Lodging is a major constraint to rice productivity and grain quality. The mechanical strength of basal internodes, particularly bending resistance (BDR), is a critical determinant of lodging resistance. In this study, we evaluated the BDR of the third and fourth basal internodes (BDR3 and BDR4) in a diverse panel of 340 rice accessions. A genome-wide association study (GWAS) identified three QTLs significantly associated with BDR3, which were defined and designated as qBDR1, qBDR4, and qBDR5. Further analysis revealed that OsWRKY102 on qBDR1 was identified as a key candidate gene. Haplotype analysis revealed distinct allelic variations between subspecies, with the elite haplotypes (Hap.1 and Hap.4) contributing to superior lodging resistance, while Hap.2 was predominantly found in lodging-susceptible Japonica accessions. CRISPR/Cas9-mediated knockout of OsWRKY102 in the ZH11 background resulted in a significant reduction of more than 50% in both BDR3 and BDR4 compared to the wild type. Detailed phenotypic characterization of the oswrky102 mutants revealed a substantial decrease in cellulose content and culm diameter, accompanied by an increase in culm wall thickness. These findings demonstrate that OsWRKY102 maintains culm mechanical strength by promoting radial expansion and cellulose accumulation. Biomechanical analysis further suggests that culm diameter and cellulose content are more critical for bending strength than wall thickness. Our results elucidate the regulatory role of OsWRKY102 in coordinating culm morphology and cell wall composition, providing a valuable genetic target for molecular breeding of high-yielding, lodging-resistant rice varieties.

Deep-space conditions exert severe stress on plant genome stability, gene expression, epigenetic modification, and cell differentiation. In this study, multiomics analysis is used to observe changes in rice at the molecular and cellular levels after deep-space flight, including an increase in the frequency and types of mutations. While overall DNA methylation levels do not significantly change, CHG methylation levels present an increase that is correlated with DNA methylation responses. RNA presents significantly elevated m6A modification levels, which positively regulate gene expression. The proportion of mesophyll cells decreases, and 188 genes are identified as affecting the differentiation of mesophyll cells. Integrated multiomics analysis supports a hypothesis that the NAC family transcription factor suppressor of variation transmission 1 (SVT1) negatively regulates MAPK pathway genes, potentially influencing differentiation of cells harbouring mutations. Overall, this study comprehensively describes the molecular map of rice after deep-space flight and proposes a putative mechanism through which SVT1 may adapt to deep-space flight by inhibiting the differentiation of cells harbouring mutations.

Salt stress is an injurious concern of global climate change that negatively impacts the growth and yield of rice plants. Identifying salt tolerance genes is essential to understanding the molecular mechanism regulating salt tolerance in rice. In this study, we treated two rice varieties, Xiangxiuzhan (XXZ) and Changxiang (CXG), with 100 mM NaCl to examine the effect on the germination and growth stages. Transcriptome analysis was investigated for changes in gene expression between the two varieties. During the germination stage, the CXG variety had higher germination potential than the XXZ variety, whereas in the growth stage, the XXZ variety showed higher survival efficiency than the CXG variety. Transcriptome analysis showed that the XXZ variety had more DEGs in grains, while CXG displayed greater DEGs in leaves and roots. Gene Ontology (GO) and KEGG pathway showed that beta-alanine metabolism, cutin biosynthesis, and plant hormone signal transduction were over-represented, whereas heatmap analysis showed cellular and environmental signal transduction. This study focuses on the molecular pathways of the salt stress tolerance mechanism of Xiangxiuzhan and Changxiang varieties.

