Functional analysis of GmMATE gene family in soybean phosphorus homeostasis and abiotic stress resilience.

The Multidrug and Toxic Compound Extrusion (MATE) transporters play critical roles in plant stress adaptation, yet their functional diversity in soybean remains underexplored. Here, we identified 121 GmMATE genes through genome-wide analysis, revealing significant expansion compared to Arabidopsis (56) and rice (46). Phylogenetic classification divided these into five clades associated with citrate efflux, flavonoid transport, disease resistance, detoxification, and hormone regulation. Evolutionary analysis highlighted tandem/segmental duplications as key drivers of GmMATE family expansion. Promoter cis-element profiling uncovered stress-responsive motifs (ABRE, ARE), suggesting hormonal and abiotic stress regulatory roles. Single-cell RNA sequencing unveiled tissue-specific expression patterns, with GmMATE12 and GmMATE85 highly expressed in seed, while GmMATE21 and GmMATE27 were enriched in root epidermis and cortex. Membrane/vacuolar localization of selected GmMATEs supported their roles in metabolite transport. Under low phosphorus (Pi), salt, and drought stresses, key GmMATEs (GmMATE12) exhibited dynamic expression shifts, validated by RT-qPCR. GmMATE12 and GmMATE50 were strongly induced under Pi deficiency, while GmMATE2 and GmMATE89 responded to NaCl and drought. Crucially, GmMATE12 overexpression improved root architecture and phosphorus use efficiency (PUE) by 30-35 % under Pi limitation, while silencing compromised these traits, suggesting its dual role in morphological and physiological adaptation. Overall, our multi-omics dissection of GmMATEs establishes a framework for leveraging transporter diversity in soybean improvement and providing actionable targets for improving soybean nutrient efficiency and stress tolerance through molecular breeding, with GmMATE12 serving as a prime target for engineering phosphorus-efficient and stress-resilient varieties.