Crop ideotype breeding aims to design plant architectures that enhance yield and resource use efficiency. Accelerating this process demands a framework for assembling accurate three-dimensional (3D) architecture. This Perspective synthesizes advances in technologies and methodologies in 3D architectural phenotyping. Rapid progress has enabled translating these advances into tangible gains in breeding efficiency. To this end, we propose integrating functional-structural plant models as an overarching framework that optimizes plant architecture combinations, shifting breeding from experience-driven to predictive ideotype design. Convergence of 3D phenotyping, plant modeling and artificial intelligence holds transformative potential to accelerate breeding cycles, enhancing productivity, sustainability, and food security.

This study aimed to evaluate rice yield attributes, loach Paramisgurnus dabryanus muscle quality, and soil biochemical composition under rice monoculture (RM), rice–loach coculture (RLC), and loach monoculture (LM). This trial was conducted for 90 days, and then rice, fish muscle and soil were obtained for analyses. The results showed that there were no significant differences in rice yield attributes between the rice–loach coculture (RLC) and rice monoculture (RM) groups. However, rice–loach coculture (RLC) improved muscle quality-related parameters, including increased hardness and springiness of loach muscle. Meanwhile, muscle metabolomic analysis showed that all the differentially expressed metabolites (DEMs) in the significantly enriched pathways of lysine degradation and lysine biosynthesis were up-regulated in the rice–loach coculture (RLC) group compared with the loach monoculture (LM) group. Furthermore, the rice–loach coculture (RLC) improved soil physicochemical properties, including an increase in microbial biomass nitrogen (MBN) content and activities of soil N-acquiring enzymes (NAG and LAP). Moreover, soil microbiome analysis showed that the abundance of Candidatus Koribacter versatilis, Acidobacteria bacterium WX27 and Pseudolabrys taiwanensis was significantly increased in the rice monoculture (RM) and rice–loach coculture (RLC) groups compared with the loach monoculture (LM) group. Pairwise Spearman’s correlation analysis of the top 30 soil microbial species and soil physicochemical properties indicated that Terrimonas sp. H1YJ31 showed a highly significant positive correlation with the soil N-acquiring enzymes (N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP) and a soil C-acquiring enzyme (exo-β-1,4-glucanase C1), whereas Gaiella occulta, Methyloceanibacter marginalis and Anaerohalosphaera lusitana had a highly significant negative correlation with S-NAG, S-LAP and S-C1. In short, the improved fish muscle quality and soil biochemical composition were ascribed to the increased hardness and springiness of loach muscle and the abundance of soil Terrimonas sp. H1YJ31.

Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore cDNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes at both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrate that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for the potential breeding of rice with ideal plant architecture.

To determine the high-efficiency nitrogen (N) compensation thresholds and root biological mechanisms of indica and japonica rice under N deficiency and compensation treatments, bucket cultivation experiments were conducted from 2021 to 2022 using the indica variety Yangxianyou 918 and the japonica variety Suxiu 867. N deficiency was imposed for 0 d, 6 d, 12 d, 18 d, 24 d, and 30 d after tillering, followed by normal or double-dose N compensation using 15N-labelled urea. Samples were collected at the heading and maturity stages to systematically analyse yield components, dry matter distribution, root physiology, N metabolism enzyme activities, and rhizosphere microbial communities were systematically analysed. Compared with the nondeficiency treatment, treatment of indica rice with double-dose N compensation after 12 d of deficiency resulted in the highest yield per plant when double-dose N compensation was applied after 12 d of deficiency, with the yield increasing by 16.3-17.0%. At this threshold, nitrate reductase activity increased by 45.9%, glutamine synthetase activity by 1.07%, dehydrogenase activity by 67%, and soluble protein content by 10.7%. Dry matter allocation supported these findings, with root and panicle dry weight increasing by 33.7% and 17.1%, respectively. In contrast, japonica rice achieved its maximum yield after 18 d of N deficiency with double-dose N compensation, which was primarily driven by the effective panicle number. Compared with those in the equal-dose treatment, the root dry weight and panicle dry weight increased by 11.1% and 14.6%, respectively, and the activities of GS, NR, DHA, soluble protein, and soil urease reached their maximum levels. Microbiome analysis revealed that the alpha diversity of rhizosphere microorganisms in indica was significantly greater than that in japonica, and bacterial communities such as Actinobacteriota, Chloroflexi, Proteobacteria, Acidobacteriota and Firmicutes were strongly correlated with yield indicators, resulting in the formation of a synergistic network of biomass-enzyme activity, and microbial N metabolism. These results suggest that indica rice may achieve high N utilization efficiency through synergistic regulation of enzyme activity and microbial diversity, whereas japonica rice may rely on stable bacterial communities. These thresholds provide a precise remedial N strategy for practical applications to mitigate yield losses caused by nitrogen deficiency in the field.

