Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination.

Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.

Enhancing rice panicle branching and grain yield through tissue-specific brassinosteroid inhibition.

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.

The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice.

Hybrid rice (Oryza sativa) generally outperforms its inbred parents in yield and stress tolerance, a phenomenon termed heterosis, but the underlying mechanism is not completely understood. Here, we combined transcriptome, proteome, physiological, and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000 (CY1000). In addition to surpassing the mean values for its two parents (mid-parent heterosis), CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents (over-parent heterosis or heterobeltiosis). Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance, acting in an overdominant fashion in CY1000. Furthermore, we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30. The salt-sensitive phenotypes were associated with the OsWRKY72paternal genotype or the OsAAT30maternal genotype in core rice germplasm varieties. OsWRKY72paternal specifically repressed the expression of OsGSTU26 under salt stress, leading to salinity sensitivity, while OsWRKY72maternal specifically repressed OsAAT30, resulting in salinity tolerance. These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice, providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

Brassinosteroid-dependent phosphorylation of PHOSPHATE STARVATION RESPONSE2 reduces its DNA-binding ability in rice.

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.

Leveraging brassinosteroids towards the next Green Revolution.

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.

MG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode.

The rice root-knot nematode (Meloidogyne graminicola) is one of the most destructive pests threatening rice (Oryza sativa L.) production in Asia; however, no rice resistance genes have been cloned. Here, we demonstrate that M. GRAMINICOLA-RESISTANCE GENE 1 (MG1), an R gene highly expressed at the site of nematode invasion, determines resistance against the nematode in several rice varieties. Introgressing MG1 into susceptible varieties increases resistance comparable to resistant varieties, for which the leucine-rich repeat domain is critical for recognizing root-knot nematode invasion. We also report transcriptome and cytological changes that are correlated with a rapid and robust response during the incompatible interaction that occurs in resistant rice upon nematode invasion. Furthermore, we identified a putative protease inhibitor that directly interacts with MG1 during MG1-mediated resistance. Our findings provide insight into the molecular basis of nematode resistance as well as valuable resources for developing rice varieties with improved nematode resistance.

Molecular mechanism of tillering response to nitrogen in rice.

Nitrogen (N) fertilizer acts as the main driving force for agricultural productivity improvement. However, overuse of N fertilizer has caused severe effects to environment and ecosystem. Thus, it is pivotal to improve nitrogen use efficiency (NUE) for future sustainable agriculture. Agronomic traits response to N are significant indices for NUE phenotyping. For example, tiller number, grain number per panicle, and grain weight are three major components for cereal yields. Although regulatory mechanisms regarding to these three traits have been largely reported, few is known about how N affects them. Tiller number is one of the most sensitive traits response to N and also plays a key role for N-promoted yield improvement. It is thereby of great significance to dissect the genetic basis underlying tillering response to N. In this review, we summarize the factors contributing to NUE as well as the regulatory mechanisms over rice tillering and emphasize how N affects rice tillering, future research directions are also discussed for further improving NUE.

Genomic decoding of breeding history to guide breeding-by-design in rice.

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design (BbD), but remains not well established. Here, we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China (NEC). We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study (GWAS)-detected quantitative trait loci (QTLs), or introgressions from indica sub-species with chronological changes in allele frequencies. Then we summarized a rice breeding trend/principle in NEC, and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in practice. Our study provides a paradigm for decoding the breeding history of a specific crop to guide BbD, which may have implications in different crop breeding.

Crosstalk between brassinosteroid signaling and variable nutrient environments.

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.

Toward improving nitrogen use efficiency in rice: Utilization, coordination, and availability.

Nitrogen (N) fertilizer drives crop productivity and underlies intensive agriculture, but overuse of fertilizers also causes detrimental effects to ecosystem. To cope with this challenge while meeting the ever-growing demand for food, it is critical and urgent to improve nitrogen use efficiency (NUE) of crops. To date, numerous efforts have been made in developing strategies for NUE improvement with different disciplines. Given the intricate and interconnected route of N for delivering its effect, it is necessary to comprehensively understand various procedures and their interplays in determining NUE. In this review, we expand the scope of NUE improvement, not only the N utilization by plants, but also the N coordination with other resources as well as the N availability in the soil, which represent the major dimensions in manipulating NUE. Moreover, both agronomic practices and genetic improvement in facilitating NUE are also included and discussed. Lastly, we provide our perspective in improving the NUE in the future, particularly highlighting the integration of various agronomic and genetic approaches for NUE improvement underlying the sustainable agriculture.

Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives.

The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture. Genetic improvement of crops with high nitrogen-use efficiency (NUE) is one of the most feasible solutions for tackling this challenge. In the last two decades, extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made, and a series of achievements have been obtained in crops, especially in rice. Here, we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice. Strategies for exploring the variants controlling NUE and breeding future crops with "less-input-more-output" for sustainable agriculture are also proposed.

Interplay between ethylene and nitrogen nutrition: How ethylene orchestrates nitrogen responses in plants.

The stress hormone ethylene plays a key role in plant adaptation to adverse environmental conditions. Nitrogen (N) is the most quantitatively required mineral nutrient for plants, and its availability is a major determinant for crop production. Changes in N availability or N forms can alter ethylene biosynthesis and/or signaling. Ethylene serves as an important cellular signal to mediate root system architecture adaptation, N uptake and translocation, ammonium toxicity, anthocyanin accumulation, and premature senescence, thereby adapting plant growth and development to external N status. Here, we review the ethylene-mediated morphological and physiological responses and highlight how ethylene transduces the N signals to the adaptive responses. We specifically discuss the N-ethylene relations in rice, an important cereal crop in which ethylene is essential for its hypoxia survival.

An activated form of NB-ARC protein RLS1 functions with cysteine-rich receptor-like protein RMC to trigger cell death in rice.

A key event that follows pathogen recognition by a resistance (R) protein containing an NB-ARC (nucleotide-binding adaptor shared by Apaf-1, R proteins, and Ced-4) domain is hypersensitive response (HR)-type cell death accompanied by accumulation of reactive oxygen species and nitric oxide. However, the integral mechanisms that underlie this process remain relatively opaque. Here, we show that a gain-of-function mutation in the NB-ARC protein RLS1 (Rapid Leaf Senescence 1) triggers high-light-dependent HR-like cell death in rice. The RLS1-mediated defense response is largely independent of salicylic acid accumulation, NPR1 (Nonexpressor of Pathogenesis-Related Gene 1) activity, and RAR1 (Required for Mla12 Resistance 1) function. A screen for suppressors of RLS1 activation identified RMC (Root Meander Curling) as essential for the RLS1-activated defense response. RMC encodes a cysteine-rich receptor-like secreted protein (CRRSP) and functions as an RLS1-binding partner. Intriguingly, their co-expression resulted in a change in the pattern of subcellular localization and was sufficient to trigger cell death accompanied by a decrease in the activity of the antioxidant enzyme APX1. Collectively, our findings reveal an NB-ARC-CRRSP signaling module that modulates oxidative state, the cell death process, and associated immunity responses in rice.