An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle

A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses

Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.

Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency

Identifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein-Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle.

Genome-wide association study for primal cut lean traits in Canadian beef cattle

This study identified genomic variants and underlying candidate genes related to the whole carcass and individual primal cut lean content in Canadian commercial crossbred beef cattle. Genotyping information of 1035 crossbred beef cattle were available alongside estimated and actual carcass lean meat yield and individual primal cut lean content in all carcasses. Significant fixed effects and covariates were identified and included in the animal model. Genome-wide association analysis were implemented using the weighted single-step genomic best linear unbiased prediction (WssGBLUP). A number of candidate genes identified linked to lean tissue production were unrelated to estimated lean meat yield and were specific to the actual lean traits. Among these, 41 genes were common for actual lean traits, on specific regions of BTA4, BTA13 and BTA25 indicating potential involvement in lean mass synthesis. Therefore, the results suggested the inclusion of primal cut lean traits as a selection objective in breeding programs with consideration of further functional studies of the identified genes could help in optimizing lean yield for maximal carcass value.

Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle

Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.

Identification and characterization of hypothalamic circular RNAs associated with bovine residual feed intake

Residual feed intake (RFI) is crucial economic indicator used for calculating the feed efficiency of growing beef cattle. circRNA plays an important biological role in gene transcriptional regulation, but little is known about its potential functional regulation underlying RFI phenotypic variation. As the core center of regulation of animal feeding, the hypothalamus is closely associated with RFI. Therefore, the present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing from hypothalamic tissue samples, in order to gain insight into the potential regulatory role of circRNAs in bovine RFI phenotypic variation. Differentially expressed genes were detected by RNA sequencing for beef cattle in the high and low RFI groups, followed by GO, KEGG enrichment, and circRNA-miRNA co-expression network analysis. A total of 257 circRNAs were differentially expressed between the two groups, with 128 significantly upregulated and 129 significantly downregulated genes in H group compared to L group. Among them, 9 unique circRNAs were present in group L and 4 unique circRNAs were present in group H. GO and KEGG enrichment analysis of the source genes of the differentially expressed circRNAs revealed that they were mainly involved in metabolic processes, such as cellular metabolic processes, cellular macromolecular metabolic processes, and regulatory pathways related to nutrient metabolism, including protein and amino acid metabolism, as well as vitamin metabolism and pancreatic secretion associated with the animal feeding behavior. The circRNAs detected in this study were mostly novel, and have not been investigated directly to be associated with the RFI phenotype. Interestingly, most miRNAs of differentially expressed circRNAs predicted based on the circRNA-miRNA co-expression network analysis by using top 50 differentially expressed circRNAs and 13 unique circRNAs, have been reported to be related to animal RFIs, implying that circRNAs in bovine hypothalamic tissue may regulate phenotypic variation in RFI through miRNAs. The study results illustrate the complex biological functions of the hypothalamus in regulating feed efficiency and showing the potential role of circRNAs in the feeding behavior regulation of livestock, which would contributing to expanding the understanding of circRNA.

Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle

Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality. Based on the inverse relationship between H3K27me3 and gene expression (i.e., epigenetic repression) and on contrasting sample groups, we computationally predicted regulatory genes that affect muscle mineral content. To this end, we applied the TRIAGE predictive method followed by a rank product analysis. This methodology can predict regulatory genes that might be affected by repressive epigenetic regulation related to mineral concentration. Annotation of orthologous genes, between human and bovine, enabled our investigation of gene expression in the Longissimus thoracis muscle of Bos indicus cattle. The animals under study had a contrasting mineral content in their muscle cells. We identified candidate regulatory genes influenced by repressive epigenetic mechanisms, linking histone modification to mineral content in beef samples. The discovered candidate genes take part in multiple biological pathways, i.e., impulse transmission, cell signalling, immunological, and developmental pathways. Some of these genes were previously associated with mineral content or regulatory mechanisms. Our findings indicate that epigenetic repression can partially explain the gene expression profiles observed in muscle samples with contrasting mineral content through the candidate regulators here identified.

Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency

Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose tissues regulate FE remains largely unknown. Therefore, this study aimed to screen potential miRNAs related to FE through miRNA sequencing. The miRNA profiles in porcine adipose tissues were obtained and 14 miRNAs were identified differentially expressed in adipose tissues of pigs with extreme differences in FE, of which 9 were down-regulated and 5 were up-regulated. GO and KEGG analyses indicated that these miRNAs were significantly related to lipid metabolism and these miRNAs modulated FE by regulating lipid metabolism. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of five randomly selected DEMs was used to verify the reliability of miRNA-seq data. Furthermore, 39 differentially expressed target genes of these DEMs were obtained, and DEMs-target mRNA interaction networks were constructed. In addition, the most significantly down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, might be the key miRNAs for FE. Our results reveal the mechanism by which adipose miRNAs regulate feed efficiency in pigs. This study provides a theoretical basis for the further study of swine feed efficiency improvement.

Network analysis reveals different hub genes and molecular pathways for pig in vitro fertilized early embryos and parthenogenotes

Maternal-to-zygotic transition (MZT) occurs when maternal transcripts decay and zygotic genome is activated gradually at early stage of embryo development. Previously, single cell RNA-seq (scRNA-seq) has helped us to uncover the MZT-associated mRNA dynamics of in vitro produced pig early embryos. Here, to further investigate functional modules and hub genes associated with MZT process, the weighted gene-coexpression network analysis (WGCNA) was performed on our previously generated 45 scRNA-seq datasets. For the in vitro fertilized embryo (IVF) group, 5 significant modules were identified (midnightblue/black/red and blue/brown modules, positively correlated with 1-cell (IVF1) and 8-cell (IVF8), respectively), containing genes mainly enriched in signaling pathways such as Wnt, regulation of RNA transcription, fatty acid metabolic process, poly(A) RNA binding and lysosome. For the parthenogenetically activated embryo (PA) group, 9 significant modules were identified (black/purple/red, brown/turquoise/yellow, and magenta/blue/green modules, positively correlated with MII oocytes, 1-cell (PA1), and 8-cell (PA8), respectively), mainly enriched in extracellular exosome, poly(A) RNA binding, mitochondrion, transcription factor activity. Moreover, some of identified hub genes within 3 IVF and 9 PA significant modules, including ADCY2, DHX34, KDM4A, GDF10, ABCC10, PAFAH2, HEXIM2, COQ9, DCAF11, SGK1, ESRRB etc., have been reported to play vital roles in different biological processes. Our findings provide information and resources for subsequent in-depth study on the regulation and function of MZT in pig embryos.

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.

Bovine rumen epithelial miRNA-mRNA dynamics reveals post-transcriptional regulation of gene expression upon transition to high-grain feeding and phytogenic supplementation

The rumen epithelium has a pivotal role in nutrient uptake and host health. This study aimed to explore the role of microRNAs (miRNAs) in the epithelial transcriptome during diet transition from forage to high-grain feeding and the modulation through supplementation with a phytogenic feed additive. Rumen biopsies were collected from 9 ruminally-cannulated non-lactating Holstein cows fed a baseline forage diet (FD) and then transitioned to high-grain feeding (HG; 65% concentrate on a dry matter basis). Cows were randomly allocated into a control group (CON, n = 5) and a group supplemented with a phytogenic feed additive (PHY, n = 4). MiRNA and mRNA sequencing was performed in parallel and transcripts were analyzed for differential expression, pathway enrichment analysis, and miRNA-mRNA interaction networks. We identified 527 miRNAs shared by all samples of the rumen epithelium, from which, bta-miR-21-5p, bta-miR-143 and bta-miR-24-3p were the most expressed. Six miRNAs were differentially expressed between CON and PHY and 8 miRNAs between FD and HG feeding, which were mainly associated with fat metabolism. Transcriptome analysis identified 9481 differentially expressed genes (DEGs) between FD and HG, whereas PHY supplementation resulted in 5 DEGs. DEGs were mainly involved in epithelium development and morphogenesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with tricarboxylic acid and short chain fatty acid (SCFA) metabolism were enriched in DEGs between diets. MiRNA target prediction and anti-correlation analysis was used to construct networks and identify DEGs targeted by DE miRNAs responsive to diet or PHY. This study allowed the identification of potential miRNA regulation mechanisms of gene expression during transition from FD to HG feeding and phytogenic supplementation, evidencing a direct role of miRNAs in host responses to nutrition.

