A promoter indel in GmSTOP1a drives soybean adaptation to low-phosphorus acidic soils in low-latitude regions

Low-phosphorus (LP) availability is a major barrier to soybean cultivation in tropical and subtropical regions, where highly weathered acidic soils strongly fix phosphate. The genetic basis driving soybean adaptation to these LP environments remains largely unclear. Here, we identify a major quantitative trait locus, Superior Phosphate Acquisition 10 (SPA10), that confers enhanced phosphate acquisition efficiency in low-latitude soils. SPA10 encodes a soybean homolog of SENSITIVE TO PROTON RHIZOTOXICITY 1 (GmSTOP1a), a transcription factor central to LP and proton toxicity responses. A naturally occurring 24-bp insertion in GmSTOP1a promoter, the haplotype prevalent in high-latitude germplasms, has impaired a GmAGL12 binding site and attenuated GmSTOP1a induction under LP condition. By contrast, the promoter haplotype lacking the 24-bp insertion, which predominates in low-latitude soybean, enables strong GmAGL12-dependent activation of GmSTOP1a and downstream genes involved in organic acid secretion, including several MATE transporters. This regulatory difference determines the capacity of soybean roots to mobilize fixed phosphorus in acidic soils. Functional validation through CRISPR knockout, overexpression lines, promoter swapping, EMSA, and DAP-seq confirms GmSTOP1a as a central regulator of LP-responsive transcriptional networks and rhizosphere chemical modification. Field trials show GmSTOP1a overexpression significantly increases seed yield without P fertilizer, demonstrating its agronomic value in P-deficient soils. Population genetic analysis reveal that the superior GmSTOP1a haplotype underwent targeted artificial selection during the historical expansion of soybean into low-latitude cultivation zones. Our findings uncover a promoter-based regulatory innovation that enabled soybean to adapt to LP acidic soils and provide a mechanistic foundation for breeding P-efficient cultivars for low-latitude cultivation.