Which key genes enable the Penaeus vannamei shrimp to thrive on 100% plant-based diets?

The economic and environmental sustainability of the international shrimp farming sector faces a critical challenge: a heavy reliance on fishmeal as the primary protein source. Currently, formulated feeds account for 40% to 60% of total production costs, while pressure on wild fish stocks underscores the urgent need for viable alternatives. Although plant-based alternatives—such as soybean and peanut meals—emerge as cost-effective and stable substitutes, the complete replacement of marine protein often introduces setbacks, notably fluctuations in growth rates and an increase in residual feed intake (RFI).

To address this dilemma, a team of scientists from Shanghai Ocean University, the Yellow Sea Fisheries Research Institute of the Chinese Academy of Fishery Sciences, and Nanjing Agricultural University utilized advanced transcriptomic tools. The study aimed to identify the exact biological mechanisms that enable specific lineages of Pacific white shrimp (Penaeus vannamei) to optimally utilize 100% plant-based diets, with findings now available in the prestigious international scientific journal Animals.

Key Study Insights

• High Individual Variability: A wide disparity in growth and feed efficiency (RFI) exists among shrimp from the same population when reared on plant-based diets.
• Identification of 7 Critical Genes: Seven “hub” genes closely linked to high efficiency on plant-based diets were discovered and validated.
• Coordination of Two Key Organs: Five of the key genes operate within the intestine and two in the hepatopancreas, regulating energy and digestion.
• Independence from Growth: The majority of these genes were demonstrated to link specifically to metabolic feed efficiency rather than directly regulating body growth.

The Antinutritional Challenge of Plant-Based Ingredients

The Pacific white shrimp (Penaeus vannamei) stands out in commercial markets due to its rapid growth and remarkable resilience; however, its digestive system originally evolved to process highly palatable marine proteins. Consequently, plant-based protein sources introduce antinutritional factors that typically trigger oxidative stress, non-specific immune responses, and intestinal inflammation in the crustacean.

Biological Efficiency: The Key Role of RFI

To counteract this impact, traditional selective breeding methods prove insufficient without a thorough understanding of the underlying biological mechanisms. In this scenario, the concept of Residual Feed Intake (RFI) becomes fundamental. RFI quantifies the difference between the feed a shrimp consumes and what it theoretically should ingest based on its weight and growth rate; thus, a negative RFI identifies a highly efficient individual—one that consumes less feed yet produces the same amount of biomass.

The Shrimp’s Metabolic Secret: Experimental Design and Transcriptomics

To unravel these mechanisms, the researchers designed an experimental feed completely free of fishmeal (0%); instead, they formulated a diet containing 37.5% soybean meal and 17% peanut meal, ensuring a 38% crude protein content. The study involving Penaeus vannamei specimens—sourced from a fast-growing commercial line—was conducted in two strategic phases:

Phase 1: Feeding Trial and Tissue Sequencing

In the first stage, 480 individuals were evaluated in individual culture units to accurately record each specimen’s actual feed consumption. After 42 days, 50 shrimp exhibiting extreme differences in their RFI (feed efficiency) were selected, and this group underwent transcriptome sequencing across three essential target tissues: the intestine, hepatopancreas, and muscle.

Phase 2: WGCNA Bioinformatic Analysis and Population Validation

Subsequently, using Weighted Gene Co-expression Network Analysis (WGCNA), the scientific team identified which gene modules were activated or inhibited based on the animal’s metabolic efficiency. To consolidate the study’s scientific rigor, the findings were validated the following year in an independent population of 450 shrimp from 30 distinct genetic families.

The Seven Molecular Drivers of Feed Efficiency

Transcriptomic analysis revealed critical findings for the sector; while muscle tissue showed no significant association with feed efficiency—likely because it serves as an effector tissue for locomotion rather than metabolic regulation—the crustacean’s intestine and hepatopancreas unveiled crucial molecular networks.

Out of an initial pool of 20 candidate genes, rigorous validation in the second independent population robustly confirmed the direct involvement of 7 specific hub genes (q < 0.1):

The 5 Gut Guardians (Pink Module)

The 2 Hepatopancreas Drivers (Dark Green Module)

• LOC113809216 (V-type proton ATPase subunit D): V-ATPases act as essential proton pumps; by acidifying lysosomal compartments, they radically increase protease activity, enabling the shrimp to cleave and digest complex plant protein chains.
• LOC113820990 (Ribonuclease kappa-B): Co-expressed in coordination with the V-ATPase pump, it appears to fulfill critical roles in cellular autophagy, nucleic acid homeostasis, and the physiological maintenance of the hepatopancreas under restrictive stress.

Practical Applications in the Aquaculture Industry

The discovery of these seven molecular biomarkers marks a pivotal milestone for marker-assisted selection (MAS) programs. By identifying early on which families or individuals exhibit higher natural expression of these hub genes when fed plant-based diets, genetic breeders can develop shrimp lines optimized to assimilate fishmeal-free feeds. This innovation will not only significantly reduce farm operating costs but also accelerate the global transition toward a shrimp farming industry with a substantially lower ecological footprint.

Challenges and Study Limitations

Despite the success of their findings, the authors cautiously clarify that additional research in massive populations with broader genetic diversity is required before commercial deployment. Furthermore, incorporating a conventional fishmeal-fed control group in subsequent experimental designs remains pending; this will precisely determine whether these seven genes specifically mediate the adaptive response to plant ingredients or if they belong to a universal digestive efficiency mechanism in the crustacean.

Conclusions

This research concludes that the efficient adaptation of Penaeus vannamei to plant-based diets is mediated by a coordinated molecular network between the intestine and the hepatopancreas. The discovery of this biological framework redefines our understanding of how marine invertebrates tolerate nutritional stress, demonstrating that both organs work in perfect synchrony to optimize mitochondrial protein transport, carbohydrate metabolism, cellular pH homeostasis, and epigenetic regulation.

Reference (open access):
Zhang, H., Xu, Y., Sui, J., Fu, Q., Liu, M., Tan, J., Kong, J., Luo, K., Meng, X., Luan, S., & Dai, P. (2026). Identification of Key Genes Associated with Feed Utilization Efficiency in Penaeus vannamei Fed a Plant-Based Diet Using WGCNA. Animals, 16(10), 1480. https://doi.org/10.3390/ani16101480

Milthon Lujan

Editor at the digital magazine AquaHoy. He holds a degree in Aquaculture Biology from the National University of Santa (UNS) and a Master’s degree in Science and Innovation Management from the Polytechnic University of Valencia, with postgraduate diplomas in Business Innovation and Innovation Management. He possesses extensive experience in the aquaculture and fisheries sector, having led the Fisheries Innovation Unit of the National Program for Innovation in Fisheries and Aquaculture (PNIPA). He has served as a senior consultant in technology watch, an innovation project formulator and advisor, and a lecturer at UNS. He is a member of the Peruvian College of Biologists and was recognized by the World Aquaculture Society (WAS) in 2016 for his contribution to aquaculture.