Nutritional Modulation, Gut, and Omics Crosstalk in Ruminants

Simple Summary

Over the last decade, animal nutrition science has been significantly developed, supported by the great advancements in molecular technologies. For scientists, the present "feedomics and nutrigenomics" era continues to evolve and shape how research is designed, performed, and understood. The new omics interpretations have established a new point of view for the nutrition–gene interaction, integrating more comprehensive findings from animal physiology, molecular genetics, and biochemistry. In the ruminant model, this modern approach addresses rumen microbes as a critical intermediate that can deepen the studies of diet–gut interaction with host genomics. The present review discusses nutrigenomics’ and feedomics’ potential contribution to diminishing the knowledge gap about the DNA cellular activities of different nutrients. It also presents how nutritional management can influence the epigenetic pathway, considering the production type, life stage, and species for more sustainable ruminant nutrition strategies.

Abstract

Ruminant nutrition has significantly revolutionized a new and prodigious molecular approach in livestock sciences over the last decade. Wide-spectrum advances in DNA and RNA technologies and analysis have produced a wealth of data that have shifted the research threshold scheme to a more affluent level. Recently, the published literature has pointed out the nutrient roles in different cellular genomic alterations among different ruminant species, besides the interactions with other factors, such as age, type, and breed. Additionally, it has addressed rumen microbes within the gut health and productivity context, which has made interpreting homogenous evidence more complicated. As a more systematic approach, nutrigenomics can identify how genomics interacts with nutrition and other variables linked to animal performance. Such findings should contribute to crystallizing powerful interpretations correlating feeding management with ruminant production and health through genomics. This review will present a road-mapping discussion of promising trends in ruminant nutrigenomics as a reference for phenotype expression through multi-level omics changes.

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.

Comparative proteomics revealed duodenal metabolic function associated with feed efficiency in slow-growing chicken

The Korat chicken (KR), developed in Thailand, is a slow-growing breed developed as an alternative breed for Thai chicken producers. The growing interest in slow-growing chicken meat, due to its unique taste, distinct texture, health benefits, and higher broiler welfare have led to higher market demand for KR. However, its low feed efficiency (FE) has a significant negative impact on farm profitability. Understanding the molecular mechanism regulating FE allows for designing a suitable selection program and contributing to breeding more efficient chicken for poultry production. Thus, the objective of our study was to investigate the proteome differences and possible pathways associated with FE in male KR using a label-free quantitative proteomic approach. Seventy-five KR males were individually evaluated for FE, and duodenum samples from 6 animals (3 high-FE and 3 low-FE chickens) were collected at 10 wk of age for differential abundant proteins (DAPs), protein networks, functional enrichment, and pathway analyses. In this study, we found 40 DAPs significantly associated with FE pathways, including glycolysis/gluconeogenesis, peroxisome, oxidative phosphorylation, tight junction, and cysteine and methionine metabolism. Thus, variations in observed DAPs or genes related to DAPs could be interesting biomarker candidates for selection for higher feed utilization efficiency in chicken.

