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

Hasan, M Shamimul; Feugang, Jean M.; Liao, Shengfa F

doi:10.1093/cdn/nzz082

Cited by 17 publications

(17 citation statements)

References 124 publications

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“…Among the transcriptomic approaches, RNA-sequencing (RNA-seq) simultaneously measures the differential expression of thousands of genes in any biological matrix. The resulting information can be used to determine the effects of a certain condition (e.g., a supplemented diet) from the perspective of the biological processes or molecular functions involved rather than from the expression levels of individual genes [2].…”

Section: Introductionmentioning

confidence: 99%

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

Pauletto

Elgendy

Ianni

et al. 2020

Animals

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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.

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Section: Introductionmentioning

confidence: 99%

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

Pauletto

Elgendy

Ianni

et al. 2020

Animals

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“…Traditionally, quantitative trait loci have been identified to accelerate the genetic control of economically important traits by means of various candidate genes, such as the ryanodine receptor ( RYR1 ), protein kinase AMP -activated non-catalytic subunit gamma 3 ( PRKAG3 ), fatty acid-binding protein 3 ( HFABP ), and melanocortin 4 receptor ( MC4R ) [ 9 , 10 ]. Recently, studies have investigated the transcript abundance of a group of candidate genes involved in metabolism, nutrient metabolites, and muscle structural genes [ 4 , 7 , 8 , 11 , 12 , 13 , 14 ]. These studies identified key regulatory genes that are significantly associated with pork quality and muscle characteristics in purebred pigs.…”

Section: Introductionmentioning

confidence: 99%

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

Kim

Markkandan²,

Lee³

et al. 2020

Animals

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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.

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“…RNA-Seq is used as a powerful approach for the identification of differential expression in response to specific nutrients and diets, compelling physiological conditions, such as disease, energy restriction, and vitamin and mineral deficiency in an organism. Recovering such an exclusively big data from RNA-Seq analysis provides robust and accurate information for animal nutritionists and eventually allows rations to be modified or personalized in order to improve objective traits of ruminants (Hasan et al, 2019). Quantitative Polymerase Chain Reaction (i.e., Real-Time PCR/qPCR) is a PCR-based technology that allows the validation of a small set of differentially expressed genes, usually recovered from large microarray or RNA-Seq studies.…”

Section: Techniques and Technologies Used For Nutrigenomics Researchmentioning

confidence: 99%

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

Kızılaslan¹,

Arzık²,

Çınar

et al. 2022

Annals of Animal Science

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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.

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

Cited by 17 publications

References 124 publications

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

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

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

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

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