Rice grain yield per unit area is jointly determined by panicle number per unit area,grain number per panicle,and grain weight.Among these components,grain number per panicle is widely regarded as the most effective contributor to yield improvement.However,enhancement of grain number is commonly coupled with penalties in other yield traits,such as grain size and spikelet fertility,posing a major challenge for yield improvement.Therefore,elucidating the molecular and genetic mechanisms underlying the coupling and trade-offs among yield components is essential for understanding crop yield formation and for enabling rational molecular design in crop improvement.

Seed weight is a key determinant of soybean yield; however, its underlying genetic regulation remains poorly understood. Here, besides the previously reported positive seed weight regulator GmST05/GmSW5, which encodes a protein homologue of Arabidopsis Mother of TFL1 and FT (MFT), we identify GmSW19 that exert negative effect on seed weight. GmSW19 belongs to the basic leucine zipper (bZIP) transcription factor family; it encoded bZIP transcription factor can represses GmSW5 expression. We further discover that the glycogen synthase kinase 3 (GSK3)-like kinase GmSK21 physically interacts with and phosphorylates GmSW19. A single nucleotide polymorphism (A to C), resulting in a T to P substitution in GmSW19, which alters its phosphorylation by GmSK21 and consequently its protein abundance. Functional analyses reveal that the GmSW19A variant represses GmSW5 and seed weight stronger than that of GmSW19C. Population analyses show that the heavy-seed allele GmSW19C has not been fully utilized in modern soybean breeding. These findings elucidate the genetic components and their possible interaction in determining seed weight and highlight the potential for enhancing yield in soybean.

ABSTRACT Nitrogen (N) and brassinosteroids (BRs) are key regulators of plant developmental plasticity in fluctuating nutrient environments, yet the direct molecular link coordinating these two signaling pathways remains elusive. Here, we report a synergistic interplay between nitrate and BR signaling that governs N utilization and lateral root development in rice (Oryza sativa L.). Nitrate activates BR response in a dose‐dependent manner, with maximal induction at 2.5 mM nitrate. Conversely, activated BR signaling enhances nitrate signaling and lateral root elongation, which strictly depends on the protein level of OsTCP19, a negative regulator of root growth. Nitrate‐induced BR signaling promotes OsTCP19 degradation within 2–4 h, while the BR signaling core kinase OsGSK2 interacts with and phosphorylates OsTCP19 at Ser141 and Thr289 to stabilize its protein. OsTCP19 directly binds to the promoters of nitrate‐responsive genes (e.g., OsNRT2.4, OsNADH‐GOGAT1, OsASN1) and root development genes (e.g., OsIAA3, OsPIN1b, OsARF19) to negatively regulate N responses and lateral root growth, respectively. Together, the OsGSK2‐OsTCP19 module establishes a direct molecular link between nitrate and BR signaling, coordinating N utilization and root plasticity in rice.

Plants dynamically adjust their root-to-shoot ratio (R:S) in fluctuating environments, a response often interpreted as adaptive resource allocation, although other explanations have also been proposed. Despite ongoing debates surrounding optimal partitioning theory, the active-regulation framework remains valuable for understanding R:S regulation, which is significant for improving plant resource use efficiency and thus fitness and productivity. This review synthesizes multi-scale advances, from physiology to molecular mechanisms, to outline the regulatory networks associated with coordinated root-shoot growth. We examine how major environmental factors such as light, temperature, osmotic stress, nitrogen, and phosphorus regulate R:S through distinct pathways, highlighting the photoreceptor-mediated carbon-nitrogen allocation, organ-specific thermomorphogenic responses, and the multi-layered osmotic stress networks. For nutrient regulation, we emphasize the OsWRI1a-RNR10-DNR1 module for tissue-specific R:S nitrogen response and the PHR1-centered phosphate starvation response network. We also summarize how endogenous hormones (auxin, cytokinin, abscisic acid, and strigolactone) and signaling hubs like TOR kinase regulate R:S. Finally, we discuss current challenges and future directions for a system-level understanding of R:S regulation and its targeted manipulation.

In the middle of the last century, the Green Revolution dramatically increased crop yields and transformed global agriculture. As current food production is increasingly challenged by the demands of the growing population, climate change, and environmental degradation, a new Green Revolution is urgently needed. This Review highlights recent progress in defining the morphological ideotypes of four major crops, and proposes essential physiological traits critical for crop improvement and environmental adaptation. We introduce two concepts: the 'architectype' representing optimized morphological features, and the 'physiotype' encompassing improved physiological traits. By integrating these concepts through advanced genomic technologies and precision management practices, the next Green Revolution could potentially enhance crop yields and resource use efficiency by over 20-30%, thereby ensuring sustainable food production.

