A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

RNA sequencing analysis revealed differentially expressed genes and their functional annotation in porcine longissimus dorsi muscle affected by dietary lysine restriction

The objective of this study was to investigate the effects of dietary lysine restriction on the global gene expression profile of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (LDD: a lysine-deficient diet; LAD: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, skeletal muscle was sampled from the longissimus dorsi of individual pigs. The muscle total RNA was isolated and cDNA libraries were prepared for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data obtained was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). A total of 80 genes (padj ≤ 0.05) were differentially expressed in the longissimus dorsi muscle of the pigs fed LDD vs. LAD, of which 46 genes were downregulated and 34 genes were upregulated. Gene Ontology (GO) analysis of the DEGs (padj ≤ 0.05) for functional annotation identified those GO terms that are mostly associated with the molecular functions of structural molecules and metabolic enzymes (e.g., oxidoreductase and endopeptidase), biological process of acute-phase response, and amino acid metabolism including synthesis and degradation in the extracellular matrix region. Collectively, the results of this study have provided some novel insight regarding the molecular mechanisms of muscle growth that are associated with dietary lysine supply.

Full-length transcriptome from different life stages of cobia (Rachycentron canadum, Rachycentridae)

Cobia (Rachycentron canadum, Rachycentridae) is one of the prospective species for mariculture. The transcriptome-based study on cobia was hampered by an inadequate reference genome and a lack of full-length cDNAs. We used a long-read based sequencing technology (PacBio Sequel II Iso-Seq3 SMRT) to obtain complete transcriptome sequences from larvae, juveniles, and various tissues of adult cobia, and a single SMRTcell generated 99 gigabytes of data and 51,205,946,694 bases. A total of 8609435, 7441673 and 9140164 subreads were generated from the larval, juvenile, and adult sample pools, with mean sub-read lengths of 2109.9, 1988.2 and 1996.2 bp, respectively. All samples were combined to increase transcript recovery and clustered into 35661 high-quality reads. This is the first report on a full-length transcriptome from R. canadum. Our results illustrate a significant increase in the identified amount of cobia LncRNAs and alternatively spliced transcripts, which will help improve genome annotation. Furthermore, this information will be beneficial for nutrigenomics and functional studies on cobia and other commercially important mariculture species.

Nutrigenomics in livestock sector and its human-animal interface-a review

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Nutrigenomics unfolds the link between nutrition and gene expression for productivity.expression profile of intramuscular.

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Nutrigenomics helps scientists discover genes and DNA in each animal's cell or tissue by assisting them in selecting nutrients.

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It brings out the importance of micronutrition for increasing animal production.

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Nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology.

Noncommunicable diseases such as cardiovascular disease, obesity, diabetes, and cancer now outnumber all other health ailments in humans globally due to abrupt changes in lifestyle following the industrial revolution. The industrial revolution has also intensified livestock farming, resulting in an increased demand for productivity and stressed animals. The livestock industry faces significant challenges from a projected sharp increase in global food and high animal protein demand. Nutrition genomics holds great promise for the future as its advances have opened up a whole new world of disease understanding and prevention. Nutrigenomics is the study of the interactions between genes and diet. It investigates molecular relationships between nutrients and genes to identify how even minor modifications could potentially alter animal and human health/performance by using techniques like proteomics, transcriptomics, metabolomics, and lipidomics. Dietary modifications mostly studied in livestock focus mainly on health and production traits through protein, fat, mineral, and vitamin supplementation changes. Nutrigenomics meticulously selects nutrients for fine-tuning the expression of genes that match animal/human genotypes for better health, productivity, and the environment. As a step forward, nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology to better understand the role of food as an epigenetic factor in the occurrence of these diseases. This review aims to provide a comprehensive overview of the fundamental concepts, latest advances, and studies in the field of nutrigenomics, emphasizing the interaction of diet with gene expression, and how it relates to human and animal health along with its human-animal interphase.

