GmBES1-1 dampens the activity of GmNSP1/2 to mediate brassinosteroid inhibition of nodulation in soybean

A Comprehensive Transcriptome Atlas Reveals the Crucial Role of LncRNAs in Maintaining Nodulation Homeostasis in Soybean

Symbiotic nitrogen fixation (SNF) provides nitrogen for soybean. A primary challenge in enhancing yield through efficient SNF lies in striking a balance between its high energy consumption and plant growth. However, the systemic transcriptional reprogramming during nodulation remains limited. Here, this work conducts a comprehensive RNA-seq of the roots, cotyledons and leaves of inoculated-soybean. This work finds 88,814 mRNAs and 6,156 noncoding RNAs (ncRNAs) across various organs. Notably, this work identifies 6,679 nodulation-regulated mRNAs (NR-mRNAs), 1,681 long noncoding RNAs (lncRNAs) (NR-lncRNAs), and 59 miRNAs (NR-miRNAs). The majority of these NR-RNAs are associated with plant-microbial interaction and exhibit high organ specificity. Roots display the highest abundance of NR-ncRNAs and the most dynamic crosstalk between NR-lncRNAs and NR-miRNAs in a GmNARK-dependent manner. This indicates that while each tissue responds uniquely, GmNARK serves as a primary regulator of the transcriptional control of nodulated-plants. Furthermore, this work proves that lnc-NNR6788 and lnc-NNR7059 promote nodulation by regulating their target genes. This work also shows that the nodulation- and GmNARK-regulated (NNR) lnc-NNR4481 negatively regulates nodulation through miR172c within a competing endogenous RNA (ceRNA) network. The spatial organ-type transcriptomic atlas establishes a benchmark and provides a valuable resource for integrative analyses of the mechanism underlying of nodulation and plant growth balance.

GmWRKY33a is a hub gene responsive to brassinosteroid signaling that suppresses nodulation in soybean (Glycine max)

Brassinosteroids (BRs) are key phytohormones influencing soybean development, yet their role in symbiosis remains unclear. Here, the RNA-Seq was used to identify important gene associated with BRs and symbiotic nitrogen fixation, and the function of candidate gene was verified by transgenic hairy roots. The result shows that the RNA-Seq analysis was conducted in which BR signaling was found to suppress nodule formation and many DEGs enriched in immunity-related pathways. WGCNA analyses led to the identification of GmWRKY33a as being responsive to BR signaling in the context of symbiosis establishment. Transgenic hairy roots analyses indicated that GmWRKY33a served as a negative regulator of the establishment of symbiosis. The qRT-PCR analysis confirmed that BR signaling upregulates GmWRKY33a, leading to nodulation suppression and activation of soybean immune responses. In summary, our research revealed that BR suppresses root nodule formation by modulating the immune signaling pathway in soybean roots. We further identified that GmWRKY33a, a crucial transcription factor in BR signaling, plays a negative role in the symbiotic establishment.

GmERF13 mediates salt inhibition of nodulation through interacting with GmLBD16a in soybean

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.

Functions and Mechanisms of Brassinosteroids in Regulating Crop Agronomic Traits

Brassinosteroids (BRs) perform crucial functions controlling plant growth and developmental processes, encompassing many agronomic traits in crops. Studies of BR-related genes involved in agronomic traits have suggested that BRs could serve as a potential target for crop breeding. Given the pleiotropic effect of BRs, a systematic understanding of their functions and molecular mechanisms is conducive for application in crop improvement. Here, we summarize the functions and underlying mechanisms by which BRs regulate the several major crop agronomic traits, including plant architecture, grain size, as well as the specific trait of symbiotic nitrogen fixation in legume crops. For plant architecture, we discuss the roles of BRs in plant height, branching number and leaf erectness, and propose how progress in these fields may contribute to designing crops with optimal agronomic traits and improved grain yield by accurately modifying BR levels and signaling pathways.

Soluble humic acid suppresses plant immunity and ethylene to promote soybean nodulation

Symbiotic nitrogen fixation (SNF) is a crucial process for nitrogen geochemical cycling and plant-microbe interactions. Water-soluble humic acid (WSHM), an active component of soil humus, has been shown to promote SNF in the legume-rhizobial symbiosis, but its molecular mechanism remains largely unknown. To reveal the SNF-promoting mechanism, we conducted transcriptomic analysis on soybean treated with WSHM. Our findings revealed that up- and downregulated differentially expressed genes (DEGs) were mainly involved in plant cell-wall/membrane formation and plant defence/immunity in the early stage, while the late stage was marked by the flavonoid synthesis and ethylene biosynthetic process. Further study on representative DEGs showed that WSHM could inhibit GmBAK1d-mediated immunity and BR signalling, thereby promoting rhizobial colonisation, infection, and nodulation, while not favoring pathogenic bacteria colonisation on the host plant. Additionally, we also found that the ethylene pathway is necessary for promoting the soybean nodulation by WSHM. This study not only provides a significant advance in our understanding of the molecular mechanism of WSHM in promoting SNF, but also provides evidence of the beneficial interactions among the biostimulator, host plant, and soil microbes, which have not been previously reported.