Differences in Liver microRNA profiling in pigs with low and high feed efficiency

Feed cost is the main factor affecting the economic benefits of pig industry. Improving the feed efficiency (FE) can reduce the feed cost and improve the economic benefits of pig breeding enterprises. Liver is a complex metabolic organ which affects the distribution of nutrients and regulates the efficiency of energy conversion from nutrients to muscle or fat, thereby affecting feed efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed efficiency through the modulation of gene expression at the post-transcriptional level. In this study, we analyzed miRNA profiling of liver tissues in High-FE and Low-FE pigs for the purpose of identifying key miRNAs related to feed efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs indicated that the target genes of DE miRNAs were significantly enriched in insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and mammalian target of rapamycin signaling pathway. To verify the reliability of sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs were confirmed to be consistent with sequencing data. DE miRNA data indicated that liver-specific miRNAs synergistically acted with mRNAs to improve feed efficiency. The liver miRNAs expression analysis revealed the metabolic pathways by which the liver miRNAs regulate pig feed efficiency.

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.

Integrated Analysis of mRNA and MicroRNA Co-expressed Network for the Differentiation of Bovine Skeletal Muscle Cells After Polyphenol Resveratrol Treatment

Resveratrol (RSV) has been confirmed to benefit human health. Resveratrol supplemented in the feeds of animals improved pork, chicken, and duck meat qualities. In this study, we identified differentially expressed (DE) messenger RNAs (mRNAs) (n = 3,856) and microRNAs (miRNAs) (n = 93) for the weighted gene co-expression network analysis (WGCNA) to investigate the co-expressed DE mRNAs and DE miRNAs in the primary bovine myoblasts after RSV treatment. The mRNA results indicated that RSV treatments had high correlations with turquoise module (0.91, P-value = 0.01) and blue module (0.93, P-value < 0.01), while only the turquoise module (0.96, P-value < 0.01) was highly correlated with the treatment status using miRNA data. After biological enrichment analysis, the 2,579 DE genes in the turquoise module were significantly enriched in the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The top two GO terms were actin filament-based process (GO:0030029) and actin cytoskeleton organization (GO:0030036). The top two KEGG pathways were regulation of actin cytoskeleton (bta04810) and tight junction (bta04530). Then, we constructed the DE mRNA co-expression and DE miRNA co-expression networks in the turquoise module and the mRNA–miRNA targeting networks based on their co-expressions in the key module. In summary, the RSV-induced miRNAs participated in the co-expression networks that could affect mRNA expressions to regulate the primary myoblast differentiation. Our study provided a better understanding of the roles of RSV in inducing miRNA and of the characteristics of DE miRNAs in the key co-expressed module in regulation of mRNAs and revealed new candidate regulatory miRNAs and genes for the beef quality traits.

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions. Blood samples were collected after the exposure to the TN and HS conditions and the relative expression of genes was measured by qPCR. The bulls exhibited lower expression of ATP1A1 in the HS condition than in the TN condition (1.98 ± 0.27 and 2.86 ± 0.26, P = 0.02), while the relative expression of NR3C1, POMC, and LEP did not differ (P > 0.05) between climatic conditions. The breed and feed intake influenced NPY and LEP expression levels (P < 0.05). Different climate conditions associated with residual feed intake can modify the gene expression patterns of ATP1A1 and NPY. The association observed among all genes studied shows that they are involved in appetite control. Bos taurus and Bos indicus bulls exhibited similar adaptability to tropical climate conditions.

Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.

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.

Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes

MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.

Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits

The study presents the miRNA profiles of two Indian sheep populations with divergent carcass and muscle traits. The RNA sequencing of longissimus thoracis muscles from the two populations revealed a total of 400 known miRNAs. Myomirs or miRNAs specific to skeletal muscles identified in our data included oar-miR-1, oar-miR-133b, oar-miR-206 and oar-miR-486. Comparison of the two populations led to identification of 100 differentially expressed miRNAs (p < 0.05). A total of 45 miRNAs exhibited a log₂ fold change of ≥ ( ±) 3.0. Gene Ontology analysis revealed cell proliferation, epithelial to mesenchymal transition, apoptosis, immune response and cell differentiation as the most significant functions of the differentially expressed miRNAs. The differential expression of some miRNAs was validated by qRT-PCR analysis. Enriched pathways included metabolism of proteins and lipids, PI3K-Akt, EGFR and cellular response to stress. The microRNA-gene interaction network revealed miR-21, miR-155, miR-143, miR-221 and miR-23a as the nodal miRNAs, with multiple targets. MicroRNA-21 formed the focal point of the network with 42 interactions. The hub miRNAs identified in our study form putative regulatory candidates for future research on meat quality traits in Indian sheep. Our results provide insight into the biological pathways and regulatory molecules implicated in muscling traits of sheep.