Understanding the dynamic responses of rice (Oryza sativa L.) to varying durations of heat stress is crucial for developing thermotolerant crops in the face of global climate trends. Here, we evaluated the responses of rice cultivar Zhonghua11 to short-term (0.5-1 h) and long-term (12-24 h) heat stress at 45 °C. Phenotypic observations showed that short-term heat stress reduced photosynthetic pigment content without major leaf morphological changes, while long-term stress caused severe leaf drying and reduced the survival rate to 13 %. Transcriptome analysis revealed persistent inhibition of chlorophyll metabolism and photosynthesis genes under heat stress. Short-term heat stress primarily induced genes involved in reactive oxygen species scavenging and heat shock proteins, while long-term stress shifted the transcriptional profile toward DNA damage repair and chloroplast reconstruction, indicating the dynamic molecular nature of rice's response. Furthermore, set of BR-linked genes were identified from transcriptome analysis and exogenous BR application was confirmed to improve plants survival rate. Functional analyses of BR-linked genes (OsBZR1, OsBU1, and OsGSR1) confirmed that BR signaling enhances thermotolerance. Based on these results, we conclude that rice employs distinct dynamic strategies to cope with heat stress of different durations. Importantly, this study clarifies rice's dynamic strategies under heat stress and highlights BR pathways as key regulators, providing a basis for breeding heat-resilient varieties.

Spatiotemporal gene expression shapes key agronomic traits, yet tissue-specific prediction remains challenging in complex crops. We present DeepWheat, a broadly applicable deep learning framework comprising DeepEXP and DeepEPI, for accurate, tissue-specific gene expression prediction. DeepEXP integrates sequence and epigenomic features to predict gene expression (PCC 0.82-0.88), while DeepEPI predicts epigenomic maps from DNA sequence to support model transfer across varieties. Validations in five wheat cultivars confirm robustness and accuracy. DeepWheat also identifies regulatory variants with strong expression effects, enabling targeted cis-regulatory elements editing and offering a powerful tool for crop functional genomics and breeding.

Brassinosteroids (BRs) play a crucial role in regulating multiple biological processes in plants, particularly those related to crop productivity and stress tolerance. During their functioning, BRs engage in extensive and intricate interactions with other phytohormones, including auxin, cytokinins, gibberellins, abscisic acid, ethylene, jasmonates, salicylic acid, and strigolactones. These interactions facilitate the integration of internal and external signals, ultimately shaping the physiological status of the plant. In this review, we introduce BR metabolism and signaling and discuss their role in modulating agronomic traits that directly contribute to grain yield in rice (Oryza sativa), the model plant for crops. We also summarize recent advances in the crosstalk between BRs and other phytohormones in regulating agronomic traits in crops. Furthermore, we highlight significant research that provides insights into developing high-yielding and stress-resistant crop varieties from the perspective of hormone crosstalk. Understanding the genetic and molecular mechanisms through which BRs and other phytohormones collaboratively control agronomic traits offers new approaches for crop improvement.

The use of gibberellin-related dwarfing genes significantly increased grain yield during the Green Revolution. Brassinosteroids (BRs) play a vital role in regulating agronomic traits and stress resistance. The potential of BR-related genes in crop improvement has been well demonstrated, positioning BRs as crucial targets for the next agricultural biotechnological revolution. However, BRs exert pleiotropic effects on plants, and thus present both opportunities and challenges for their application. Recent research suggests promising strategies for leveraging BR regulatory molecules for crop improvement, such as exploring function-specific genes, identifying beneficial alleles, inducing favorable mutations, and optimizing spatial hormone distribution. Advancing our understanding of the roles of BRs in plants is imperative to implement these strategies effectively.

