While the genetic regulation of nodule formation has been well explored, the molecular mechanisms by which abiotic stresses, such as salt stress, impede nodule formation remain largely elusive. Here, we identify four APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors, GmERF13s, that are induced by salt stress and play key roles in salt-repressed nodulation. Loss of GmERF13 function increases nodule density, while its overexpression suppresses nodulation. Moreover, salt stress-inhibited nodule formation is greatly attenuated in GmERF13 loss-of-function mutants, whereas it becomes more pronounced when GmERF13 is overexpressed. Furthermore, GmERF13s can interact with Lateral Organ Boundaries Domain 16 (GmLBD16a), which attenuates GmLBD16a’s binding capacity on Expansin17c (GmEXP17c) promoter. Additionally, salt-induced GmERF13s expression relies on abscisic acid signaling, with direct promotion facilitated by GmABI5, illustrating their direct involvement in enhancing GmERF13s expression. Collectively, our study reveals a molecular mechanism by which salt stress impedes nodulation through the GmERF13-GmLBD16a-GmEXP17 module in soybean.

Stay-green syndrome (SGS) resistant germplasms serve as the cornerstone for soybean improvement. A comprehensive assessment was conducted on a panel of 1553 germplasms to evaluate their resistance to SGS through natural inoculation. Over a three-year period, one landrace, ZaoShuHeiDou, emerged as resilient to SGS, displaying a significantly reduced risk of SGS (p < 0.05) compared to its counterparts. The broad-sense heritability of SGS resistance was 0.86. Notably, landraces demonstrated a substantially lower incidence of SGS compared to improved cultivars. Furthermore, the severity of SGS correlated with several key traits pertinent to soybean improvement efforts. In field trials, the application of insecticides effectively mitigated SGS severity, whereas the use of organic fertilizers and soil sterilization had no discernible impact. A total of 83 DNA samples were successfully amplified from SGS-afflicted plants using specific primers for soybean stay-green associated virus (SoSGV), and a SoSGV LCU-1 strain was isolated. The qPCR analysis confirmed a positive correlation between SGS severity and the relative SoSGV copy number in afflicted plants. The findings of this study lay a solid foundation for the development of SGS-resistant cultivars and the exploration of underlying resistance mechanisms.

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.

The value of a novel soybean male-sterile mutation ms_LC01 in breeding practice was determined by its outcrossing properties. Then, the effects of different planting arrangements on the pod set characteristics of male-sterile plants were assessed by using orthogonal experiments at two sites. At the same time, the effects of ms_LC01 male sterility on other traits were assessed in two C₂F₂ populations. In addition, the nectar secretion and natural outcross of male-sterile plants from four ms_LC01 lines were compared with one ms1 line and one ms6 line. The results of the orthogonal experiment showed that the pod numbers and pod set rates of male-sterile plants were decisively different between the two experimental sites but not between the two levels of the other factors. Both increasing the ratio of paternal parent to maternal parent and planting the parental seeds in a mixed way, the proportion of seeds pollinated by the target parent pollen could be increased. Except for the pod number per plant trait, there was no significant difference between male-sterile plants and their fertile siblings. The amount of nectar significantly differed among the lines. Compared with ms1 and ms6 male-sterile plants, the four ms_LC01 lines possessed significantly more or similar numbers of pod sets. The results of this study lay a foundation for the future use of this mutant in soybean breeding.