Alternative polyadenylation (APA) is a widespread post-transcriptional regulation that generates transcripts with variable 3 ' untranslated region (UTR) lengths. In this study, poly(A)-tag sequencing (PAT-seq) was performed during the process of Magnaporthe oryzae infection of rice. Genome-wide dynamic changes of APA profiles were identified during the response, with widespread shortening of gene transcripts. Shortened genes were found to function in biological processes associated with stress responses. Importantly, the changes of 3 ' UTR length were negatively related to the expression levels of the corresponding genes. In addition, we found that the expression levels of miRNAs that bind to the 3 ' UTRs of the APA genes were negatively correlated with the expression levels of the corresponding APA genes. This correlation suggests a potential regulatory strategy where immune-related genes might evade miRNA-mediated repression via 3 ' UTR shortening. To assess the biological impact of these APA dynamics, we functionally characterised a representative candidate, Os05g0509500, that exhibits complex and dynamic APA site switching upon infection. Knockout of Os05g0509500 via CRISPR/Cas9 revealed its positive regulatory role in rice blast, offering initial insights into the function of APA in this disease. Several core polyadenylation protein factors were significantly differentially expressed during the rice response. Our results revealed that the precise transcriptome-wide poly(A) site selection of genes during rice blast challenge, and the relationships between miRNAs and targeted APA genes, are tightly regulated. Such a mechanism provides a new perspective for designing novel strategies to control rice blast disease.

Ustilaginoidea oryzae, the ascomycete fungus responsible for Rice False Smut (RFS), devastates global rice yields via rice panicles infection, threatening food security. To address the critical need for early pathogen detection, we developed an ultrasensitive electrochemical genosensor utilizing a gold-palladium bimetallic nanoparticle (Au-PdNPs) decorated violet phosphorene/boron nitride (VP/BN) nanohybrid. The VP/BN support, synthesized via sonication-assisted liquid-phase exfoliation, enabled the uniform anchoring of Au-PdNPs through chemical reduction, creating an enhanced conductive interface. Thiolated DNA probes immobilized on Au-PdNPs via Au-S bonds enabled specific recognition of U. oryzae DNA through hybridization. This design achieved exceptional sensitivity with a broad linear range (0.1 mu M to 10 pM) and ultralow detection limit (3.67 pM), surpassing some traditional detection methods reported at present in speed and cost-efficiency. The genosensor exhibited high specificity against non-target sequences and delivered 96.6-98 % recovery in spiked rice samples, validating its effectiveness in practical applications. By integrating nanomaterials with electrochemical amplification, this work paves the way for field-deployable portable U. oryzae diagnostics in the future, offering a transformative strategy to mitigate economic and agricultural impacts.

Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes that modulates gene expression by generating transcript variants. The development of young panicles in rice is a critical stage that determines grain number and weight. However, the regulatory mechanisms and inheritance patterns of APA during this process remain poorly understood. In this study, full-length isoform sequencing (Iso-seq) and metabolome were employed to investigate APA dynamics in the young panicle of hybrid rice variety Wufengyou T025 and in parent lines, Wufeng B and Changhui T025. This analysis revealed that approximately 80% of genes possessed two or more polyadenylation (pA) sites. These APA genes were predominantly enriched in the pathways associated with rice spikelet development, including response to external photoperiod changes, energy production and transportation, protein signal exchange, and amino acid metabolism. Notably, transcripts with a shortened 3'-untranslated region (3'UTR) exhibited elevated expression levels of their corresponding genes, suggesting that APA plays an important role in modulating gene expression. Furthermore, the variable 3'UTR of the 25% differentially expressed APA genes contained numerous miRNA binding sites, including osa-miR1848 and osa-miR5075, which are known to influence spikelet development. In the offspring, the expression levels of core APA factors during young panicle development were generally downregulated compared to the parental lines. Additionally, metabolomic analysis identified 209 and 164 differentially abundant metabolites in the offspring relative to Wufeng B and Changhui T025, respectively. Intriguingly, some of the enriched metabolic pathways overlapped with those of differentially expressed APA genes, implying that APA may influence small-molecule metabolites in pathways related to spike development. Collectively, these findings are valuable for understanding the regulation of APA and its genetic basis in young panicle development, offering new insights into the molecular mechanisms underlying this critical development stage.

Rice (Oryza sativa L.) is a staple food crop globally, and identifying genes governing grain yield is critical for food security. Although heat shock proteins (HSPs) are known for their roles in stress tolerance, the molecular mechanisms by which they regulate yield formation remain unclear. In this study, we generated knockout and overexpression lines for OsHSP20 (encoding a member of the Hsp20/alpha crystallin family, LOC_Os10g30162.1. It is also one of the four candidate genes discovered during our fine mapping of major QTLs for photosynthetic rate in rice.) and performed integrated analyses combining field phenotyping, multi-stress assays, and transcriptomics. Phenotypic analyses revealed that OsHSP20 deficiency resulted in compromised plant architecture, leaf morphology, tillering, and panicle development, leading to a significant reduction in grain setting rate; Conversely, OsHSP20 overexpression enhanced drought tolerance. Mechanistically, transcriptomic and functional analyses demonstrated that OsHSP20 maintains protein homeostasis under drought stress via its chaperone activity, this function orchestrates a coordinated regulatory network involving lipid barrier formation, antioxidant defense, and carbon allocation. Our findings establish OsHSP20 as a positive regulator of both yield and drought resilience, improving crop adaptability by balancing growth and stress responses; In addition, our previous research has shown that OsHSP20 is actually one of the important components of the main QTL for rice photosynthetic rate. Therefore, this study can provide new genetic resources and theoretical basis for cultivating rice varieties with high-yield, stress resistant, and high photosynthetic rate.

ATP-citrate lyase (ACL) is a key enzyme that catalyzes the synthesis of cytosolic acetyl-CoA, providing an essential precursor for lipid metabolism and protein modification. While prior studies have implicated ACLA in rice anther development, its regulatory role in tapetal programmed cell death (PCD) and pollen wall formation remains unclear. In this study, we identified a novel ACLA allelic mutant, acla, from the rice variety Wuyunjing 7. In this mutant, the tapetum undergoes premature degradation during the late meiotic phase, accompanied by the absence of Ubisch bodies, disordered pollen exine structure, and microspore abortion. Biochemical assays revealed a significant reduction in ACL enzyme activity in the acla mutant. Transcriptome analysis further demonstrated systematic dysregulation of genes involved in reactive oxygen species (ROS) homeostasis, lipid metabolism, ubiquitination, and cell death-related pathways. Protein–protein interaction assays confirmed that ACLA directly interacts with TDR and PTC1, two core transcription factors that regulate tapetal PCD, as well as CAD8C, a key enzyme in phenylpropanoid metabolism. Subcellular localization and bimolecular fluorescence complementation (BiFC) assays further demonstrated that ACLA co-localizes and directly interacts with these proteins in the nucleus. Collectively, these results suggest that ACLA may participate in anther development through two potential routes. One provides acetyl-CoA to sustain metabolism and another interacts with tapetum-development-related transcription factors and metabolic enzymes, thereby potentially involving a transcription-metabolism synergistic regulatory network. These findings provide new experimental evidence for understanding the molecular mechanisms underlying male fertility in rice.

