Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

In situ spatial transcriptomic analysis of human skeletal muscle using the Xenium platform

Traditional transcriptomic studies often overlook the complex heterogeneity of skeletal muscle, as they typically isolate RNA from mixed muscle fibre and cell populations, resulting in an averaged transcriptomic profile that obscures fibre type-specific differences. This study assessed the potential of the recently developed Xenium platform for high-resolution spatial transcriptomic analysis of human skeletal muscle histological sections. Human vastus lateralis muscle samples from two individuals were analysed using the Xenium platform and Human Multi-Tissue and Cancer Panel targeting 377 genes complemented by staining of successive sections for Myosin Heavy Chain isoforms to differentiate between type 1 and type 2 muscle fibres. Manual segmentation of muscle fibres allowed accurate comparisons of transcript densities across fibre types and subcellular regions, overcoming limitations in the platform's automated segmentation. The analysis revealed higher transcript density in type 1 fibres, particularly in nuclear and perinuclear areas, and identified 191 out of 377 genes with differential expression between muscle fibres and perimysium. Genes such as PROX1, S100A1, LGR5, ACTA2, and LPL exhibited higher expression in type 1 fibres, whereas PEBP4, CAVIN1, GATM, and PVALB in type 2 fibres. We demonstrated that the Xenium platform is capable of high-resolution spatial in situ transcriptomic analysis of skeletal muscle histological sections. This study demonstrates that, with manual segmentation, the Xenium platform effectively performs fibre type-specific transcriptomic analysis, providing new insights into skeletal muscle biology.

Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions

Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.

Soybean molasses increases subcutaneous fat deposition while reducing lipid oxidation in the meat of castrated lambs

This study aimed to evaluate the effect of including soybean molasses (SM) on performance, blood parameters, carcass traits, meat quality, fatty acid, and muscle (longissimus thoracis) transcriptomic profiles of castrated lambs. Twenty Dorper × Santa Inês lambs (20.06 ± 0.76 kg body weight [BW]) were assigned to a randomized block design, stratified by BW, with the following treatments: CON: 0 g/kg of SM and SM20: 200 g/kg of SM on dry matter basis, allocated in individual pens. The diet consisted of 840 g/kg concentrate and 160 g/kg corn silage for 76 d, with the first 12 d as an adaptation period and the remaining 64 d on the finishing diet. The SM20 diet increased blood urea concentration (P = 0.03) while reduced glucose concentration (P = 0.04). Lambs fed SM showed higher subcutaneous fat deposition (P = 0.04) and higher subcutaneous adipocyte diameter (P < 0.01), in addition to reduced meat lipid oxidation (P < 0.01). SM reduced the quantity of branched-chain fatty acids in longissimus thoracis (P = 0.05) and increased the quantity of saturated fatty acids (P = 0.01). In the transcriptomic analysis, 294 genes were identified as differentially expressed, which belong to pathways such as oxidative phosphorylation, citric acid cycle, and monosaccharide metabolic process. In conclusion, diet with SM increased carcass fat deposition, reduced lipid oxidation, and changed the energy metabolism, supporting its use in ruminant nutrition.

Transcriptome profile of skeletal muscle using different sources of dietary fatty acids in male pigs

Pork is of great importance in world trade and represents the largest source of fatty acids in the human diet. Lipid sources such as soybean oil (SOY), canola (CO), and fish oil (FO) are used in pig diets and influence blood parameters and the ratio of deposited fatty acids. In this study, the main objective was to evaluate changes in gene expression in porcine skeletal muscle tissue resulting from the dietary oil sources and to identify metabolic pathways and biological process networks through RNA-Seq. The addition of FO in the diet of pigs led to intramuscular lipid with a higher FA profile composition of C20:5 n-3, C22:6 n-3, and SFA (C16:0 and C18:0). Blood parameters for the FO group showed lower cholesterol and HDL content compared with CO and SOY groups. Skeletal muscle transcriptome analyses revealed 65 differentially expressed genes (DEG, FDR 10%) between CO vs SOY, and 32 DEG for CO vs FO, and 531 DEG for SOY vs FO comparison. Several genes, including AZGP1, PDE3B, APOE, PLIN1, and LIPS, were found to be down-regulated in the diet of the SOY group compared to the FO group. The enrichment analysis revealed DEG involved in lipid metabolism, metabolic diseases, and inflammation between the oil groups, with specific gene functions in each group and altered blood parameters. The results provide mechanisms to help us understand the behavior of genes according to fatty acids.

RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids

Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms' variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets.

Transcriptomics and Lipid Metabolomics Analysis of Subcutaneous, Visceral, and Abdominal Adipose Tissues of Beef Cattle

Fat deposition traits are influenced by genetics and environment, which affect meat quality, growth rate, and energy metabolism of domestic animals. However, at present, the molecular mechanism of fat deposition is not entirely understood in beef cattle. Therefore, the current study conducted transcriptomics and lipid metabolomics analysis of subcutaneous, visceral, and abdominal adipose tissue (SAT, VAT, and AAT) of Huaxi cattle to investigate the differences among these adipose tissues and systematically explore how candidate genes interact with metabolites to affect fat deposition. These results demonstrated that compared with SAT, the gene expression patterns and metabolite contents of VAT and AAT were more consistent. Particularly, SCD expression, monounsaturated fatty acid (MUFA) and triglyceride (TG) content were higher in SAT, whereas PCK1 expression and the contents of saturated fatty acid (SFA), diacylglycerol (DG), and lysoglycerophosphocholine (LPC) were higher in VAT. Notably, in contrast to PCK1, 10 candidates including SCD, ELOVL6, ACACA, and FABP7 were identified to affect fat deposition through positively regulating MUFA and TG, and negatively regulating SFA, DG, and LPC. These findings uncovered novel gene resources and offered a theoretical basis for future investigation of fat deposition in beef cattle.

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.

Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle

Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (-0.47), ribeye area (REA) and protein 4 (prot4) (-0.33), REA and protein 2 (prot2) (-0.3), carcass and prot4 (-0.31), carcass and prot2 (-0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (-0.25). Positive correlations were observed among the four protein factors (0.45-0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR &lt; 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.

Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases

Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science.

Explaining Unsaturated Fatty Acids (UFAs), Especially Polyunsaturated Fatty Acid (PUFA) Content in Subcutaneous Fat of Yaks of Different Sex by Differential Proteome Analysis

Residents on the Tibetan Plateau intake a lot of yak subcutaneous fat by diet. Modern healthy diet ideas demand higher unsaturated fatty acids (UFAs), especially polyunsaturated fatty acid (PUFA) content in meat. Here, the gas chromatography (GC) and tandem mass tag (TMT) proteomic approaches were applied to explore the relationship between the proteomic differences and UFA and PUFA content in the subcutaneous fat of yaks with different sex. Compared with male yaks (MYs), the absolute contents of UFAs, monounsaturated fatty acids (MUFAs) and PUFAs in the subcutaneous fat of female yaks (FYs) were all higher (p < 0.01); the relative content of MUFAs and PUFAs in MY subcutaneous fat was higher, and the value of PUFAs/SFAs was above 0.4, so the MY subcutaneous fat is more healthy for consumers. Further studies showed the transcriptional regulation by peroxisome proliferator-activated receptor delta (PPARD) played a key role in the regulation of UFAs, especially PUFA content in yaks of different sex. In FY subcutaneous fat, the higher abundance of the downstream effector proteins in PPAR signal, including acyl-CoA desaturase (SCD), elongation of very-long-chain fatty acids protein 6 (ELOVL6), lipoprotein lipase (LPL), fatty acid-binding protein (FABP1), very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 (HACD3), long-chain fatty acid CoA ligase 5 (ACSL5) and acyl-CoA-binding protein 2 (ACBP2), promoted the UFAs’ transport and synthesis. The final result was the higher absolute content of c9-C14:1, c9-C18:1, c9,c12-C18:2n-6, c9, c12, c15-C18:3n-3, c5, c8, c11, c14, c17-C20:5n-3, c4, c7, c10, c13, -c16, c19-C22:6n-3, UFAs, MUFAs and PUFAs in FY subcutaneous fat. Further, LPL, FABP1, HACD3, ACSL1 and ACBP2 were the potential biomarkers for PUFA contents in yak subcutaneous fat. This study provides new insights into the molecular mechanisms associated with UFA contents in yak subcutaneous fat.

Integrated analysis of expression profiles with meat quality traits in cattle

MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.