Light intensity is important for the growth of medicinal plants and the accumulation of active ingredients. This study integrated physiological and transcriptomic analyses to investigate the effects of six light intensities (25, 50, 100, 200, 400, and 600 µmol·m-2·s-1) on the morphology, physiology, and medicinal active components of Dendrobium nobile Lindl (D. nobile). The results indicated that 200 µmol·m-2·s-1 was the optimum light intensity, significantly promoting plant height (33.11

Genomic selection (GS) is a promising tool to accelerate genetic gain for complex traits. In this study, we evaluated the potential of GS for the improvement of seven lodging-related traits in double-cropping rice in Southern China using 438 rice accessions. The traits examined included the length and bending resistance of the third and fourth internodes (IL3, IL4, BR3, BR4), plant height (PH), and the ratio of internode length to plant height (IL3/PH, IL4/PH). Significant phenotypic differences were observed for all traits between the two seasons. In comparisons of cross-validation and independent prediction, GBLUP and BayesLASSO outperformed LightGBM across all traits in both seasons. Across all evaluated traits, prediction accuracies (Pearson’s r) ranged from 0.33 to 0.78 in cross-validation and from 0.28 to 0.75 in independent prediction using the GBLUP model. Bending resistance exhibited lower prediction accuracy due to its lower genomic heritability. Correlation analysis revealed that plant height was not significantly correlated with culm bending resistance, suggesting that these traits are genetically independent. We utilized GBLUP models trained on our experimental data to predict the genomic estimated breeding values (GEBVs) of the 3000 Rice Genomes Project (3kRG) dataset. The results demonstrated that GS can efficiently enrich the proportion of highly lodging-resistant accessions, increasing it from 31.40% in the base 3kRG population to a maximum of 83.00% among the top 200 selected individuals. Furthermore, indirect selection for traits with higher heritability, such as IL and IL/PH, was more effective at screening highly lodging-resistant cultivars than direct selection for BR. Our research demonstrates the feasibility of applying genomic selection for the breeding of lodging-resistant varieties in double-cropping rice and provides a foundation for further applications.

IntroductionPlant disease segmentation in real-world agricultural environments poses significant technical challenges, including complex backgrounds, diverse lesion morphologies, and extreme class imbalance.MethodsIn this paper, we propose an integrated solution, STAR-Net, which combines a novel network architecture with a dynamic training strategy. The architecture features an innovative Heterogeneous Branch Attention Aggregation (HBAA) module to robustly represent multi-scale and multi-morphology features. The training strategy employs a Dynamic Phase-Weighted Loss (DPW-Loss) to navigate the complexities of imbalanced data.ResultsOur method achieves a state-of-the-art average mIoU of 93.36% on the NLB dataset. This result demonstrates its superior ability to precisely segment diseases with specific elongated morphologies. Furthermore, the model obtains a competitive average mIoU of 41.13% on the highly challenging PlantSeg dataset. This result validates its robustness in complex 'in-the-wild' scenarios.DiscussionOur work presents a powerful, well validated, and synergistic solution for plant disease segmentation. It also paves the way for practical applications in precision agriculture.

Grain chalkiness compromises rice appearance quality and market value. The genetic basis of chalkiness reduction in indica rice remains less well understood than that in japonica. Modern Guangdong indica varieties released since the 1980s have long, translucent grains with low chalkiness, making them a suitable system to dissect quality improvement in indica. Here, we analyse whole-genome variation in 154 Guangdong indica varieties and 229 genetically diverse international indica accessions. Integrating population genomics, haplotype association analysis, and endosperm expression profiling, we identify four major chalkiness-associated genes, Wx, Chalk5, OsDER1, and OsATG8b, showing strong genetic differentiation consistent with breeding selection in Guangdong germplasm. Superior haplotypes at all four loci are significantly associated with reduced chalkiness in multi-year phenotyping in Guangzhou and in independent trials from the Philippines. Analysis of HuangHuaZhan pedigree further reveals stepwise pyramiding and fixation of these haplotypes during grain-quality improvement. Across other indica-growing provinces in southern China, favorable haplotypes at Wx and OsDER1 are largely fixed in cultivated varieties, whereas those at Chalk5 and OsATG8b remain less deployed. Variants in these four genes also enable efficient prediction of chalkiness across multiple machine learning models. Together, these results illustrate how breeding enriched favorable haplotypes for low chalkiness in indica rice.

