Oxidizing the odds: FAD-linked oxidase flavoenzymes empower cotton for cadmium-free harvests

Anthropogenic activities enhance the concentration of trace elements in environment like highly carcinogenic Cadmium (Cd), which adversely affect the plant growth and development. They deliberately accumulate defense compounds e.g., flavonoids, terpenoids, and alkaloids to ensure resilience in such adverse conditions. Current study explores the adaptive evolution, structural complexity, and functional roles of Flavin Adenine Dinucleotide (FAD)-linked oxidase genes in widespread leading cash crop cotton. As a non-edible, hyperaccumulator halophyte crop, cotton is an excellent candidate for phytoremediation of Cd-polluted soils by manipulating stress resistant genetic material. They utilize FAD as a cofactor to drive oxidative reactions, including benzylisoquinoline alkaloid biosynthesis, which plays a critical role in cellular signaling pathways, stress responses and metabolic processes. A total of 387 FADs retrieved from four cotton species were distributed into seven families and twelve subfamilies. They underwent large scale expansion under intense purifying selection with lineage-specific gene loss and retention, reflecting their ongoing evolution for functional advancements to adopt altering environment. High throughput transcriptomic, functional enrichment and qRT-PCR validation revealed their multifaceted roles in growth, development and stress responses. Overexpression of GhBBE59 ( BBE7 ) in Arabidopsis enhanced Cd tolerance by 25 % marked by a 20 % reduction in malondiadehyde (MDA) and 25 % higher superoxide dismutase (SOD) activity compared to wild type plants. While its knockdown in cotton, reduced Proline accumulation by 60 % and increased electrolyte leakage by 2 fold, rendering plants hypersensitity to Cd stress. Transcriptomic and biochemical analyses demonstrated that BBE7 modulates redox homeostasis via 25 % higher glutathione accumulation and hormonal crosstalk, mitigating oxidative damage. Functional analyses further revealed the pivotal role of BBE7 in regulation of oxidative stress, antioxidant production, epigenetic modifications and proline accumulation, thereby enhancing stress resilience. These findings hold substantial promise for reducing cadmium accumulation in soils, thereby mitigating its entry into the food chain and associated health risks. The implications of current study extend beyond fundamental research, addressing real-world challenges associated with environmental stresses and sustainable agriculture practices by enabling safer cultivation in polluted environments. Graphical abstract representing the scheme of study and short summary of key findings. • Cotton's GhBBE59 gene enhances cadmium tolerance via redox and hormonal crosstalk. • Genome-wide analysis identifies 387 FAD oxidases with lineage-specific evolution in cotton. • GhBBE59 silencing increases cadmium sensitivity; overexpression boosts plant resilience. • FAD oxidases modulate Proline and antioxidants to mitigate cadmium-induced oxidative stress. • GhBBE59 -engineered cotton enables eco-friendly phytoremediation of cadmium-polluted soils.