Metabolic Engineering
Volume 96, 2026.
Combining pathway engineering and precursor enrichment to build a multi-trait soybean platform for aquaculture feed applications
Hyojin Kim, Truyen Quach, Kiyoul Park, Ming Guo, Hae Jin Kim, Hanh Nguyen, Huu Tam Nguyen, Rebecca E. Cahoon, Shirley Sato, Johnathan A. Napier, Chi Zhang, Tom Elmo Clemente, Edgar B. Cahoon
Engineering Pink Soybeans for Aquaculture Feed
Soy-based ingredients, often in the form of soybean protein concentrate (SPC), are widely incorporated into aquaculture feed because of their high protein content and favorable amino acid profile. However, conventional soybean meal lacks key nutrients for marine diets, including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and astaxanthin, the red pigment that gives shrimp, salmon, and trout their pink color.
These nutrients are usually added to aquafeeds from fish oil, algae, or chemical synthesis, but these sources face constraints in sustainability, cost, and scalability. Marine based ingredients also pose the risk of heavy metal accumulation, which affects feed quality and safety. These issues indicate a need to develop alternative sources of these nutrients, including engineered plant-based platforms such as soybeans.
PSI’s Edgar Cahoon and Chi Zhang, in collaboration with Tom Clemente of the UNL Plant Transformation Core Research Facility and Johnathan Napier of Rothamsted Research in the UK, set out to engineer a line of soybeans to co-produce eicosapentaenoic acid (EPA), astaxanthin, and tocotrienols, a form of vitamin E that protects the stability of the aquafeeds and fish.
They inserted nine genes from microbes and other plants into a line of soybeans. The engineered line successfully produced all three nutrients, turning the seeds a pink color showing astaxanthin, but was low (~3.8%) in EPA. It also had a lower overall oil content and struggled to germinate successfully. The team discovered a metabolic bottleneck associated with a limited ALA precursor supply.
To address the bottleneck without adding more transgenes, the team crossed the engineered line with a high-ALA soybean variety to expand the precursor pool. The result was a fourfold increase in EPA accumulation, reaching up to 14% of total fatty acids, while maintaining the astaxanthin and tocotrienol production. This produced a unique multi-trait seed in which the compounds act synergistically to create a soybean-based feed that more closely matches the composition of marine-based diets, and reduces the need for added fish oil, synthetic pigment, or vitamin E supplements.
This work shows that combining metabolic engineering with a breeding strategy can substantially increase the accumulation of high-value lipids and antioxidants in soybean seeds, improving quality and crop performance in a scalable solution for sustainable plant-based aquafeed production.
Read the article in Metabolic Engineering.