High temperature stress is one of the important abiotic stresses for plants, which affects their in the growth and development as well as physiology. In this experiment, the appearance and morphology, physiology and biochemistry, and leaf anatomical structure of Dendrobium nobile Lindl(D. nobile) were systematically studied under high temperature stress by taking D. nobile. Firstly, the semi-lethal temperature of D. nobile was 43.08 ℃ according to the rate of cellular injury and the Logistic equation, then, 25 ℃ was chosen as the control, and the other 30 ℃, 35 ℃, and 40 ℃ were set up as the high temperature treatments. The results showed that the root, stem and leaf dry weights of the plants were significantly different under high temperature treatments at 35 °C and 40 °C compared with the control, with a decrease of 23.12

The high-frequency induction rate of haploid is crucial for double haploid (DH) breeding. The combination of multiple haploid-induced genes, such as ZmPLA1/MATL/NLD and ZmDMP, can synergistically enhance the haploid induction rate (HIR) in maize. However, the potential synergistic effects between OsMATL and OsDMP genes in rice remain unclear. Knocking out OsMATL in both HuaHang No.48 (HH48) and Nipponbare (NIP) cultivars resulted in reduced seed setting rate (SSR) and haploid induction (HI). Notably, in this study, the HI capacity of OsMATL knockout mutants in indica rice surpassed that of japonica rice knockout mutants, with the proton active site in the third exon exhibiting a higher HIR compared to the first and fourth exons. Furthermore, when OsDMP1 or OsDMP3 was combined with OsMATL, they increased HIR, and an antagonistic relationship was observed between HIR and SSR in HH48 matl4dmp1 and HH48 matl4dmp3. In rice, the proton active site in the third exon of OsMATL exhibited higher induction efficiency, and OsDMP1 or OsDMP3 exerted a synergistic effect with OsMATL. These findings provide a foundation for further research on DH breeding in rice.

Flowering time is a critical agronomic trait with a profound effect on the productivity and adaptability of rapeseed (Brassica napus L.). Strategically advancing flowering time can reduce the risk of yield losses due to extreme climatic conditions and facilitate the cultivation of subsequent crops on the same land, thereby enhancing overall agricultural efficiency. In this review, we synthesize current information on flowering time regulation in rapeseed through an integrated analysis of its genetic, hormonal, and environmental dimensions, emphasizing their crosstalk and implications for yield. We consolidate multi-omics evidence from population genetics, functional genomics, and systems biology to create a haplotype-based framework that overcomes the trade-off between flowering time and yield, providing support for the precision breeding of early-maturing cultivars. The insights presented here could inform future research on flowering time regulation and guide strategies for increasing rapeseed productivity.

Light intensity plays a pivotal role in modulating the development and secondary metabolite production of medicinal plants. This research thoroughly examines the impact of varying light levels (50 [A], 100 [B], 200 [C], 400 [D], and 600 [E] μmol m−2 s−1) on Dendrobium denneanum, focusing on its morphological traits, physiological and biochemical responses, and secondary metabolite content. Our findings indicate that an intermediate light intensity of 400 μmol m−2 s−1 markedly improves stem diameter, leaf dimensions (length and width), and the synthesis of photosynthetic pigments, including chlorophyll a, chlorophyll b, and carotenoids, with pronounced effects observed during later treatment phases. At 400 μmol m−2 s−1, antioxidant enzyme activities (CAT, POD, SOD) reached their highest levels, while malondialdehyde (MDA) levels were the lowest, indicating efficient reactive oxygen species (ROS) scavenging capacity. Soluble sugars and proteins accumulated significantly at 400 μmol m−2 s−1, supporting metabolic homeostasis and stress tolerance. Secondary metabolites (flavonoids and polyphenols) peaked at 400 μmol m−2 s−1. Principal component analysis (PCA) and resistance contribution diagrams revealed that 400 μmol m−2 s−1 achieved the highest composite scores across morphological, physiological, and metabolic indicators. This study not only pinpoints an optimal light condition for maximizing growth, ornamental characteristics, and the yield of valuable medicinal compounds in Dendrobium denneanum but also offers a scientific basis for precise, resource-efficient cultivation. These insights are valuable for enhancing the sustainable production and quality consistency of this and potentially other economically important medicinal and ornamental plants, supporting both the phytopharmaceutical and horticultural industries.

