Search Results (238)

Rice blast and bacterial blight are two major diseases that seriously threaten rice production. Developing rice germplasm with enhanced resistance to multiple diseases while maintaining favorable agronomic traits is essential for sustainable breeding. In this study, two rice landraces from Motuo County, Xizang Autonomous Region, China, Benglinba and Gare, were used to simultaneously edit OsERF922 and Xa41 using a structurally optimized dual-target CRISPR/Cas9 vector, pRGEB32-2T. A total of 32 and 28 T₀ transgenic plants were generated in the Benglinba and Gare backgrounds, respectively. Targeted mutagenesis generated eight homozygous oserf922 mutants and three homozygous xa41 mutants in Benglinba, and four and five homozygous mutants in Gare. Twelve double homozygous mutant lines (nine Benglinba and three Gare) were selected for further analysis. Disease resistance assays showed that these double mutants exhibited significantly enhanced resistance to the rice blast fungus strain GDYJ7 and the bacterial blight pathogen strain GDXO-1, with markedly reduced lesion size or lesion length compared with wild-type plants (p < 0.001, Student’s t-test). Importantly, three independent T-DNA-free double mutant lines from each genetic background displayed no significant differences from their corresponding wild types in major agronomic traits, including plant height, effective panicle number, panicle length, seed-setting rate, or thousand-grain weight (p > 0.05). Grain quality parameters, such as brown rice rate, milled rice rate, amylose content, and gel consistency, were also unaffected. Overall, this study generated rice materials with enhanced resistance to rice blast and bacterial blight while maintaining elite agronomic and quality traits, providing valuable germplasm resources and a feasible strategy for the precise improvement of disease resistance in rice landraces from Xizang Autonomous Region. Full article

Rice is a key food crop worldwide, but its yield and quality are severely constrained by insect pests. As environmental and regulatory restrictions on chemical pesticides grow, developing insect-resistant rice varieties has become a sustainable way to protect food security. This review covers recent progress in functional genomics and molecular marker mapping related to insect resistance in rice. We highlight the identification, cloning, and functional analysis of resistance genes targeting major pests, including the brown planthopper, rice gall midge, white-backed planthopper, small brown planthopper, and rice leaf roller. Several important resistance genes (such as Bph14, Bph3, and Bph29) have been cloned, and their roles in rice immunity have been clarified—covering insect feeding signal recognition, activation of salicylic acid and jasmonic acid pathways, and regulation of MAPK cascades, calcium signaling, and reactive oxygen species production. We also discuss how molecular marker-assisted selection, gene pyramiding, and transgenic techniques are used in modern rice breeding. Finally, we address future challenges and opportunities, stressing the importance of utilizing wild rice germplasm, understanding insect effector–plant immune interactions, and applying molecular design breeding to create long-lasting insect-resistant rice varieties that can withstand changing pest pressures and climate conditions. Full article

Background: The coordinated improvement of yield, quality and resistance is a primary goal in rice breeding. Gene editing technology is a novel method for precise multiplex gene improvement. Methods: In this study, we constructed a multiplex CRISPR/Cas9 vector targeting yield-related genes (GS3, OsPIL15, Gn1a), fragrance gene (OsBADH2) and rice blast resistance gene (Pi21) to pyramid traits for enhanced yield, quality, and disease resistance in rice. A tRNA-assisted CRISPR/Cas9 multiplex gene editing vector, M601-OsPIL15/GS3/Gn1a/OsBADH2/Pi21-gRNA, was constructed. Genetic transformation was performed using the Agrobacterium-mediated method with the japonica rice variety Xin Dao 53 as the recipient. Mutation editing efficiency was detected in T₀ transgenic plants. Grain length, grain number per panicle, thousand-grain weight, 2-acetyl-1-pyrroline (2-AP) content, and rice blast resistance of homozygous lines were measured in the T₃ generations. Results: Effectively edited plants were obtained in the T₀ generation. The simultaneous editing efficiency for all five genes reached 9.38%. The individual gene editing efficiencies for Pi21, GS3, OsBADH2, Gn1a, and OsPIL15 were 78%, 63%, 56%, 54%, and 13%, respectively. Five five-gene homozygous edited lines with two genotypes were selected in the T₂ generation. In the T₃ generation, compared with the wild-type (WT), the edited homozygous lines showed increased grain number per panicle (14.60–25.61%), increased grain length (7.39–11.16%), increased grain length–width ratio (8.37–13.02%), increased thousand-grain weight (3.79–9.15%), a 42–64 folds increase in the fragrant substance 2-AP content, and significantly enhanced rice blast resistance. Meanwhile, there were no significant changes in other agronomic traits. Conclusions: CRISPR/Cas9-mediated multiplex gene editing technology enabled the simultaneous editing of genes related to rice yield, quality, and disease resistance. This provides an effective approach for obtaining new japonica rice germplasm with blast resistance, long grains, and fragrance. Full article

Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops. Full article

Small-grained rice varieties are highly valued in hybrid seed production and food markets because of their unique advantages in mechanized seed production and cooking qualities. Developing new varieties combining small grain size with high nutritional and cooking quality represents an important breeding objective. The OsVIN2 gene has been identified as a key regulator involved in carbohydrate metabolism and grain development in rice. In this study, a CRISPR/Cas9-mediated gene-editing approach was employed to precisely modify the OsVIN2 gene in the restorer line MH86 of high-quality rice varieties. Compared with the wild-type plants, the frameshift mutant seeds showed a significant reduction in length and width by 19.9% and 15.2%, respectively, leading to a 39.2% decrease in thousand-grain weight. Notably, the mutant exhibited improved quality traits, including a decrease of 16.6% in amylose content, an increase of 11.0% protein, and a 77.5% and 84.7% decrease in chalkiness rate and chalkiness degree, respectively. These results demonstrate that targeted editing of OsVIN2 is a promising approach for creating novel small-grained rice germplasm with superior quality attributes. Full article

Sometimes, crop breeding varieties demonstrate high resistance to target insects under laboratory conditions but exhibit significantly low resistance in the field. This research aimed to explain this phenomenon based on inter-species interactions among insects, as herbivory by one insect species can trigger physiological changes in plants that enhance their attraction to other insect species. The striped stem borer (SSB), Chilo suppressalis (Walker), and the brown planthopper (BPH), Nilaparvata lugens (Stål), are pests of rice (Oryza sativa L.) that cause major losses in grain production. In this study, we investigated BPH performance and behavior on the planthopper-resistant rice variety “Mudgo” with pre-feeding of SSB. BPHs showed better growth and development, as well as feeding behavior, on SSB-damaged plants compared to undamaged plants. Then, gene expression and phytohormone analysis revealed that jasmonic acid (JA) biosynthesis was induced by SSB feeding. The JA pathway is a central defense signaling hub in rice responding to chewing herbivores like SSB; however, our findings reveal that its induction can have contrasting ecological consequences, inadvertently reducing resistance to a subsequent piercing-sucking pest (BPH). Finally, we discovered that volatile emissions induced by SSB damage attracted BPH and benefited its development. In summary, we found that JA biosynthesis triggered by SSB herbivory played a vital role in rice defense against BPH. This provides insight into the molecular and biochemical mechanisms underlying BPH preferences for SSB-damaged rice plants. Our study emphasizes the crucial role of inter-species interactions in enhancing host plant resistance to insect pests and evaluating germplasm resistance. These findings can serve as a basis for controlling BPH. Full article

The morphology of rice grains represents one of the most vital agronomic characteristics, significantly impacting both grain productivity and the subsequent milling and nutritional quality of the crop. A comprehensive understanding of the genetic basis and molecular drivers of grain shape is vital for the targeted breeding of high-performance rice lines with consistent yield stability. To pinpoint the genomic regions influencing grain dimensions, we conducted a genome-wide association analysis across a panel of 231 distinct rice accessions, focusing on the discovery of loci associated with length and width. Our analysis revealed four consistent quantitative trait loci (QTLs) distributed across chromosomes 3, 4, and 11. Notably, grain length was associated with qGL3.1, qGL3.2, and qGL11. The first two were co-localized with GS3 and SMG3, respectively, whereas qGL11 likely constitutes a novel locus. One QTL, qGW4, which governs grain width, was found to co-localize with the gene OsOFP14. Haplotype analysis further revealed that the characteristic haplotypes of the candidate genes for qGL3.1, qGL3.2, and qGW4 were enriched in eight germplasm accessions (including Newbonnet, Skybonnet, and Lemont), all of which exhibit a slender-grain phenotype. This finding suggests that the specific combination of these characteristic haplotypes is a common genetic signature of slender-grain rice, serving as a potential gene combination for the targeted improvement of rice grain shape. Our results reveal valuable QTLs and candidate genes and highlight specific germplasm resources that can be readily applied in marker-assisted breeding to improve rice grain shape. Full article

Shanlan upland rice is a unique genetic resource from the mountainous regions of Hainan, China, yet its genetic diversity and agronomic potential remain poorly characterized. This study systematically evaluated 114 Shanlan upland rice landraces using phenotypic assessment and 38 genome-wide Insertion/Deletion (InDel) markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, and yield components. The molecular analysis revealed a moderate level of genetic diversity (average PIC = 0.43) and consistently grouped the landraces into three distinct genetic subpopulations. To facilitate efficient germplasm management, we developed a DNA fingerprinting system using a reduced set of 19 core InDel markers, which was integrated with a phenotypic QR code database. Furthermore, a network-based strategy identified a core collection of 54 accessions, streamlining the resource for future breeding and conservation efforts. These findings provide a robust molecular framework for the conservation and genetic improvement of Shanlan upland rice. Full article

