The core premise of nutrigenomics is deceptively simple. Nutrients do not merely fuel a fish; they act as chemical signals that switch genes on and off, reshaping metabolism, immunity, and growth at the molecular level. The field emerged in the late 1990s at the intersection of nutritional science and genomics, and it has since migrated from human medicine into livestock and, more recently, into aquaculture. Farmed fish are an especially attractive target because their diets are entirely controlled by producers. If researchers can identify which genes respond to which dietary ingredients, they can in principle design feeds that maximize feed conversion efficiency, strengthen disease resistance, and even alter the nutritional profile of the fillet that reaches the consumer’s plate. The retracted review argued that this approach could transform aquaculture into a precision discipline, where rations are tailored to the genome of each species rather than formulated by trial and error.

The technological engine behind this vision is a battery of omics tools. Whole genome sequencing has supplied reference assemblies for major farmed species, while RNA sequencing, or transcriptomics, allows scientists to measure which genes are active in fish fed different diets, exposing the molecular fingerprints of each ration. Proteomics extends the analysis to the proteins those genes produce, and metabolomics captures the biochemical end products of metabolism, closing the loop between gene and physiology. Perhaps the most disruptive entry is CRISPR gene editing, which enables researchers to deliberately disable or modify genes suspected of governing feed efficiency, fatty acid synthesis, or stress tolerance, then observe the consequences. The review highlighted these tools as the foundation for identifying the genetic pathways that control how fish digest proteins, metabolize lipids, and mount immune responses, turning what was once an opaque black box into an experimentally tractable system.

Among the nutritional pathways receiving the most attention, lipid metabolism stands out. Lipids are a principal energy source for many fish, and the genes governing fatty acid synthesis, elongation, and desaturation determine whether a farmed fish can build health-promoting omega-3 fatty acids such as EPA and DHA from plant-based feed ingredients. The review cited work on hybrid grouper showing that high-lipid diets cause hepatic fat accumulation and that bile acids modulate this process. Carbohydrate metabolism presents a parallel puzzle: carnivorous fish express low levels of amylase and glucokinase and therefore handle starch poorly. A single-nuclei RNA sequencing study of largemouth bass fed high-carbohydrate diets revealed disturbed hepatic energy metabolism and activation of oxidative stress and liver fibrosis pathways, while whole genome resequencing combined with RNA sequencing linked genes such as fabp6, lpcat2, pla2g1b, and pentose phosphate pathway genes to growth performance under carbohydrate-rich, thermally fluctuating conditions.

Species-specific findings form the empirical backbone of the field. In Atlantic salmon, research has concentrated on lipid metabolism and immune function, including the identification of genes involved in omega-3 biosynthesis and pathogen resistance. One frequently cited study replaced fish oil with vegetable oil in salmon diets and used liver transcriptomics to track the consequences: genes for fatty acid biosynthesis, inflammation, and oxidative stress, including fasn, cox2, and pparα, shifted expression, signaling a fundamental rewiring of lipid handling. Tilapia has served as a model for testing plant-based alternative feeds on nutrient utilization and growth, while catfish studies have uncovered nutrigenomic pathways tied to hypoxia tolerance and feed efficiency, informing breeding programs for hardier strains. Carp, with their natural talent for carbohydrate metabolism, are being studied as candidates for sustainable plant-based feeding, a trait that could ease pressure on wild-capture fisheries that supply fishmeal.

The larval stage of farmed fish has emerged as a particularly sensitive window where nutrition leaves lasting genomic marks. Larvae are typically reared on live feeds such as rotifers and artemia, enriched with phospholipids, fatty acids, and micronutrients that support growth, survival, and disease resistance. Researchers formulating a microdiet of 22 percent lipid and 52 percent protein for pike silverside larvae found differential gene expression and overexpression of apoptotic, DNA damage repair, and oxidative stress genes, which correlated with suboptimal growth and survival, prompting a recommendation to reduce lipid content. De novo transcriptomic sequencing of tropical gar embryos and larvae identified nutrigenomic markers spanning cell cycle, digestion, muscle development, and behavioral genes. In Atlantic cod larvae, RNA sequencing and qPCR revealed that fast-moving copepod prey stimulated swimming activity, boosting glycolysis and oxidative phosphorylation in muscle cells but also elevating reactive oxygen species, a burden that prey nutritional quality must counterbalance. Adding alpha lipoic acid to pike silverside microdiets improved larval survival and feed efficiency by modulating mitochondrial biogenesis and DNA repair.