The seedling stage is critically important for the development of rice plants, and rapid shoot growth has a major effect on plant morphology and yield potential. In this study, we identified a major and stable quantitative trait loci (QTL), qSL10, on chromosome 10, that controls shoot growth during the seedling stage using a high-resolution genetic map of recombinant inbred lines (RILs). Through differential gene expression and sequence analysis, we identified the candidate gene OsSL10 within the qSL10 region. OsSL10 was differentially expressed in the shoots of rice varieties with varying shoot growth rates. Functional validation using CRISPR/Cas9-mediated knockout and overexpression lines confirmed that OsSL10 regulates shoot length; knockout lines showed reduced shoot growth, and the growth of overexpression lines was enhanced. These findings highlight that OsSL10 is a key regulator of seedling shoot development; OsSL10 provides a promising target for improving seedling vigor in rice. Furthermore, the identification of new QTLs for seedling growth provides valuable insights into the genetic mechanisms governing early rice development, as well as opportunities for the breeding of high-yielding rice varieties.

RNA m6A modification plays a crucial role in plant growth and crop yield. Proteins that can recognize m6A modifications, known as m6A reader proteins, are essential for the regulatory functions of m6A in gene expression. Among mRNA modification, methylation of internal adenosine N6 positions (m6As) is the most prevalent. The functional impact of m6A modifications largely relies on reader proteins. In this study, we identified OsYTH10, a member of the rice YTH domain family protein, as a key player for recognizing and binding to mRNA m6A modification sites. The m6A-binding activity of OsYTH10 is mediated by its YTH structural domain. Knockout mutation of OsYTH10 results in early flowering in rice. Through FA-CLIP and m6A-seq analysis, we discovered that OsYTH10 binds to m6A in the 3'UTR region of mRNA. Our findings reveal that OsYTH10 stabilizes the mRNAs of target genes OsDTH7 and OsGI, thereby regulating the normal flowering process in rice under prolonged sunlight conditions. This study sheds light on the critical role of OsYTH10 in m6A-mediated gene regulation and its impact on flowering time in rice.Key messageA crucial RNA N6-methyladenosine (m6A) reader protein OsYTH10 in rice was identified to physically binds mRNA's 3'UTR via its YTH domain, stabilizing OsDTH7 and OsGI transcripts to accelerate flowering under long-day conditions.

Awn length is a significant agronomic trait in rice. To analyze the genetic mechanism of awn length in the chromosome segment substitution line 29 (CSSL29) derived from 9311 (recipient) into Nipponbare (NIP, donor), an F2 segregated population was constructed from 9311 (indica) and CSSL29. The population and candidate genes were analyzed using quantitative trait loci sequencing (QTL-seq), yeast two-hybrid assays, and 3 k and 10 k rice population databases. The results indicated that the awn length in the F2 segregating population followed a normal distribution, and the long-awn phenotype in CSSL29 was controlled by multiple genes. Through BSA sequencing data, a major QTL qAWN4 associated with rice awn length was identified on chromosome 4, containing the cloned gene An-2. Further investigation of the CSSL29 long-awn substitution segment revealed the presence of the awn length gene An-1, with both genes exhibiting an additive effect on the regulation of the long-awn phenotype. Yeast two-hybrid experiments confirmed no interaction between An-2 and An-1, suggesting that additive effect awn length regulation is not mediated through simple protein-to-protein binding. Population genetic analysis indicated that the An-2 allele was artificially selected during domestication but did not significantly differ between indica and japonica subspecies. These findings enhance our understanding of the genetic regulation of rice awn length and the domestication of long-awn rice, laying the groundwork for future research in this area.

The discovery of male sterile lines in rice laid a foundation for the successful use of heterosis in rice, greatly improved the yield per unit area of rice, and provided a strong guarantee for solving the problems of food security. As a male reproductive organ, anther development is closely related to pollen fertility. Clarifying the mechanism of anther development is of great theoretical and practical significance for rice production. In the antioxidant system, the production and clearance of reactive oxygen species (ROS) are in a state of dynamic equilibrium. In order to further explore ROS homeostasis in the development of rice anthers, this review summarizes the research progress of 21 ROS homeostasis regulation genes related to rice anther development. Among these isolated genes, three ROS-clearance genes (OsRboh1, OsRboh3 and OsHXK1) and six ROS-clearance genes (OsCATB/2, cCu/Zn-SOD1, OsALDH2b, OsCOX11, OsMT-1-4b and OsMT2b), which mainly encode enzymes, can directly regulate the content of ROS. Three genes (OsMADS3, bHLH142 and OsAGO2), encoding transcription factors, can affect anther development by directly regulating the expression of ROS homeostasis genes. It also includes 9 genes (OsSAPK2, OsRACK1B, DTC1, EDT1, OsHSP60-3B, OsBP1, ADT1, OsTMS19, and DPS1) that encode other proteins, which mainly regulate ROS levels and pollen formation through protein-protein interactions. Finally, the in-depth study of ROS homeostasis genes in rice anthers is prospected, with an aim to provide new ideas and references for revealing the molecular mechanism of rice anther development.