Common Gene Modules Identified for Chicken Adiposity by Network Construction and Comparison

Excessive fat deposition can cause chicken health problem, and affect production efficiency by causing great economic losses to the industry. However, the molecular underpinnings of the complex adiposity trait remain elusive. In the current study, we constructed and compared the gene co-expression networks on four transcriptome profiling datasets, from two chicken lines under divergent selection for abdominal fat contents, in an attempt to dissect network compositions underlying adipose tissue growth and development. After functional enrichment analysis, nine network modules important to adipogenesis were discovered to be involved in lipid metabolism, PPAR and insulin signaling pathways, and contained hub genes related to adipogenesis, cell cycle, inflammation, and protein synthesis. Moreover, after additional functional annotation and network module comparisons, common sub-modules of similar functionality for chicken fat deposition were identified for different chicken lines, apart from modules specific to each chicken line. We further validated the lysosome pathway, and found TFEB and its downstream target genes showed similar expression patterns along with chicken preadipocyte differentiation. Our findings could provide novel insights into the genetic basis of complex adiposity traits, as well as human obesity and related metabolic diseases.

Interplay among miR-29 family, mineral metabolism, and gene regulation in Bos indicus muscle

An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.\\An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.

Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows

The aim of this study was to detect the genomic region or regions associated with metabolic clusters in early-lactation Holstein cows. This study was carried out in 2 experiments. In experiment I, which was carried out on 105 multiparous Holstein cows, animals were classified through k-means clustering on log-transformed and standardized concentrations of blood glucose, insulin-like growth factor I, free fatty acids, and β-hydroxybutyrate at 14 and 35 d in milk (DIM), into metabolic clusters, either balanced (BAL) or other (OTR). Forty percent of the animals were categorized in the BAL group, and the remainder were categorized as OTR. The cows were genotyped for a total of 777,962 SNP. A genome-wide association study was performed, using a case-control approach through the GEMMA software, accounting for population structure. We found 8 SNP (BTA11, BTA23, and BTAX) associated with the predicted metabolic clusters. In experiment II, carried out on 4,267 second-parity Holstein cows, milk samples collected starting from the first week until 50 DIM were used to determine Fourier-transform mid-infrared (FT-MIR) spectra and subsequently to classify the animals into the same metabolic clusters (BAL vs. OTR). Twenty-eight percent of the animals were categorized in the BAL group, and the remainder were classified in the OTR category. Although daily milk yield was lower in BAL cows, we found no difference in daily fat- and protein-corrected milk yield in cows from the BAL metabolic cluster compared with those in the OTR metabolic cluster. In the next step, a single-step genomic BLUP was used to identify the genomic region(s) associated with the predicted metabolic clusters. The results revealed that prediction of metabolic clusters is a highly polygenic trait regulated by many small-sized effects. The region of 36,258 to 36,295 kb on BTA27 was the highly associated region for the predicted metabolic clusters, with the closest genes to this region (ANK1 and miR-486) being related to hematopoiesis, erythropoiesis, and mammary gland development. The heritability for metabolic clustering was 0.17 (SD 0.03), indicating that the use of FT-MIR spectra in milk to predict metabolic clusters in early-lactation across a large number of cows has satisfactory potential to be included in genetic selection programs for modern dairy cows.