Fat Deposition in the Muscle of Female and Male Yak and the Correlation of Yak Meat Quality with Fat

This study aimed to explore the differences in fat deposition between female (FYs) and male yaks (MYs). Compared with MYs, the tenderness, L*, marbling, absolute content of fat, and most fatty acids (FAs) of longissimus dorsi (LD) in FYs were higher or better (p < 0.05), whereas the relative content of polyunsaturated fatty acids (PUFAs) and n-3 PUFAs were lower (p < 0.01). The absolute content of fat, C18:0, cis-C18:2, cis-C18:1, and C24:0 were positively correlated with L*_{45 min}, b*_{24 h}, tenderness, and marbling score of LD in FYs and MYs (p < 0.05), respectively. LPL, FATP2, ELOVL6, HADH, HACD, and PLINS genes play a crucial role in improving the marbling score and tenderness of yak meat. The results of gene expression and protein synthesis showed the effect of gender to FA biosynthesis, FA transport, lipolysis, and FA oxidation in the adipose tissue of yak was realized by the expressions of ME1, SCD, ACSL5, LPL, FABP1, PLIN4, and PLIN2 in peroxisome proliferators-activated receptor (PPAR) signaling. This study established a theoretical basis for the improvement of the meat quality of yak and molecular breeding.

Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (p-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition.

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (F_ST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

Functional contexts of adipose and gluteal muscle tissue gene co-expression networks in the domestic horse

A gene's response to an environment is tightly bound to the underlying genetic variation present in an individual's genome and varies greatly depending on the tissue it is being expressed in. Gene co-expression networks provide a mechanism to understand and interpret the collective transcriptional responses of genes. Here, we use the Camoco co-expression network framework to characterize the transcriptional landscape of adipose and gluteal muscle tissue in 83 domestic horses (Equus caballus) representing 5 different breeds. In each tissue, gene expression profiles, capturing transcriptional response due to variation across individuals, were used to build two separate, tissue-focused, genotypically-diverse gene co-expression networks. The aim of our study was to identify significantly co-expressed clusters of genes in each tissue, then compare the clusters across networks to quantify the extent that clusters were found in both networks as well as to identify clusters found in a single network. The known and unknown functions for each network were quantified using complementary, supervised and unsupervised approaches. First, supervised ontological enrichment was utilized to quantify biological functions represented by each network. Curated ontologies (GO and KEGG) were used to measure the known biological functions present in each tissue. Overall, a large percentage of terms (40.3% of GO and 41% of KEGG) were co-expressed in at least one tissue. Many terms were co-expressed in both tissues, however a small proportion of terms exhibited single tissue co-expression suggesting functional differentiation based on curated, functional annotation. To complement this, an unsupervised approach not relying on ontologies was employed. Strongly co-expressed sets of genes defined by Markov clustering identified sets of unannotated genes showing similar patterns of co-expression within a tissue. We compared gene sets across tissues and identified clusters of genes the either segregate in co-expression by tissue or exhibit high levels of co-expression in both tissues. Clusters were also integrated with GO and KEGG ontologies to identify gene sets containing previously curated annotations versus unannotated gene sets indicating potentially novel biological function. Coupling together these transcriptional datasets, we mapped the transcriptional landscape of muscle and adipose setting up a generalizable framework for interpreting gene function for additional tissues in the horse and other species.

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.

Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.

Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.

Proteome alterations associated with the oleic acid and cis-9, trans-11 conjugated linoleic acid content in bovine skeletal muscle

Oleic acid (OA) and cis-9, trans-11 conjugated linoleic acid (c9t11-CLA) are fatty acids found in beef with beneficial effects in human health. This study investigated differentially abundant proteins (DAPs) in skeletal muscle of bovines with extreme values of OA, and c9t11-CLA. For each one of the fatty acids, twenty muscle samples were divided into two groups (N = 10_High; N = 10_Low) and analyzed by high definition mass spectrometry. We identified 103 and 133 DAPs between the groups for each fatty acid. We found 64 and 45 up-regulated and 39 and 68 down-regulated proteins for OA and c9t11-CLA, respectively. Comparative analysis between proteomic and transcriptomic data revealed eight and ten genes with a consistent between mRNA expression levels and protein abundance for OA and c9t11-CLA, respectively. Unconventional myosin-Id (MYO1D), mineralocorticoid receptor (NR3C2), geranylgeranyl transferase type-2 subunit-alpha (RABGGTA), and uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA) were found as putative candidate proteins for OA content. Fatty acid synthase (FASN), tubulin alpha-4A chain (TUBA4A), vinculin (VCL), NADH dehydrogenase 1 alpha subcomplex 5 (NDUFA5), and prefoldin subunit 6 (PFDN6) for c9t11-CLA. Our findings contribute to a deeper understanding of the molecular mechanisms behind the regulation of the OA and c9t11-CLA content in cattle skeletal muscle. SIGNIFICANCE: Questions about the association between meat intake and disease incidence in humans has driven animal scientist to pursue a better understanding of the biological processes associated with differences in the intramuscular fat composition. The beneficial effects of oleic acid and conjugated linoleic acid in human health have been demonstrated by improving the immune system and preventing atherosclerosis, different types of cancers, hypertension, and diabetes. Previous genome-wide association and gene expression studies identified genomic regions and differentially expressed genes associated with the fatty acid profile in skeletal muscle. In this work, differences were evaluated at the protein level. The use of a label-free quantitative proteomic approach, compared with muscle transcriptome results obtained by RNA-sequencing, allowed us to earn new insights into the variability in fatty acid deposition in skeletal muscle of farm animals. This study opens new avenues to explore the effect of the fatty acids in the skeletal muscle of livestock animals, which is associated with nutritional values of the meat, and perhaps to understand the mechanisms correlated with metabolic diseases in other species.

