• S. Boobalan, E. Prabu*, K. Manikandan and S. Jeyaprakash Sabari
    Tamil Nadu Dr. J. Jayalalithaa Fisheries University
  • In print edition October,2020

Aquaculture has lagged far behind medical research in applying genetics improvement techniques. However last 25 year was favorable period for the development of aquaculture genomics. Nutritional science has long tradition for recommending specific diets to the farmed fishes for getting more production. Nutrigenomics is the application of high throughput genomics tool in nutritional research. Nutrigenomics is the study of “how foods affect genes and how individual differences in genetic makeup affect the ways in which animals respond to nutrients with regard to health”. Communication is an essential part of scientific life and many would regard research that is not passed on to others as being incomplete. Hence the present discussion is the bridge in between genome based technology and aquaculture nutrition programs.


Nutrigenomics is a branch of nutritional genomics and is the study of the effects of foods and food constituents on gene expression. Nutrigenomics is establishing the effects of ingested nutrients and other food components on gene expression and gene regulation. It will also determine the individual nutritional requirements based on the genetic makeup of the animal as well as the association between diet and chronic diseases. It will identify the genes involved in physiological responses to diet and the genes in which small changes, called polymorphisms and the influence of environmental factors on gene expression.

Origin of Nutrigenomics

The concept that diet influences health is an ancient one. Nutrigenomics includes known interactions between food and inherited genes, called inborn errors of metabolism, that have long been treated by manipulating the diet. The Human Genome Project of the 1990s, which sequenced the entire DNA in the human genome, jump- started the science of nutrigenomics.

Nutrigenomics brings along new terminology, novel experimental techniques and a fundamentally new approach to nutrition research, such as high- throughput technologies that enables the global study of gene expression in a cell or organism. Hence to see how molecular approach is useful in fish nutrition, the current discussion is with some recent studies on nutritional regulation of candidate gene expression.

The term genomics describes the process by which all genes present in the genome of a given species can be mapped, sequenced and characterized. Nutrigenomics applies high-throughput molecular biology techniques including sequencing and genotyping (genomics), transcriptomics, proteomics, and metabolomics. By combining information from transcriptomics, proteomics, metabolomics, and bioinformatics one can gain a comprehensive understanding of nutrient related homeostasis. Nutrigenomics brings along new terminology, novel experimental techniques and a fundamentally new approach to nutrition research, such as high-throughput technologies that enables the global study of gene expression in a cell or organism.

Nutrigenomics deal with few important concepts

1. Specific dietary profiles can modulate the delicate balance between health and disease acting either directly or indirectly on gene expression.
2. The individual genetic makeup that is the presence of polymorphisms in nutrient regulated genes affects individual risk of diseases.
3. Personalized diets which take into account individual genotype represent the ultimate goal of Nutrigenomics.

Genomics and Aquaculture

Functional genomics – the combination of genomics, proteomics, transcriptomics, and metabolomics has expanded rapidly over the last decade, but research on important aquaculture species is still relatively uncommon. Nutrigenomics uses a number of “omic” disciplines.

OMICS Technology

The terms 'Ome' and 'Omics' are derivations of the suffix -ome, which has been appended to a variety of previously existing biological terms to create names for fields of endeavor like genome, proteome, transcriptome and metabolome that are either speculative or have some tangible meaning in particular contexts. The new "global" methods of measuring families of cellular molecules, such as RNA, proteins, and intermediary metabolites have been termed "omic" technologies, based on their ability to characterize all, or most, members of a family of molecules in a single analysis. 'Omic' technologies include genomics, transcriptomics (gene expression profiling), proteomics and metabolomics. The recent availability of masses of omic data is responsible for the major growth spurt of systems biology.

1. Transcriptomics The complete collection of gene transcripts in a cell or a tissue at a given time. Transcriptomics is the study of the ‘transcriptome.’ The term transcriptome is now widely understood to mean the complete set of all the ribonucleic acid (RNA) molecules expressed in some given entity, such as a cell, tissue, or organism. Transcriptomics encompasses everything relating to RNAs. This includes their transcription and expression levels, functions, locations, trafficking, and degradation. It also includes the structures of transcripts and their parent genes with regard to start sites 5′ and 3′ end sequences, splicing patterns, and post transcriptional modifications. Transcriptomics covers all types of transcripts, including messenger RNAs (mRNAs), microRNAs (miRNAs), and different types of long non coding RNAs (lncRNAs). Modern transcriptomics uses high-throughput methods to analyze the expression of multiple transcripts in different physiological or pathological conditions and this is rapidly expanding our understanding of the relationships between the transcriptome and the phenotype across a wide range of living entities.

2. Proteomics The study of proteomes (the complete collection of proteins in a cell or tissue at a given time), which attempts to determine their role inside cells and the molecules with which they interact. Proteomics holds great promise for discoveries in nutrition research. Integrated with other advanced technologies (genomics, transcriptomics, metabolomics, and bioinformatics) and systems biology, proteomics will greatly facilitate the discovery of key proteins that function to regulate metabolic pathways and whose synthesis, degradation, and modifications are affected by specific nutrients or other dietary factors. This will aid in rapidly enhancing our knowledge of the complex mechanisms responsible for nutrient utilization, identifying new biomarkers for nutritional status and disease progression, and designing a contemporary paradigm for dietary prevention and intervention of disease.

