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.