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression

Background

Fatty acid composition contributes greatly to the quality and nutritional value of meat. However, the molecular regulatory mechanisms underlying fatty acid accumulation in poultry have not yet been cleared. The aims of this study were to characterize the dynamics of fatty acid accumulation in duck breast muscle and investigate its correlations with gene expression.

Results

Here, we analyzed the fatty acid profile and transcriptome of breast muscle derived from Pekin ducks and mallards at the ages of 2 weeks, 4 weeks, 6 weeks and 8 weeks. Twenty fatty acids were detected in duck breast muscle, with palmitic acid (C16:0, 16.6%~ 21.1%), stearic acid (C18:0, 9.8%~ 17.7%), oleic acid (C18:1n-9, 15.7%~ 33.8%), linoleic acid (C18:2n-6, 10.8%~ 18.9%) and arachidonic acid (C20:4n-6, 11.7%~ 28.9%) as the major fatty acids. Our results showed that fatty acid composition was similar between the two breeds before 6 weeks, but the compositions diverged greatly after this point, mainly due to the stronger capacity for C16:0 and C18:1n-9 deposition in Pekin ducks. By comparing the multistage transcriptomes of Pekin ducks and mallards, we identified 2025 differentially expressed genes (DEGs). Cluster analysis of these DEGs revealed that the genes involved in oxidative phosphorylation, fatty acid degradation and the PPAR signaling pathway were upregulated in mallard at 8 weeks. Moreover, correlation analysis of the DEGs and fatty acid composition traits suggested that the DEGs involved in lipogenesis, lipolysis and fatty acid β-oxidation may interact to influence the deposition of fatty acids in duck breast muscle.

Conclusions

We reported the temporal progression of fatty acid accumulation and the dynamics of the transcriptome in breast muscle of Pekin ducks and mallards. Our results provide insights into the transcriptome regulation of fatty acid accumulation in duck breast muscle, and will facilitate improvements of fatty acid composition in duck breeding.

Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus

Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors. To unveil the genetic factors involved in muscle mineral concentration, we applied a pairwise differential gene expression analysis in groups of Nelore steers genetically divergent for nine different mineral concentrations. Here, based on significant expression differences between contrasting groups, we presented candidate genes for the genetic regulation of mineral concentration in muscle. Functional enrichment and protein-protein interaction network analyses were carried out to search for gene regulatory processes concerning each mineral. The core genetic regulation for all minerals studied, except Zn, seems to rest on interactions between components of the extracellular matrix. Regulation of adipogenesis-related pathways was also significant in our results. Antagonistic patterns of gene expression for fatty acid metabolism-related genes may explain the Cu and Zn antagonistic effect on fatty acid accumulation. Our results shed light on the role of these minerals on cell function.