Utilizing the underutilized plant resources for development of life style foods: Putting nutrigenomics to use

Sufficient amount of minerals, vitamins, and proteins in human diet play indispensable role in maintaining the active metabolism for better human health. All the essential nutrients that are requisite for an individual's survival are acquired from plants as well as animals. Micronutrients and macronutrients directly influence the metabolic pathways and their deficiencies play a substantial role in development of manifold disorders. In addition to environmental factors, quality and quantity of foods are key factors in maintaining the human health. Transition from healthy to diseased state is concurrent with the pattern of gene expression that is largely influenced by nutrition and environment. A combined approach to study the influence of nutrition on expression of numerous genes can be well explored through nutrigenomic studies. Nutrigenomics includes studies wherein applied genomics is used to investigate nutritional science to understand the compartmentalization of genes that influence the cause of diet-related complications. This review describes the role of underutilized crops as frontline foods to circumvent the health complications through the nutrigenomic studies. Further dynamics of nutrigenomic tools to study the impact of nutrition on the changing pattern of genome stability and gene expression for developing precise safety measures against wide range of health ailments linked to metabolic networks. Additionally, this review provides detailed information on nutrigenomic studies undertaken to unravel the potential of underutilized crops to augment the human health and to carry the agronomic/genomic approaches to enhance nutritional profile of underutilized crops to overcome diet-related disorders.

Genome-wise engineering of ruminant nutrition- nutrigenomics: applications, challenges, and future perspectives – a review

Use of genomic information in ruminant production systems can help relieve concerns related to food security and sustainability of production. Nutritional genomics (i.e., Nutrigenomics) is a field of research that is interested in all types of reciprocal interactions between nutrients and genomes of organisms, i.e., variable patterns of gene expression and effect of genetic variations on the nutritional environment. Devising a revolutionizing analytical approach to traditional ruminant nutrition research, the relatively novel area of ruminant nutrigenomics has several studies concerning different aspects of animal production systems. This paper aims to review the current nutrigenomics research in the frame of how nutrition of ruminants can be modified accounting for individual genetic backgrounds and gene/diet relationships behind productivity, quality, efficiency, disease resistance, fertility, and GHG emissions. Furthermore, current challenges facing ruminant nutrigenomics are evaluated and future directions for the novel area are strongly argued by this review.

Transcriptome Profiling Associated with Carcass Quality of Loin Muscles in Crossbred Pigs

Carcass quality traits, such as lean depth and loin depth, are of extreme economic importance for the swine industry. This study aimed to identify the gene expression pattern related to carcass quality in crossbred pigs ((Landrace × Yorkshire) × Duroc). In total, 20 crossbred pigs were used in this study and they were divided into two groups (class I grade, n = 10; class II grade, n = 10) based on the carcass grades. Total RNA samples extracted from the loin muscles of both groups were submitted for RNA-seq. The quality assessment of the sequencing reads resulted in 25,458 unigenes and found 12,795 candidate coding unigenes with homology to other species after annotation. Differentially expressed gene (DEG) analysis of the two groups revealed 282 up-regulated and 189 down-regulated genes (p ≤ 0.01), linked to tissue development, striated muscle tissue development, tissue morphogenesis, and lipid metabolic process gene ontology (GO) terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis highlighted genes related to the calcium signaling pathway, melanogenesis, the sphingolipid signaling pathway, the apelin signaling pathway, and the mTOR signaling pathway. We constructed an expressed gene profile, which may serve as a resource for genomic studies focused on uncovering the molecular mechanisms underlying carcass quality in crossbred pigs.