The Rapid Viscosity Analyzer (RVA) has emerged as a useful tool for comprehensive and objective evaluation of rice eating and cooking quality (ECQ), offering precise quantification of starch viscosity properties during simulated cooking processes. To dissect the genetic basis of ECQ, we performed genome-wide association studies (GWAS) on 439 genetically diverse rice accessions across two environments and identified 10 robust quantitative trait loci (QTLs) associated with RVA profile parameters. Six loci (qRVA-1.1, qRVA-1.2, qRVA-3, qRVA-5, qRVA-8 and qRVA-11) were linked to six RVA profile properties, displaying their importances in the regulation of RVA parameters. Notably, qRVA-6.1 co-localizes with Wx locus, a canonical regulator of amylose content (AC) and gel consistency (GC), and influenced breakdown value (BDV), cold paste viscosity (CPV), consistence value (CSV), hot paste viscosity (HPV) and setback value (SBV). Two novel loci, qRVA-2 and qRVA-10 were associated with retrogradation dynamics (SBV/CSV) and starch stability (BDV/CPV), respectively. Through haplotype-based analysis, we prioritized six candidate genes (LOC_Os01g65780, LOC_Os01g65880, LOC_Os02g53620, LOC_Os03g40440, LOC_Os10g34520 and LOC_Os11g01580) harboring nonsynonymous mutations or structural variations significantly altered RVA profiles, highlighting their potential as key regulators of starch viscosity properties. By integrating RVA phenotyping with genetic mapping, this study provides novel insights into the molecular mechanisms underlying ECQ and delivers valuable QTLs and candidate genes for breeding rice varieties with superior culinary characteristics.

Identifying genes resistant to anaerobic germination can provides key genetic targets for breeding direct seeding rice varieties with anaerobic tolerance. In this study, genome-wide association analysis (GWAS) was performed on coleoptile length (CL) of 591 natural rice populations under anaerobic conditions, and a total of 34 significant QTLs were identified, with eight of them co-localized with previous studies. Furthermore, through meta-analysis of 156 initial QTLs from 21 independent studies related to anaerobic germination, 37 MQTLs were identified, including 4 core MQTLs. Integration of GWAS with meta-analysis revealed the overlap between the physical interval of qCL9.5 on chromosome 9 and MQTL9.2, highlighting it as a reliable locus. Notably, our analysis pinpointed the dehydration-responsive element-binding protein 6 gene, OsDREB6, as a potential regulator impacting anaerobic germination in rice seeds. Phenotypic analysis revealed that the ko-osdreb6-1 and ko-osdreb6-2 mutants exhibited significantly increased CL and germination sprout length under aerobic treatment for 4 days compared to WT. In contrast, disruption of OsDREB6 caused reduced CL in plants seeds under under anaerobic 4-day treatment and anaerobic 3-day treatment after seed dehiscence. Additionally, the relative coleoptile lengths of the mutants after 4 days between anaerobic and aerobic treatments were significantly lower than those of WT. RNA-seq and MapMan analysis of the ko-osdreb6-1 suggested that OsDREB6 may regulate the coleoptile elongation under anaerobic conditions by affecting the expression of related genes involved in the sucrose and starch metabolism. Overall, our study demonstrated that the effectiveness of combining GWAS with meta-analysis of QTL in identifying genetic loci and key genes for improving anaerobic germination tolerance in direct seeding rice breeding.