Beyond growth, nutrigenomics is being deployed to armor fish against disease through diet rather than drugs. Functional feeds enriched with probiotics, prebiotics, or plant-derived bioactive compounds have been shown to reshape the expression of immune-related genes. In rainbow trout, dietary supplementation with the probiotic Lactobacillus rhamnosus upregulated genes governing gut barrier function, including mucins and tight junction proteins, alongside immune genes such as cytokines and toll-like receptors. In Pacific white shrimp, vitamin C supplementation upregulated antioxidant defenses, including sod and cat, and immune genes including toll-like receptors and penaeidins, increasing resistance to the pathogenic bacterium Vibrio parahaemolyticus. Selenium studies in rainbow trout demonstrated that organic selenomethionine significantly upregulated antioxidant genes such as gpx1 and sod2, reducing markers of oxidative stress, while laminarin, a bioactive polysaccharide from brown algae, altered immune gene expression in abalone. Microalgal diets rich in Isochrysis galbana upregulated energy metabolism genes in Pacific oysters, and vitamin C-enriched diets in tilapia boosted SOD and CAT expression while dialing down the stress marker HSP70.

The human-health dimension of this research extends to biofortification and contaminant control. Because omega-3 fatty acids reduce cardiovascular risk and support cognitive function, researchers are pursuing fish strains genetically optimized for EPA and DHA production, including transgenic strategies that stimulate desaturase gene expression. Nutrigenomic approaches may also identify genes governing the metabolism and detoxification of heavy metals and pesticides, opening a route to fish lines that accumulate fewer contaminants and meet stricter food safety standards. The review even sketched a vision of regionally tailored products, fish engineered or selectively bred to carry more selenium or vitamin A precursors, addressing specific nutrient deficiencies in particular populations. By contrast, plant protein substitution is not without molecular cost: in zebrafish fed soybean meal, transcriptomics revealed altered lipid homeostasis through genes such as ppara, fabp2, mttp, and cyp7a1, along with mild intestinal inflammation marked by elevated pro-inflammatory cytokines.

The retraction of this particular review does not settle any of these scientific questions, but it does underscore the scrutiny that fast-moving fields attract, and it coincides with a candid discussion of the field’s unresolved problems. The review itself acknowledged that RNA sequencing and CRISPR remain expensive, that bioinformatics capacity is a bottleneck for many aquaculture facilities, and that genetically modified fish raise public acceptance concerns, biodiversity risks, and ecological hazards if transgenic animals escape and interbreed with wild populations. Looking forward, it pointed to artificial intelligence and machine learning for predicting gene-nutrient interactions and optimizing feed formulas, multi-omics integration for holistic views of fish biology, and cross-sector partnerships to build affordable technologies and responsible regulatory frameworks. Readers should consult the publisher’s retraction notice before relying on any claim from the withdrawn article, but the underlying research program it surveyed, from copepod-fed cod larvae to CRISPR-edited salmon, continues to advance in the peer-reviewed literature, carrying the promise of seafood that is healthier for people and gentler on the planet.

Subject of Research: Fish nutrigenomics and its application to sustainable aquaculture nutrition

Article Title: RETRACTED ARTICLE: Fish nutrigenomics: unravelling the genetic code for sustainable aquaculture and improved nutritional benefits

Article References: Iqbal, G., Wani, M. N., Piyushbhai, M. K., Dar, S. A., & Sharma, A. (2025). RETRACTED ARTICLE: Fish nutrigenomics: unravelling the genetic code for sustainable aquaculture and improved nutritional benefits. Blue Biotechnology, 2(1), Article 19. https://doi.org/10.1186/s44315-025-00043-9

Image Credits: AI Generated

DOI: 10.1186/s44315-025-00043-9

Keywords: nutrigenomics, aquaculture, fish nutrition, genomics, CRISPR, RNA sequencing, omega-3 fatty acids, feed efficiency, disease resistance, transcriptomics, sustainable food, retraction