Genomic dissection of divergent selection reveals a roadmap for reciprocal improvement of Chinese and American soybean
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.
Authors
- Tianqing Zheng (ORCID: https://orcid.org/0000-0002-6313-3068)
- Zhongren Zhang (ORCID: https://orcid.org/0000-0002-4996-7912)
- Chengzhi Jiao (ORCID: https://orcid.org/0000-0002-7037-5217)
- Guoyu Hu (ORCID: https://orcid.org/0009-0004-3537-849X)
- Guangnan Xing (ORCID: https://orcid.org/0000-0002-2507-9195)
- Delin Li (ORCID: https://orcid.org/0000-0002-3689-3790)
- Chaosen Zhao (ORCID: https://orcid.org/0000-0001-6298-8796)
- Xiaojian Fang (ORCID: https://orcid.org/0000-0003-4685-1241)
- Yan Long (ORCID: https://orcid.org/0009-0001-0655-515X)
- Like Liu (ORCID: https://orcid.org/0009-0002-1481-7065)
- Xiaobo Wang (ORCID: https://orcid.org/0000-0002-2810-9249)
- Yanfei Li (ORCID: https://orcid.org/0000-0001-5566-7222)
- Xing Wang (ORCID: https://orcid.org/0000-0002-9214-2385)
- Lijuan Qiu (ORCID: https://orcid.org/0000-0001-5777-3344)
- Yu Tian (ORCID: https://orcid.org/0000-0002-2765-0156)
- Qiang Wang (ORCID: https://orcid.org/0009-0008-0197-4532)
- Hongmei Qiu (ORCID: https://orcid.org/0000-0001-6951-0218)
- Long Miao (ORCID: https://orcid.org/0009-0000-5470-2882)
- Xueqing Wang (ORCID: https://orcid.org/0009-0008-9388-4656)
- Hao Zhang (ORCID: https://orcid.org/0009-0003-0723-6964)
- Xin Jing (ORCID: https://orcid.org/0009-0006-3673-0701)
- Yinghui Li (ORCID: https://orcid.org/0000-0001-8940-1924)
- Yumin Wang (ORCID: https://orcid.org/0009-0007-7261-7084)
- Wen Huang (ORCID: https://orcid.org/0009-0000-3778-0520)
Institutions
- Nanjing Agricultural University (CN)
- Anhui Agricultural University (CN)
- Liaocheng University (CN)
- Heilongjiang Provincial Academy of Agricultural Sciences (CN)
- Jilin Academy of Agricultural Sciences (CN)
- Anhui Academy of Agricultural Sciences (CN)
- Sweet Potato Research Institute (CN)
- Institute of Crop Sciences (CN)
- Hebei Academy of Agriculture and Forestry Sciences (CN)
- Jiangxi Academy of Agricultural Sciences (CN)
Publication Details
- Journal
- Journal of Integrative Plant Biology
- Published
- 2026-10-15
- DOI
- https://doi.org/10.1111/jipb.70421
- Primary Topic
- Soybean genetics and cultivation
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Key Research and Development Program of China
- Agricultural Science and Technology Innovation Program