industry. This study aimed to evaluate the relationship between the expression levels of the CAST gene and the FA composition in the longissimus thoracis (LL) muscle, to identify novel variants of CAST, and to perform association analysis with the FA composition in grazing Sonid lambs. The correlation results showed that high expression levels of CAST are correlated with better FA compositions and classes in LL. For association studies, the results showed that c.1210C>T and c.1437G>A in LD-M, and c.2097C>T mutations are associated with some compositions and classes of FA in the LL of grazing Sonid sheep. Two missense c.646G>C (G216R) and c.1210C>T (R404C) mutations were predicted to influence the Calpain_inhib domains of CAST. Thus, the correlation results and associated mutations are expected to be genetic selection markers for the FA composition and meat quality of grazing Sonid lamb muscle and provide new insights into sheep meat quality traits influenced by the ovine CAST gene.

Relationships between the Mini-InDel Variants within the Goat CFAP43 Gene and Body Traits

The cilia- and flagella-associated protein 43 (CFAP43) gene encodes a member of the cilia- and flagellum-associated protein family. Cilia on the cell surface influence intercellular signaling and are involved in biological processes such as osteogenesis and energy metabolism in animals. Previous studies have shown that insertion/deletion (InDel) variants in the CFAP43 gene affect litter size in Shaanbei white cashmere (SBWC) goats, and that litter size and body traits are correlated in this breed. Therefore, we hypothesized that there is a significant relationship between InDel variants within the CFAP43 gene and body traits in SBWC goats. Herein, we first investigated the association between three InDel variant loci (L-13, L-16, and L-19 loci) within CFAP43 and body traits in SBWC goats (n = 1827). Analyses revealed that the L-13, L-16, and L-19 loci were significantly associated with chest depth, four body traits, and three body traits, respectively. The results of this study are in good agreement with those previously reported and could provide useful molecular markers for the selection and breeding of goats for body traits.

Lipidomics and Transcriptome Reveal the Effects of Feeding Systems on Fatty Acids in Yak’s Meat

The differences of fatty acids in yak’s meat under graze feeding (GF) and stall feeding (SF) regimes and the regulation mechanism of the feeding system on the fatty acids content in yak ’s meat was explored in this study. First, the fatty acids in yak’s longissimus dorsi (LD) muscle were detected by gas liquid chromatography (GLC). Compared with GF yaks, the absolute content of ΣSFAs, ΣMUFAs, ΣUFAs, ΣPUFAs and Σn-6PUFAs in SF yak’s LD were higher, whereas Σn-3PUFAs was lower; the relative content of ΣMUFAs, ΣPUFAs, Σn-3PUFAs and ΣUFAs in SF yak’s LD were lower, whereas ΣSFAs was higher. The GF yak’s meat is healthier for consumers. Further, the transcriptomic and lipidomics profiles in yak’s LD were detected by mRNA-Sequencing (mRNA-Seq) and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), respectively. The integrated transcriptomic and lipidomics analysis showed the differences in fatty acids were caused by the metabolism of fatty acids, amino acids, carbohydrates and phospholipids, and were mainly regulated by the FASN, FABP3, PLIN1, SLC16A13, FASD6 and SCD genes in the PPAR signaling pathway. Moreover, the SCD gene was the candidate gene for the high content of ΣMUFA, and FADS6 was the candidate gene for the high content of Σn-3PUFAs and the healthier ratio of Σn-6/Σn-3PUFAs in yak meat. This study provides a guidance to consumers in the choice of yak’s meat, and also established a theoretical basis for improving yak’s meat quality.