The GmGDPD family regulates phosphorus efficiency in soybean and enables precision breeding with domestication-lost alleles.

Phosphorus (P) deficiency severely limits soybean productivity, yet the genetic basis of P efficiency remains underexplored. Here, we systematically identified 27 GmGDPD genes in soybean (Glycine max), revealing that family expansion was driven by segmental/tandem duplication events, accompanied by functional diversification through acquisition of protein kinases, catalytic domain-like kinase and GUB_WAK_bind domains. Transcriptome and reverse transcription quantitative PCR analyses demonstrated that genes, including GmGDPD2/9/12/14, were significantly induced under low Pi stress, correlating with enhanced root apical meristem activity. Haplotype association analysis across 559 soybean accessions identified elite haplotypes (GmGDPD4-Hap4, GmGDPD9-Hap3, GmGDPD14-Hap4, and GmGDPD12-Hap4) associated with enhanced Pi efficiency traits. Notably, these superior haplotypes were enriched in wild soybeans (Glycine soja) but drastically reduced in cultivated varieties due to domestication bottlenecks. A high-accuracy kompetitive allele-specific PCR marker targeting GmGDPD2-Hap5 enabled rapid screening of Pi-efficient germplasm. Hydroponic validation confirmed that Hap5 materials significantly enhanced root traits under low Pi conditions, with 41% longer roots, 36% larger root surface area, 31% the relative root volume, and 100% relative root tip number compared to non-Hap5 genotypes. Evolutionary analyses highlighted soybean-specific domain innovation in the GmGDPD members, suggesting adaptive roles in coordinating phospholipid metabolism and kinase signaling under Pi stress. Our findings propose an allele-replenishment strategy to reintroduce wild-derived Pi-efficient alleles into modern cultivars, bridging the gap between domestication-driven allele loss and sustainable breeding. The functional markers and mechanistic insights established here advance precision breeding for reducing fertilizer dependency while stabilizing yields in Pi-deficient soils, offering a genomic toolkit for soybean improvement.