The rapid elongation of rice (Oryza sativa) coleoptile is pivotal for the plant plumule to evade hypoxia stress induced by submergence, a condition often arising from overirrigation, ponding, rainstorms, or flooding. While brassinosteroids (BRs) are recognized for their diverse roles in plant growth and development, their influence on coleoptile elongation under hypoxic conditions remains largely unexplored. In this study, we demonstrate the significant requirement of BRs for coleoptile elongation in deep water. During coleoptile development, Glycogen Synthase Kinase3-Like Kinase2 (GSK2), the central inhibitor of BR signaling in rice, undergoes substantial suppression in deep water but induction in air. In contrast, the dephosphorylated form of BRASSINAZOLE RESISTANT1 (OsBZR1), representing the active form of the key BR signaling transcription factor, is induced in water but suppressed in air. Remarkably, the knockout of GSK3-like kinase genes significantly enhances coleoptile elongation in deep water, strongly indicating a vital contribution of BR response to hypoxia-stimulated coleoptile elongation. Transcriptome analysis uncovers both BR-associated and BR-independent hypoxia responses, implicating substance metabolism, redox reactions, abiotic stress responses, and crosstalk with other hormones in the regulation of BR-induced hypoxia responses. In summary, our findings suggest that rice plumules rapidly elongate coleoptiles through the activation of BR response in deep water, enabling them to escape from submergence-induced hypoxia stress.

Brassinosteroids (BRs) are widely used as plant growth regulators in modern agriculture. Understanding how BRs regulate nutrient signaling is crucial for reducing fertilizer usage. Here we elucidate that the central BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 (GSK2) interacts directly with and phosphorylates PHOSPHATE STARVATION RESPONSE2 (OsPHR2), the key regulator of phosphate (Pi) signaling, to suppress its transcription factor activity in rice (Oryza sativa). We identify a critical phosphorylation site at serine residue S269 of OsPHR2 and demonstrate that phosphorylation by GSK2 or phosphor-mimic mutation of S269 substantially impairs the DNA-binding activity of OsPHR2, and thus diminishes expression of OsPHR2-induced genes and reduces Pi levels. Like BRs, Pi starvation noticeably induces GSK2 instability. We further show that this site-specific phosphorylation event is conserved in Arabidopsis (Arabidopsis thaliana), but varies among the PHR-family members, being present only in most land plants. These results unveil a distinctive post-transcriptional regulatory mechanism in Pi signaling by which BRs promote Pi acquisition, with a potential contribution to the environmental adaptability of plants during their evolution.

Crop yield potential is constrained by the inherent trade-offs among traits such as between grain size and number. Brassinosteroids (BRs) promote grain size, yet their role in regulating grain number is unclear. By deciphering the clustered-spikelet rice germplasm, we show that activation of the BR catabolic gene BRASSINOSTEROID-DEFICIENT DWARF3 ( BRD3 ) markedly increases grain number. We establish a molecular pathway in which the BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 phosphorylates and stabilizes OsMADS1 transcriptional factor, which targets TERMINAL FLOWER1 -like gene RICE CENTRORADIALIS2 . The tissue-specific activation of BRD3 in the secondary branch meristems enhances panicle branching, minimizing negative effects on grain size, and improves grain yield. Our study showcases the power of tissue-specific hormonal manipulation in dismantling the trade-offs among various traits and thus unleashing crop yield potential in rice.

Brassinosteroids (BRs) are a class of steroid hormones with great potential for use in crop improvement. De-repression is usually one of the key events in hormone signaling. However, how the stability of GSK2, the central negative regulator of BR signaling in rice (Oryza sativa), is regulated by BRs remains elusive. Here, we identify the U-box ubiquitin ligase TUD1 as a GSK2-interacting protein by yeast two-hybrid screening. We show that TUD1 is able to directly interact with GSK2 and ubiquitinate the protein. Phenotypes of the tud1 mutant are highly similar to those of plants with constitutively activated GSK2. Consistent with this finding, GSK2 protein accumulates in the tud1 mutant compared with the wild type. In addition, inhibition of BR synthesis promotes GSK2 accumulation and suppresses TUD1 stability. By contrast, BRs can induce GSK2 degradation but promote TUD1 accumulation. Furthermore, the GSK2 degradation process is largely impaired in tud1 in response to BR. In conclusion, our study demonstrates the role of TUD1 in BR-induced GSK2 degradation, thereby advancing our understanding of a critical step in the BR signaling pathway of rice.

The Green Revolution,which took place in the 1960s,was instrumental in increasing grain yields and mitigating the world's food crisis.Breeding semi-dwarfing crops was a critical activity that significantly improved lodging resistance,field management,and harvesting convenience.Subsequent molecular genetic studies revealed that the semi-dwarfing genes used in rice and wheat,two major staple crops,are related to the plant hormone gibberellin(GA).

Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.