3. Metabolomics The study of the metabolomics, which is the entire metabolic content of a cell or organism, at a given time. Currently, nutritional metabolomics research in aquaculture is an emerging field. As an emerging tool in nutrition research, metabolomics offers a unique potential to unravel the complex intertwining mechanisms involved in nutrient utilization, reproduction, growth and disease progression. Through the catabolic breakdown of macromolecules in foods and direct incorporation of smaller components, the metabolome is the receiving depot for the raw materials required by cells to synthesize new products. These materials are essential for the formation and repair of body tissues and the production of energy to support and maintain life. As signaling molecules and enzymatic cofactors, metabolites are involved in the synthesis, degradation and modification of proteins, which regulate gene expression and metabolic pathways. It is the intricate combination of these multifaceted processes which are required for biological systems to maintain homoeostasis. Metabolomics can provide important mechanistic insights to identify how regulation of homoeostatic control is disturbed in the early phases of diet-related diseases. This knowledge could be used to identify the new metabolic biomarkers for health and nutritional status and to develop strategies for the dietary prevention and intervention of diseases. Future nutrition research in aquaculture will undoubtedly be radically advanced through the application of metabolomic approaches.

Status of nutrigenomics research in aquaculture

In recent years, several research institutes and commercial feed and additive companies around the world including India have been engaged in understanding the relation between dietary/nutritional factors and metabolic or physiological effects at the molecular level. These studies have contributed towards a better understanding of specific metabolic pathways and towards assessing the nutritional control of the expression of genes corresponding to the metabolic steps involved. The muscle-growth-related gene expression is gaining better understanding in assessing the optimum amino acid requirement in fish species. Meanwhile, the immune related-gene expression had much focus in analyzing the health status of several fin fish and shell fish species.

Table 1: Nutritionally regulated genes expressed in farmed fish species
Genes Species Nutritional regulation
Muscle growth
Myogenic regulatory factors Nile tilapia + by dietary lysine levels
Myogenic regulatory factors Nile tilapia + by dietary Histidine levels
Myogenic regulatory factors Nile tilapia + by dietary tryptophan levels
Amylase (intestine/pancreas) European seabass + by dietary carbohydrate levels
Trypsin (intestine/pancreas European seabass + by dietary protein levels
Nutrient transport
Sodium-phosphate co-transporter Rainbow trout + by dietary phosphorus levels
Lipoprotein lipase (mesenteric fat tissue) Gilthead sea bream - by dietary plant protein inclusion
Protein metabolism
Glutamine synthase (liver) Rainbow trout - by dietary plant protein inclusion
Atrogin (muscle) Rainbow trout - by refeeding
Lipid metabolism
Cholesterol biosynthetic genes (liver) Atlantic salmon + by dietary vegetable oil inclusion
Delta-6 desaturase (liver) Rainbow trout + by dietary vegetable oil inclusion
Glucose metabolism
Glucokinase (liver) Rainbow trout + by dietary carbohydrate levels
Glucose-6-phosphatase (liver) Rainbow trout No regulation by dietary carbohydrate levels
Hormonal actions
Growth hormone receptor (mesenteric fat tissue) Rainbow trout + by dietary protein levels
Insulin-like growth factor I (liver) Atlantic salmon + by dietary lysine levels
Note: +, induction of gene expression; -, inhibition of gene expression

New tools available in modern research allow nutritionists to screen genetic background through transcriptomics, proteomics and metabolomics and develop dietary strategies targeted nutrition. In fact, nutrigenomics approach can be divided into 3 ways (1) Gene switching, (2) Emphasis gene-protein relation and (3) Influence of food ingredients on gene expression. To evaluate the interaction between diets and genes, DNA microarray techniques and quantitative real-time Polymerase Chain Reaction (PCR) can be applied. Two dimensional gel electrophoresis might be an important tool to explore the effect of individual amino acid on protein composition that leads to safe usage of transgenic fish in our nutrition.

To fully understand the repercussions of aquaculture feeds on fish physiology, a shift in approach is required to determine the molecular and cellular pathways that regulate responses to different diets. The new omics technologies, especially transcriptomics coupled with full genome sequences, offer enormous potential to investigate the complex relationship between fish nutrition and immunity, both in health and disease. However even though the field is advancing rapidly, there are a number of major gaps in the knowledge that need to be addressed. One of the major challenges is for example the relationship between the nutritional content of aquaculture feeds, fish intestinal microbiota and the resultant metabolites, and how these metabolites modified differently by different diets impact fish heath and their resistance to pathogens. Fish microbiota studies are advancing with deep sequencing approaches, but as yet there is little interpretation of the findings of such studies in the context of fish immune status and health. Understanding the mechanisms that underpin the links between diet, intestinal microbiota and fish health will almost certainly become a major focus in the next few years.

The final future perspective is how these omics technologies can be integrated with the ambition of generating predictive models for diet, immune system and health outcomes. Such work requires improved genome annotation, the knowledge of immune cell type-specific responses and mathematical computational expertise, which can then be combined and used to dissect the molecular mechanisms underlying the diet-immunity interactions, leading to improved health of farmed fish and sustainable aquaculture.

*Corresponding author:

E. Prabu,