The Role of MicroRNAs in Muscle Tissue Development in Beef Cattle

In this review, we highlight information on microRNA (miRNA) identification and functional characterization in the beef for muscle and carcass composition traits, with an emphasis on Qinchuan beef cattle, and discuss the current challenges and future directions for the use of miRNA as a biomarker in cattle for breeding programs to improve meat quality and carcass traits. MicroRNAs are endogenous and non-coding RNA that have the function of making post-transcriptional modifications during the process of preadipocyte differentiation in mammals. Many studies claim that diverse miRNAs have an impact on adipogenesis. Furthermore, their target genes are associated with every phase of adipocyte differentiation. It has been confirmed that, during adipogenesis, several miRNAs are differentially expressed, including miR-204, miR-224, and miR-33. The development of mammalian skeletal muscle is sequentially controlled by somite commitment into progenitor cells, followed by their fusion and migration, the proliferation of myoblasts, and final modification into fast- and slow-twitch muscle fibers. It has been reported that miRNA in the bovine MEG3-DIO3 locus has a regulatory function for myoblast differentiation. Likewise, miR-224 has been associated with controlling the differentiation of bovine adipocytes by targeting lipoprotein lipase. Through the posttranscriptional downregulation of KLF6, miR-148a-3p disrupts the proliferation of bovine myoblasts and stimulates apoptosis while the miR-23a~27a~24-2 cluster represses adipogenesis. Additional to influences on muscle and fat, bta-mir-182, bta-mir-183, and bta-mir-338 represent regulators of proteolysis in muscle, which influences meat tenderness.

Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.

Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep

In the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected six lambs with very high (n = 3) and very low (n = 3) RFI values and analyzed their liver transcriptomes. A total of 101 differentially expressed genes were identified, of which 40 were upregulated and 61 were downregulated in the low-RFI group compared with that in the high-RFI group. The downregulated genes were mainly concentrated in immune function pathways, while the upregulated genes were mainly involved in energy metabolism pathways. Two differentially expressed genes, ADRA2A (encoding adrenoceptor alpha 2A) and RYR2 (ryanodine receptor 2), were selected as candidate genes for FE and subjected to single nucleotide polymorphism scanning and association analysis. Two synonymous mutations, ADRA2A g.1429 C > A and RYR2 g.1117 A > C, were detected, which were both significantly associated with the feed conversion rate. These findings provide a deeper understanding of the molecular mechanisms regulating FE, and reveal key genes and genetic variants that could be used to genetically improve FE in sheep.

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.

Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake

Background

Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals.

Results

A greater abundance of 14–3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14–3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14–3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression.

Conclusion

Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5890-z) contains supplementary material, which is available to authorized users.

Comprehensive analysis of differentially expressed profiles of non‑coding RNAs in peripheral blood and ceRNA regulatory networks in non‑syndromic orofacial clefts

Non-syndromic orofacial clefts (NSOC), which include cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO), are common congenital birth defects in humans. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs or miRs) play important roles in NSOC; however, the potential regulatory associations between them remain largely unknown. In this study, we performed next-generation RNA sequencing (RNA-seq) to identify transcriptome profiles, including mRNAs, lncRNAs and miRNAs, in patients with CL/P and CPO. A total of 36 lncRNAs, 1,341 mRNAs and 60 miRNAs were found to be differentially expressed in the CL/P group compared to the control group, and 57 lncRNAs, 1,255 mRNAs and 162 miRNAs were found to be differentially expressed in the CPO group compared to the control group. Subsequently, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to validate the expression of selected lncRNAs, miRNAs and mRNAs. In addition, bioinformatics methods were employed to explore the potential functions of ncRNAs and to construct lncRNA-miRNA-mRNA regulatory networks. To the best of our knowledge, this is the first study to comprehensively analyze regulated non-coding RNAs (ncRNAs) in CL/P and CPO, providing a novel perspective on the etiology of NSOC and laying the foundation for future research into the potential regulatory mechanisms of ncRNAs and mRNAs in NSOC.