Co-Expression Networks Reveal Potential Regulatory Roles of miRNAs in Fatty Acid Composition of Nelore Cattle

Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in skeletal muscle associated with FA content. miRNA and mRNA expression data were obtained from skeletal muscle of Nelore cattle that had extreme genomic breeding values for OA and CLA. Insulin and MAPK signaling pathways were identified by WGCNA as central pathways associated with both of these fatty acids. Co-expression network analysis identified bta-miR-33a/b, bta-miR-100, bta-miR-204, bta-miR-365-5p, bta-miR-660, bta-miR-411a, bta-miR-136, bta-miR-30-5p, bta-miR-146b, bta-let-7a-5p, bta-let-7f, bta-let-7, bta-miR 339, bta-miR-10b, bta-miR 486, and the genes ACTA1 and ALDOA as potential regulators of fatty acid synthesis. This study provides evidence and insights into the molecular mechanisms and potential target genes involved in fatty acid content differences in Nelore beef cattle, revealing new candidate pathways of phenotype modulation that could positively benefit beef production and human consumption.

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r  > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.

Promoting the Outgrowth of Neurites on Electrospun Microfibers by Functionalization with Electrosprayed Microparticles of Fatty Acids

Controlling the outgrowth of neurites is important for enhancing the repair of injured nerves and understanding the development of nervous systems. Herein we report a simple strategy for enhancing the outgrowth of neurites through a unique integration of topographical guidance and a chemical cue. We use electrospray to easily functionalize the surface of a substrate with microparticles of natural fatty acids at a controllable density. Through a synergistic effect from the surface roughness arising from the microparticles and the chemical cue offered by the fatty acids, the outgrowth of neurites from PC12 cells is greatly enhanced. We also functionalize the surfaces of uniaxially aligned, electrospun microfibers with the microparticles and further demonstrate that the substrates can guide and enhance directional outgrowth of neurites from both PC12 multicellular spheroids and chick embryonic dorsal root ganglia bodies.

Differentially expressed coding and noncoding RNAs in CoCl2-induced cytotoxicity of C2C12 cells

Aim: We aimed to explore potential regulators of coding and noncoding RNAs (ncRNAs) in Co(II) ion-induced myo cytotoxicity. Materials & methods: We confirmed the toxic effects of Co(II) on mouse skeletal C2C12 myotubes by CoCl2, and performed the expression profiles of circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and mRNAs using microarray analysis. We constructed co-expression, competing endogenous RNA and cis/trans regulation networks for ncRNAs, and filtered 71 candidate circRNAs with coding potential. Results: We identify 605 differentially expressed circRNAs, 4409 long noncoding RNAs and 3965 mRNAs. We also provided several ncRNAs regulation networks and presumed functions of circRNAs with coding potential. Conclusion: Our findings may reveal novel regulatory mechanisms underlying the noxious effects of CoCl2 in skeletal muscle.

Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle

BACKGROUND

Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer's payment. The selection of these traits has not been satisfactory since they are expressed later in the animal's life and multigene regulated. So, next-generation technologies have been applied in this area to improve animal's selection and better understand the molecular mechanisms involved in the development of these traits. Correlation network analysis, performed by tools like WGCNA (Weighted Correlation Network Analysis), has been used to explore gene-gene interactions and gene-phenotype correlations. Thus, this study aimed to identify putative candidate genes and metabolic pathways that regulate REA and BFT by constructing a gene co-expression network using WGCNA and RNA sequencing data, to better understand genetic and molecular variations behind these complex traits in Nelore cattle.

RESULTS

The gene co-expression network analysis, using WGCNA, were built using RNA-sequencing data normalized by transcript per million (TPM) from 43 Nelore steers. Forty-six gene clusters were constructed, between them, three were positively correlated (p-value< 0.1) to the BFT (Green Yellow, Ivory, and Light Yellow modules) and, one cluster was negatively correlated (p-value< 0.1) with REA (Salmon module). The enrichment analysis performed by DAVID and WebGestalt (FDR 5%) identified eight Gene Ontology (GO) terms and three KEGG pathways in the Green Yellow module, mostly associated with immune response and inflammatory mechanisms. The enrichment of the Salmon module demonstrated 19 GO terms and 21 KEGG pathways, related to muscle energy metabolism, lipid metabolism, muscle degradation, and oxidative stress diseases. The Ivory and Light yellow modules have not shown significant results in the enrichment analysis.

CONCLUSION

With this study, we verified that inflammation and immune response pathways modulate the BFT trait. Energy and lipid metabolism pathways, highlighting fatty acid metabolism, were the central pathways associated with REA. Some genes, as RSAD2, EIF2AK2, ACAT1, and ACSL1 were considered as putative candidate related to these traits. Altogether these results allow us to a better comprehension of the molecular mechanisms that lead to muscle and fat deposition in bovine.