Rice (Oryza sativa L.) seed shattering is an important agronomic trait closely associated with yield. This study identified the interaction between Oryza sativa HOMEOBOX 71 (OSH71) and the essential seed shattering gene quantitative trait locus of seed shattering on chromosome 1 (qSH1) in rice. Mutants of OSH71 exhibited defects in abscission zone development, leading to reduced seed shattering. Importantly, both qSH1 and OSH71 directly bound to the promoter of xyloglucan endotransglucosylase/hydrolase (OsXTH12) and activated its expression, with their interaction further enhancing promoter activity. OsXTH12 mutants showed decreased seed shattering, which was consistent with the findings for OSH71 mutants. Glucuronidase staining assays revealed OSH71 and OsXTH12 genes were highly induced in the abscission zone of young panicles, indicating the role of the qSH1-OSH71-OsXTH12 module in abscission zone development. OsXTH12-overexpressing lines showed a decrease in hemicellulose content in the abscission zone, leading to increased seed shattering in rice. Furthermore, ethylene levels increased in the OsXTH12-overexpressing lines. This study investigated the molecular mechanisms by which the qSH1-OSH71-OsXTH12 pathway regulates rice seed shattering, laying the foundation for deciphering the molecular modules involved in rice seed shattering regulation.

Direct seeding of rice (DS) has been widely adopted due to reduced labor cost and simpler cultivation practices. However, anaerobic flooding conditions reduce seed germination and seedling establishment. Here, a genome-wide association study (GWAS) of four coleoptile traits using 572 rice accessions subjected to 3 d of anaerobic conditions was conducted. The traits were coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD). Ninety two QTL were identified, with 59 overlapping with previously reported loci. Two rice varieties (C126 and C261) with contrasting coleoptile lengths were selected for multi-omics analyses. A specific anaerobic-responsive blue module was identified by weighted gene co-expression network analysis (WGCNA). Thirty six candidate genes were screened, including OsMYB48 that was predominantly localized in the nucleus. Loss-of-function OsMYB48 mutants exhibited significantly increased coleoptile length relative to the control under 4 d of anaerobic conditions. Endogenous hormone measurements revealed that the content of 1-aminocyclopropanecarboxylic acid (ACC), the ethylene precursor, was significantly increased in the ko-osmyb48-1 mutants. Ethylene-related genes OsACS1 and OsACO2 were also upregulated in the mutants. OsMYB48 DAP-seq identified 31 potential target genes, including WB1 and OsBURP16. Hence, anaerobic-responsive gene OsMYB48 likely acts as a transcriptional repressor of coleoptile elongation under anaerobic germination conditions, probably via the ethylene signaling pathway. This work provides a theoretical basis and genetic resources for breeding rice lines with high germination when directly sown. (c) 2025 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Lodging is the bending, collapse of stems or the uprooting of plants typically triggered by external forces like rain, irrigation, wind or dense canopy structures. It is a common physiological disorder affecting a variety of cereal and oil crops, such as maize, rice, wheat and rapeseed. Lodging reduces photosynthetic efficiency, nutrient transport and hampers mechanical harvesting resulting in substantial yield and economic loss. Therefore, enhancing lodging resistance has become a key strategy for improving yield and sustainable agriculture in rapeseed. This review analyzes the factors causing lodging in rapeseed, including root and stem lodging, and discussed key traits such as stem diameter, plant height, and internode length influencing resistance. The biochemical and physiological basis of lodging resistance is also explored, with a focus on lignin composition in stem cell walls. Furthermore the genetic basis is discussed, including quantitative trait loci (QTLs) and genes associated with stem strength. The review also considers how mapping these QTLs and identifying candidate genes can be applied to improve lodging resistance in rapeseed. In conclusion, this review underscores the critical role of lodging resistance in Brassica napus (B. napus) and provides a detailed mechanism of its physiological and mechanical basis. Lodging is a multifactorial challenge influenced by plant traits and mechanical stress, but it can be mitigated through integrated genetic and agronomic approaches. Graphical abstract shows the factors and benefits influencing crop lodging, Highlighting key elements like genetic factors and agronomic practices. It showcases benefits such as improved crop yield and enhanced grain quality, crucial for effective lodging management.