This study presents a detailed analysis of the molecular mechanisms involved in heat stress tolerance in rice, focusing on the endoplasmic reticulum (ER) protein processing pathway. Through RNA sequencing (RNA-seq), we identified differentially expressed genes in two rice varieties, BNP162 and BNP206, emphasizing the importance of ER quality control mechanisms in maintaining cellular balance during heat stress. We identified three novel genes, Os11g0244200, Os01g0135800, and Os04g0445100, belonging to the Hsp20/alpha crystallin family, which are upregulated in response to heat stress. These genes play essential roles in protein stabilization, folding, and preventing aggregation, critical functions for maintaining protein balance under stress conditions. The upregulation of these genes highlights their potential in enhancing thermotolerance, a key trait for rice cultivation in the face of global climate change challenges. Our findings suggest that these novel genes could be promising targets for genetic manipulation to enhance heat tolerance in rice, contributing to the development of heat-resistant rice varieties. This research provides new insights into the molecular mechanisms of heat stress adaptation and lays a solid foundation for future studies aimed at improving crop resilience to environmental stress.

This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice–frog–loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 104 individuals/667 m2), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice–frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice–frog–loach integrated systems was determined to be 1.0 × 104 individuals/667 m2. This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities.

In humans, cadmium (Cd) toxicity caused by contaminated environments is associated with numerous chronic diseases. Breeding rice with low Cd accumulation is now deemed critical for sustainable agriculture development. Here, we elucidate the crucial functions of UCLACYANIN 23 (UCL23), a small copper protein, in Cd absorption, tolerance, and accumulation through modulation of reactive oxygen signals in rice. Additionally, we demonstrate that WRKY51 binds to promoters of UCL23 and miR528, a post-transcriptional regulator of UCL23, thereby contributing to Cd regulation in a dual-modulatory manner. Furthermore, we show that the natural variation of UCL23 is important for the differential accumulation of Cd in rice grains. Finally, we reveal that Indica rice harboring the major Japonica haplotype of UCL23 significantly reduces Cd uptake in roots and Cd accumulation in grains. Together, our study not only reveals a regulatory cascade in Cd regulation but also provides valuable resources for breeding low-Cd rice cultivars.

The regulation of seed size in rice represents a significant concern within the domain of developmental biology. Nevertheless, our understanding of the mechanisms by which plants determine seed size remains limited, despite its critical importance. The transcriptome and proteome sequencing of rice kernels, derived from the recombinant inbred line (RIL) population between the large-grain line AD3 and the small-grain line AD148, were conducted at the third stage of spikelet development (stage Sp 3: formation of lemma primordium), the sixth stage of spikelet development (stage Sp 6: formation of stamen primordia), as well as nine days post anthesis (9DPA). During the stage Sp 3 and stage Sp 6, the differentially expressed genes were predominantly associated with metabolic pathways, secondary metabolite synthesis, and nitrogen metabolism. In contrast, at 9DPA, these genes were primarily involved in cysteine and methionine metabolism, biosynthesis, and protein processing. This observation indicates that the differences in grain size between the large-grain line AD3 and the small-grain line AD148 result from distinct biological processes occurring both during the early stages of glume development and the grain filling stage. Furthermore, eight genes have been identified as potential regulators of grain development, providing valuable information on the underlying mechanisms of grain development in rice.To identify the key genes, pathways, and regulatory networks controlling rice grain size by integrating transcriptomic and proteomic analyses of large-grain (AD3) and small-grain (AD148) lines at critical developmental stages.