Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

Soybean (Glycine max [L.] Merr.) is a food and oil crop whose growth and yield are influenced by root and nodule development. In the present study, GmNMHC5 was found to promote the formation of nodules in overexpressing mutants. In contrast, the number of nodules in Gmnmhc5 edited with CRISPR/Cas9 decreased sharply. In 35S:GmNMHC5 mutants, expression levels of genes involved in nodulation were significantly up-regulated. Both in vitro and in vivo biochemical analyses showed that GmNMHC5 directly interacted with GmGAI (a DELLA protein), and the content of gibberellin 3 (GA₃) in overexpressing mutants was lower than that in the wild type. These results revealed that GmNMHC5 participates in the classical GA signaling pathway, and may regulate the content of GA₃ to match the optimal concentration required for nodule formation, thereby promoting nodulation by directly interacting with GmGAI. A model illustrating the mechanism by which GmNMHC5 promotes soybean nodulation is presented.

Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding. Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding. We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China. Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations: Northeast China (NE) versus the Huang-Huai-Hai River Valley and South China (HS). A total of 309 selective regions were identified as being impacted by geographical origins. The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population. To study the association between phenotypic differences and geographical origins, we recorded the vegetative period under different growing conditions for two years, and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin. By iteratively calculating accumulated genetic diversity, we established a platform panel of cultivars and have proposed a novel breeding strategy named “Potalaization” for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the “plateau” for accumulating elite loci and traits, breeding novel widely adapted cultivars, and upgrading breeding technology. In addition to providing new genomic information for the soybean research community, the “Potalaization” strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.

Staygreen syndrome or Zhengqing in soybean has recently become a major issue for Chinese growers in the Huang-Huai-Hai river basin. Although previous studies revealed that staygreen can be induced when pods/seeds are damaged, it is unknown whether virus infection or insect infestation causes staygreen. To determine whether viral infection causes staygreen, a survey of soybean staygreen incidence in the Huang-Huai-Hai river basin was conducted in 2016 and 2017. Diseased samples were collected and analyzed using DAS-ELISA for Soybean mosaic virus, Watermelon mosaic virus, Bean pod mottle virus, Cucumber mosaic virus, and Bean common mosaic virus. The survey showed that the severity of soybean staygreen syndrome was most prevalent in Beijing, Henan, Shaanxi, and some parts of Shandong provinces, with yield losses from 0 to nearly 100%, but only a small fraction of samples were positive for the tested viruses. A field cage experiment and an insecticide treatment field trial were conducted to determine the contribution of the bean bug, Riptortus pedestris, to staygreen incidence. The field cage experiment showed that R. pedestris treatment resulted in shorter plants, more empty pods, increased numbers of abnormal seeds, and decreased yields. The field experiment showed that there were fewer R. pedestris and less soybean staygreen incidence in fields treated with insecticide than in untreated control fields. Together, these results suggest that R. pedestris infestation rather than virus infection induces staygreen syndrome and that growers in this region can mitigate staygreen syndrome via bean bug control.

Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids, and saponins, were quantified in 763 soybean samples collected from widely distributed regions across China from 2010 to 2013. A majority of the tested bioactive components showed generally declining trends from the north (high latitude) to the south (low latitude). A positive relationship between total oligosaccharides (TO) and altitude was observed. Total isoflavones (TI), phospholipids (TP) and TO were negatively correlated with cumulative temperature above or equal to 15 ℃ (AT₁₅) and mean daily temperature (MDT), but positively correlated with diurnal temperature range (DTR) and hours of sunshine (HS). Total saponins (TS) were negatively correlated with MDT but positively correlated with rainfall (RF), whereas TO were negatively correlated with RF. Path-coefficient analysis showed that, besides genotype differences, temperature and HS during the reproductive period influenced TI and TP contents, while temperature and RF influenced TS and TO. The effects of weather factors on soybean bioactive components in diverse regions of China were characterized. These findings will be helpful in promoting soybean production for functional food purposes.

Soybean (Glycine max (L.) Merr.) is a non-native and non-staple crop in sub-Saharan Africa (SSA) with potential to be a commercial crop owing to its wide range of uses as food, feed, and industrial raw material. Soybean was first introduced to SSA by Chinese traders in the 19th century and was cultivated as an economic crop as early as 1903 in South Africa. In the past four decades, soybean cultivation area and production in SSA has increased exponentially, from about 20,000 ha and 13,000 t in the early 1970s to 1,500,000 ha and 2,300,000 t in 2016. Soybean yield has been stagnant in SSA for decades at about 1.1 t ha⁻¹, much lower than the world average, representing one of the most challenging issues in the soybean industry in SSA. The low soybean yield in SSA can be attributed to the use of poor-performing varieties and to the limited application of fertilizers and rhizobial inoculants in soils with no history of soybean production. South Africa, Nigeria, Zambia, and Uganda are the leading soybean producers in SSA. Soybean research in SSA is conducted by international and national research institutions, including IITA, national soybean improvement programs, universities, and the private sector. Between 1970 and 2011, 195 soybean varieties were released by IITA, private breeders, and national soybean improvement programs in SSA. This paper reviews the history and current state of soybean production and of the utilization and adoption of tropical varieties in SSA, addresses the major soybean yield-limiting factors across the region, and discusses the potential of the soybean industry in SSA. It also highlights soybean improvement efforts and lessons learned from previous soybean improvement efforts and the current progress of some national soybean improvement programs in SSA. Opportunities for scaling up tropical soybean as a major crop across SSA countries are promising.

Leaves provide substances and signals for pod and seed development in soybean. However, the regulatory feedbacks of pod and seed to leaf development remain unclear. We investigated the effects of pod and seed on leaf senescence by conducting pod removal and seed injury experiments. Pod removal and seed injury delayed leaf senescence and caused the staygreen phenotype of leaves. There were dosage effects of pod number on the extent of staygreen in depodded plants. The concentrations of chlorophyll (SPAD value, an index of relative chlorophyll content), soluble protein, and soluble sugar in the leaves of depodded plants were higher than those of intact plants. During seed development, the content of IAA decreased, while that of ABA increased. This trend was more pronounced in intact than in depodded and seed-injured plants. The GA₃/ABA ratio decreased gradually in all treatments. The content of GA₃ was relatively stable and was higher in intact than in depodded plants. The expression levels of four senescence-related genes, GmSARK, GmSGR1, GmCYN1, and GmNAC, declined in depodded or seed-injured treatments and were positively correlated with the number of leaves retained on plants. GmFT2a, the major flowering-promoting gene, was expressed at a higher level while E1, a key flowering inhibitory gene, was expressed at a lower level in depodded than in intact plants. We propose that the pod or seed can regulate leaf development. When the seed is aborted owing to disease infection or pest attack, the leaves stay green because of the absence of the seed signals for senescence.