Nutrigenomic Effects of Long-Term Grape Pomace Supplementation in Dairy Cows

Simple Summary

The aim of this study was to evaluate the effect of grape pomace (GP), the polyphenol-rich agricultural by-product, on dairy cows’ whole-blood transcriptome, milk production and composition. Twelve lactating Holstein-Friesian cows were randomly assigned to two groups; the first received a GP-supplemented diet for 60 days (group GP), whereas the second was given only a basal diet (CTR). The results reveal 40 protein-coding genes differentially expressed in the GP group when compared with the CTR group, but no effects were noticed on milk production, concentrations of crude protein, fat, casein, lactose and urea, or somatic cell count. Compared to CTR, GP had a transcriptomic signature mainly reflecting a reinforced immunogenic response.

Abstract

The increasing demand for more animal products put pressure on improving livestock production efficiency and sustainability. In this context, advanced animal nutrition studies appear indispensable. Here, the effect of grape pomace (GP), the polyphenol-rich agricultural by-product, was evaluated on Holstein-Friesian cows’ whole-blood transcriptome, milk production and composition. Two experimental groups were set up. The first one received a basal diet and served as a control, while the second one received a 7.5% GP-supplemented diet for a total of 60 days. Milk production and composition were not different between the group; however, the transcriptome analysis revealed a total of 40 genes significantly affected by GP supplementation. Among the most interesting down-regulated genes, we found the DnaJ heat-shock protein family member A1 (DNAJA1), the mitochondrial fission factor (MFF), and the impact RWD domain protein (IMPACT) genes. The gene set enrichment analysis evidenced the positive enrichment of ‘interferon alpha (IFN-α) and IFN-γ response’, ‘IL6-JAK-STAT3 signaling’ and ‘complement’ genes. Moreover, the functional analysis denoted positive enrichment of the ‘response to protozoan’ and ‘negative regulation of viral genome replication’ biological processes. Our data provide an overall view of the blood transcriptomic signature after a 60-day GP supplementation in dairy cows which mainly reflects a GP-induced immunomodulatory effect.

Dietary lysine affects amino acid metabolism and growth performance, which may not involve the GH/IGF-1 axis, in young growing pigs1

Lysine is the first limiting amino acid (AA) in typical swine diets. Our previous research showed that dietary lysine restriction compromised the growth performance of late-stage finishing pigs, which was associated with the changes in plasma concentrations of nutrient metabolites and hormone insulin-like growth factor 1 (IGF-1). This study was conducted to investigate how dietary lysine restriction affects the plasma concentrations of selected metabolites and three anabolic hormones in growing pigs. Twelve individually penned young barrows (Yorkshire × Landrace; 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (n = 6). Two corn and soybean meal based diets were formulated to contain 0.65% and 0.98% standardized ileal digestible lysine as a lysine-deficient (LDD) and a lysine-adequate (LAD) diets, respectively. During the 8-week feeding trial, pigs had ad libitum access to water and their respective diets, and the growth performance parameters including average daily gain (ADG), average daily feed intake (ADFI), and gain-to-feed ratio (G:F) were determined. At the end of the trial, jugular vein blood was collected for plasma preparation. The plasma concentrations of free AA and six metabolites were analyzed with the established chemical methods, and the hormone concentrations were analyzed with the commercial ELISA kits. Data were analyzed with Student's t-test. The ADG of LDD pigs was lower (P < 0.01) than that of LAD pigs, and so was the G:F (P < 0.05) since there was no difference in the ADFI between the two groups of pigs. In terms of free AA, the plasma concentrations of lysine, methionine, leucine, and tyrosine were lower (P < 0.05), while that of β-alanine was higher (P < 0.01), in the LDD pigs. The total plasma protein concentration was lower (P < 0.02) in the LDD pigs, whereas no differences were observed for the other metabolites between the two groups. No differences were observed in the plasma concentrations of growth hormone (GF), insulin, and IGF-1 between the two groups as well. These results indicate that the lack of lysine as a protein building block must be the primary reason for a reduced body protein synthesis and, consequently, the compromised G:F ratio and ADG. The changes in the plasma concentrations of total protein and four AA suggest that the compromised growth performance might be associated with some cell signaling and metabolic pathways that may not involve the GH/IGF-1 axis.