Abstract: Soybean (Glycine max [L.] Merr.) was domesticated in China over five millennia ago; yet, its global expansion has resulted in two distinct, independently evolved breeding pools in China and the Americas. While regional breeding has optimized specific traits, a comprehensive roadmap for the reciprocal exchange of these “breeding-specific” beneficial alleles is lacking. Here, we performed a large-scale genomic dissection of 2,377 soybean accessions, integrating 8.4 million high-quality SNPs with multi-environment phenotyping across 11 locations. Through genome-wide association studies (GWAS), we identified 261 significant loci (223 novel) governing six key agronomic traits, revealing that Chinese and American germplasms have accumulated distinct sets of beneficial alleles of seed size/protein in China and oil/yield in the Americas. To harness this untapped potential, we developed the Soybean Targeted Improvement Navigation System (STINS), a framework integrating population genomics, GWAS, and genomic selection (GS). We demonstrate the potential of targeted beneficial allele introgression between populations via gene modification for rapid trait improvement. Proof-of-concept functional evaluation through CRISPR/Cas9-mediated knockout of GmST05 in an American cultivar and overexpression of a resistant GmSNAP18 haplotype in a Chinese cultivar provided experimental support for STINS-predicted targets for protein content and SCN resistance improvement. Our study provides a navigable genomic resource for “knowledge-driven design breeding”, offering a blueprint for the global exchange of elite alleles to ensure future food security.

Key words: beneficial alleles, genomic selection, GWAS, soybean, STINS