Brassinosteroid（BR） represents a group of steroid hormones that regulate plant growth and development as well as environmental adaptation.The fluctuation of external nutrient elements is a situation that plants frequently face in the natural environment,in which nitrogen（N） and phosphorus（P） are two of the most critical nutrients restraint of the early growth of plants.As the macronutrients,N and P are highly required by plants,but their availability or solubility in the soil is relatively low.Since iron（Fe） and P always modulate each other’s content and function in plants mutually antagonistically,the regulatory mechanisms of Fe and P are inextricably linked.Recently,BR has emerged as a critical regulator in nutrient acquisition and phenotypic plasticity in response to the variable nutrient levels in Arabidopsis and rice.Here,we review the current understanding of the crosstalk between BR and the three major nutrients（N,P,and Fe）,highlighting how nutrient signaling regulates BR synthesis and signaling to accommodate plant growth and development in Arabidopsis and rice.

Japonica/geng and indica/xian are two major rice (Oryza sativa) subspecies with multiple divergent traits, but how these traits are related and interact within each subspecies remains elusive. Brassinosteroids (BRs) are a class of steroid phytohormones that modulate many important agronomic traits in rice. Here, using different physiological assays, we revealed that japonica rice exhibits an overall lower BR sensitivity than indica. Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms. Among these, we demonstrate that the C38/T variant in BR Signaling Kinase2 (OsBSK2), causing the amino acid change P13L, plays a central role in mediating differential BR signaling in japonica and indica rice. OsBSK2L13 in indica plays a greater role in BR signaling than OsBSK2P13 in japonica by affecting the auto-binding and protein accumulation of OsBSK2. Finally, we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice, including grain shape, tiller number, cold adaptation, and nitrogen-use efficiency. Our study suggests that the natural variation in OsBSK2 plays a key role in the divergence of BR signaling, which underlies multiple divergent traits between japonica and indica.

Brassinosteroid (BR) phytohormones play crucial roles in regulating internode elongation in rice (Oryza sativa). However, the underlying mechanism remains largely unclear. The dwarf and low-tillering (dlt) mutant is a mild BR-signaling-defective mutant. Here, we identify two dlt enhancers that show more severe shortening of the lower internodes compared to the uppermost internode (IN1). Both mutants carry alleles of ORYZA SATIVA HOMEOBOX 15 (OSH15), the founding gene for dwarf6-type mutants, which have shortened lower internodes but not IN1. Consistent with the mutant phenotype, OSH15 expression is much stronger in lower internodes, particularly in IN2, than IN1. The osh15 single mutants have impaired BR sensitivity accompanied by enhanced BR synthesis in seedlings. DLT physically interacts with OSH15 to co-regulate many genes in seedlings and internodes. OSH15 targets and promotes the expression of the BR receptor gene BR INSENSITIVE1 (OsBRI1), and DLT facilitates this regulation in a dosage-dependent manner. In osh15, dlt, and osh15 dlt, BR levels are higher in seedlings and panicles, but unexpectedly lower in internodes compared with the wild-type. Taken together, our results suggest that DLT interacts with OSH15, which functions in the lower internodes, to modulate rice internode elongation via orchestrating BR signaling and metabolism.

Plant hormone cytokinin signals through histidine-aspartic acid (H-D) phosphorelay to regulate plant growth and development. While it is well known that the phosphorelay involves histidine kinases, histidine phosphotransfer proteins (HPs), and response regulators (RRs), how this process is regulated by external components remains unknown. Here we demonstrate that protein phosphatase with kelch-like domains (PPKL1), known as a signaling component of steroid hormone brassinosteroid, is actually a cryptic inhibitor of cytokinin phosphorelay in rice (Oryza sativa). Mutation at a specific amino acid D364 of PPKL1 activates cytokinin response and thus enlarges grain size in a semi-dominant mutant named s48. Overexpression of PPKL1 containing D364, either with the deletion of the phosphatase domain or not, rescues the s48 mutant phenotype. PPKL1 interacts with OsAHP2, one of authentic HPs, and D364 resides in a region resembling the receiver domain of RRs. Accordingly, PPKL1 can utilize D364 to suppress OsAHP2-to-RR phosphorelay, whereas mutation of D364 abolishes the effect. This function of PPKL1 is independent of the phosphatase domain that is required for brassinosteroid signaling. Importantly, editing of the D364-residential region produces a diversity of semi-dominant mutations associated with variously increased grain sizes. Further screening of the edited plants enables the identification of two genotypes that confer significantly improved grain yield. Collectively, our study uncovers a noncanonical cytokinin signaling suppressor and provides a robust tool for seed rational design.

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems1,2: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT)3,4. A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.