Timing of Exposure to High-Concentrates versus High-Quality Forages on Growth and Marbling Deposition in Steers

Forty Angus-cross steers (280 ± 21.4 kg BW, 8 mo.) were used to examine the effects of exposure to 2 diets [high concentrate diets (CONC) versus high quality forages (FOR)] during 2 time periods [early (EARLY; at 30-d post weaning) or late (LATE; just prior to slaughter)] on animal growth, marbling deposition and tenderness. Steers were blocked by weight and randomly assigned to four dietary treatments: 1) CONC-FOR, 2) CONC-CONC, 3) FOR-CONC, or 4) FOR-FOR. Exposure to CONC during the EARLY or LATE period increased (P < 0.05) growth and fat deposition compared to FOR-FOR. Hot carcass weight was greater (P < 0.05) for CONC-CONC and FOR-CONC steers than FOR-FOR and CONC-FOR due to changes in dressing percent. Marbling score was greater (P < 0.05) for CONC-CONC and CONC-FOR compared to FOR-FOR. Exposure to CONC during the EARLY period (CONC-FOR and CONC-CONC) increased (P < 0.05) n-6 polyunsaturated fatty acids (PUFA) deposition in longissimus muscle (LM) and subcutaneous adipose tissue (SQ); whereas, exposure to CONC during the LATE period (CONC-CONC and FOR-CONC) reduced (P < 0.05) n-3 PUFA, trans-11 octadecenoic acid and cis-9 trans-11 isomer of conjugated linoleic acid (CLA). Warner-Bratzler shear force at d 2 and 7 of postmortem aging in ribeye steaks from CONC-CONC and FOR-CONC was greater (P < 0.05) than FOR-FOR and CONC-FOR. Lipogenic gene expression was up-regulated (P < 0.05) and lipolytic gene expression was downregulated (P < 0.06) in SQ from CONC-CONC and FOR-CONC compared to FOR-FOR. Overall, exposure to CONC in both periods increased growth rate and marbling deposition but LATE exposure had the greatest impact on adipose lipogenesis and lipolysis, fatty acid composition, and tenderness.

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

Background

Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with intramuscular fat (IMF) content traits.

Results

We performed an integrative eQTL study in skeletal muscle to identify putative regulatory regions and factors associated with intramuscular fat content traits. Data obtained from skeletal muscle samples of 192 animals was used for association analysis between 461,466 SNPs and the transcription level of 11,808 genes. This yielded 1268 cis- and 10,334 trans-eQTLs, among which we identified nine hotspot regions that each affected the expression of > 119 genes. These putative regulatory regions overlapped with previously identified QTLs for IMF content. Three of the hotspots respectively harbored the transcription factors USF1, EGR4 and RUNX1T1, which are known to play important roles in lipid metabolism. From co-expression network analysis, we further identified modules significantly correlated with IMF content and associated with relevant processes such as fatty acid metabolism, carbohydrate metabolism and lipid metabolism.

Conclusion

This study provides novel insights into the link between genotype and IMF content as evident from the expression level. It thereby identifies genomic regions of particular importance and associated regulatory factors. These new findings provide new knowledge about the biological processes associated with genetic variants and mechanisms associated with IMF deposition in mammals.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4871-y) contains supplementary material, which is available to authorized users.

Widespread modulation of gene expression by copy number variation in skeletal muscle

Copy number variation (CNV) is a frequently observed deviation from the diploid state due to duplication or deletion of genomic regions. Although intensively analyzed for association with diseases and production traits, the specific mechanisms and extent by which such variations affect the phenotype are incompletely understood. We present an integrative study on CNV and genome-wide gene expression in Brazilian Bos indicus cattle. We analyzed CNVs inferred from SNP-chip data for effects on gene expression measured with RNA-seq in skeletal muscle samples of 183 steers. Local effects, where expression changes coincided with CNVs in the respective genes, were restricted to immune genes. Distal effects were attributable to several high-impact CNVs that modulated remote expression in an orchestrated and intertwined fashion. These CNVs were located in the vicinity of major skeletal muscle pathway regulators and associated genes were enriched for proteolysis, autophagy, and muscle structure development. From association analysis between CNVs and several meat quality and production traits, we found CNV-associated expression effects to also manifest at the phenotype level. Based on genome sequences of the population founders, we further demonstrate that CNVs with impact on expression and phenotype are passed on from one generation to another.

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Background

Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits.

Results

By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis.

Conclusion

In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3897-x) contains supplementary material, which is available to authorized users.