Metabolic engineering of soybean for improving grain quality for animal consumption

Soybean is one of the main sources of vegetable protein used in animal feed, but its nutritional value is limited by the presence of antinutritional factors, such as protease inhibitors (Kunitz and Bowman-Birk), lectins, phytic acid, raffinose family oligosaccharides (RFOs), and saponins, which reduce the digestibility and absorption of nutrients. In recent decades, advances in metabolic engineering and functional genomics have allowed the targeting of biochemical pathways to increase the content and quality of proteins while simultaneously reducing these undesirable compounds. This work reviews the main progress achieved through transgenesis, induced mutagenesis, and precision gene editing, highlighting the role of tools such as RNAi, CRISPR/Cas9, and AlphaFold2-guided gene editing in modifying genes involved in carbon and nitrogen metabolism and storage proteins. Recent studies demonstrate that the silencing of negative regulatory genes, such as <i>CIF1</i> and <i>AIP2</i>, can elevate the protein content of seeds, while the editing of sugar transporters <i>SWEET10a</i> and <i>SWEET10b</i> allows the modulation of the oil-protein balance. Simultaneously, the inactivation of genes related to antinutritional factors has significantly reduced the expression of compounds such as phytate and protease inhibitors. The integration of new approaches, such as promoter engineering and Prime Editing, promises to further enhance the precision of genetic modifications, minimizing pleiotropic effects. Taken together, these strategies consolidate metabolic engineering as a promising tool for the development of soybean cultivars with higher protein content and quality, and with lower content of antinutritional factors, optimizing their use in animal feed.