Nucleotide-binding leucine-rich repeat (NLR) genes play a critical role in plant effector-triggered immunity (ETI) against pathogen invasion. However, the regulatory mechanisms governing NLR expression and functional dynamics, particularly in head-to-head NLR gene pairs, remain poorly understood. In this study, we investigated the regulatory mechanisms, subcellular localization and functional pathways associated with Pik-H4 gene pair. Bidirectional Pik-H4 promoter (PPik-H4) strengths were found across the whole plants and exhibited co-expressed patterns in tissues and cells, and the PPik-H4 activity was upregulated in vascular bundles during blast fungus invasion. Additionally, altering the co-expression of Pik1-H4 and Pik2-H4 via overexpression in rice or Nicotiana benthamiana did not compromise the immune response. Promoter analysis identified two minimal promoter regions that are essential for bidirectional transcription, and mutagenesis of the bidirectional TATA box confirmed its role in gene regulation. This dual-function promoter coordinates Pik-H4 expression in both directions, a regulatory innovation previously unreported in NLR-mediated immunity. In planta subcellular localization revealed Pik1-H4 relocates to vesicles, indicating its role in effector recognition, while Pik2-H4 predominantly accumulated in the nucleus. These new discoveries of Pik protein extended the putative immune function of NLR pairs. Transcriptome analysis demonstrated that Pik-H4-mediated resistance induces significant transcriptome reprogramming between 12- and 24-h postinoculation. In summary, these findings provide novel insights into the regulatory complexity and functional divergence within NLR bidirectional gene pairs in response to pathogen invasion.

KEY MESSAGE:A novel allele of Badh2, badh2-I11 undergoes alternative splicing and leads to reduced Badh2 expression and enhanced 2-AP accumulation in rice. Aroma is a crucial quality trait in rice and is primarily regulated by the Badh2 gene located on chromosome 8. In this study, we identified a novel allele of Badh2, badh2-I11, in the aromatic rice variety, Hei126 (H126). This allele harbors a 55-bp deletion in intron 11, inducing alternative splicing, that generates both wild-type transcripts and aberrant transcripts containing a premature stop codon. Consequently, Badh2 mRNA levels are reduced, leading to moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of an F2 population derived from a cross between Huahang 48 (non-aromatic, Badh2/Badh2) and H126 (aromatic, badh2-I11/badh2-I11) revealed a genotypic segregation ratio 1:2:1 (Badh2/Badh2: Badh2/badh2-I11: badh2-I11/badh2-I11), consistent with Mendelian inheritance for a single codominant locus. The corresponding phenotypic ratio of non-aromatic to aromatic plants was 3:1. We developed a codominant InDel marker for efficient screening of badh2-I11 in breeding populations. This intermediate aromatic phenotype establishes H126 as a unique germplasm resource, accumulating 2-AP while retaining partial Badh2 function. Our findings elucidate a novel molecular mechanism of aroma production mediated by intronic alternative splicing and provide valuable genetic resources and molecular tools for aromatic rice breeding.

This study aimed to develop an aromatic thermosensitive genic male sterile (TGMS) line in indica rice using CRISPR/Cas9 technology. The TMS5 and FGR in the high-quality conventional rice variety Huahang 48 were targeted for editing using CRISPR/Cas9 technology. CRISPR/Cas9 vectors designed for TMS5 and FGR were constructed and introduced into rice calli through Agrobacterium-mediated transformation. Transgenic seedlings were subsequently regenerated, and the target sites of the edited plants were analyzed via sequencing. A total of fifteen T0 double mutants were successfully obtained. Three mutants without T-DNA insertion were screened in the T1 generation by the PCR detection of hygromycin gene fragments, and homozygous mutants without T-DNA insertion were screened in the T2 generation by the sequencing analysis of the mutation sites, named Huahang 48s. Huahang 48s exhibited complete sterility at 24 °C and pollen transfer at 23 °C. The 2-acetyl-1-pyrroline (2-AP) content was detected in the young panicles, leaves, and stems of Huahang 48s. The leaves of Huahang 48s had the highest 2-AP content, contrasting with the absence of 2-AP in HuaHang 48. F1 hybrids that crossed Huahang 48s with two high-quality restorer lines were superior to the two parents in terms of yield per plant and 1000-grain weight. Huahang 48s has a certain combining ability and application potential in two-line cross breeding. The successful application of CRISPR/Cas9 technology in Huahang 48 established a foundation for developing aromatic TGMS lines, providing both theoretical insights and practical materials for breeding efforts.