Phospholipase D (PLD) genes play key roles in plant abiotic stress responses, but the systematic identification of the maize (Zea mays) PLD family and its cold tolerance mechanism remain unclear. Using 26 maize genomes (pangenome), we identified 21 ZmPLD members via Hidden Markov Model (HMM) search (Pfam domain PF00614), including five private genes—avoiding gene omission from single reference genomes. Phylogenetic analysis showed ZmPLD conservation with Arabidopsis and rice PLDs; Ka/Ks analysis revealed most ZmPLDs under purifying selection, while three genes (including ZmPLD15) had positive selection signals, suggesting roles in maize adaptive domestication. For ZmPLD15, five shared structural variations (SVs) were found in its promoter; some contained ERF/bHLH binding sites, and SVs in Region1/5 significantly regulated ZmPLD15 expression. Protein structure prediction and molecular docking showed conserved ZmPLD15 structure and substrate (1,2-diacyl-sn-glycero-3-phosphocholine) binding energy across germplasms. Transgenic maize (B73 background) overexpressing ZmPLD15 was generated. Cold stress (8–10 °C, 6 h) and recovery (24 h) on three-leaf seedlings showed transgenic plants had better leaf cell integrity than wild type (WT). Transgenic plants retained 45.8% net photosynthetic rate (Pn), 47.9% stomatal conductance (Gs), and 55.8% transpiration rate (Tr) versus 7.6%, 21.3%, 13.8% in WT; intercellular CO₂ concentration (Ci) was maintained properly. This confirms ZmPLD15 enhances maize cold tolerance by protecting photosynthetic systems, providing a framework for ZmPLD research and a key gene for cold-tolerant maize breeding. Full article

Nitrogen (N) is an essential nutrient for the growth and development of rice. However, excessive N fertiliser application and low N Use Efficiency (NUE) have led to serious environmental problems and threatened agricultural sustainability. In this study, we compared the physiological and transcriptomic profiles of roots of two cultivars exposed to normal nitrogen (NN) and low nitrogen (LN). The results showed that the LN treatment suppressed root growth and severely affected enzymatic activities in the roots of both rice cultivars compared to the NN treatment. Moreover, HJ753 exhibited significantly higher activities of NITRATE REDUCTASE (NR) and GLUTAMINE SYNTHETASE (GS) in its roots than DJ8 under both LN and NN conditions. Transcriptomic analysis identified 23,205 genes across all samples, with more than 5000 differentially expressed genes (DEGs) detected in response to LN stress in both cultivars. The KEGG analysis revealed that the DEGs were primarily involved in DNA replication, tryptophan metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and N metabolism. Under LN stress, most genes associated with tryptophan metabolism and phenylpropanoid biosynthesis pathways remained stable or were upregulated in both cultivars. In contrast, genes related to auxin signalling transduction, N metabolism, and N utilisation exhibited significant genotype-specific expression patterns between HJ753 and DJ8. In conclusion, this study elucidated the genotypic differences in root development and N response mechanisms under LN stress at the molecular level, providing new insights into the regulatory mechanisms of N efficiency that may be used to develop and support the breeding of N-efficient rice cultivars. Full article

The average pairwise dissimilarity (APD) between one plant sample and other assayed samples based on genetic markers was developed in 2006 to assess genetic distinctness and genetic redundancy in a plant germplasm collection. With the availability of abundant genomic variants across a genome, APD can be expanded to measure individual genomic distinctness. This study was conducted to assess the applicability of APD estimates in measuring the individual genomic distinctness of 1789 indica and 854 japonica rice samples based on published genome-wide single-nucleotide polymorphism (SNP) and structural variant (SV) data. It was found that the acquired APD estimates were weakly or not correlated between the SNP and SV data sets in the indica or japonica samples, respectively. For the indica samples, the APD estimates based on the SNP and SV data ranged from 0.1779 to 0.3277 and from 0.2297 to 0.4096, respectively. For the japonica samples, the SNP-based and SV-based APD estimates varied from 0.1774 to 0.3029 and from 0.1534 to 0.3459, respectively. These APD estimates were highly negatively correlated with the estimates of individual inbreeding coefficients and can identify the most genomically distinct rice germplasm that are compatible with those revealed through principal component analysis. Also, a reliable APD estimation was found to require 5000 to 10,000 random genomic SNPs or SVs. These findings together are significant, not only in demonstrating the informativeness of APD estimates in the identification of individuals with variable genomic distinctness, but also in providing guidance for APD applications to measure individual genomic distinctness. Full article

Rapid and accurate phenotypic screening of rice germplasms is crucial for identifying potential sources of rice sheath blight resistance. However, visual and/or caliper-based estimations of coalescing, necrotic, diseased lesions of rice sheath blight (ShB)-infected plants are time-consuming, labor-intensive, and subject to human rater subjectivity. Here, we propose the use of RGB images and image processing techniques to quantify ShB disease progression in terms of lesion height and diseased area. To be specific, we developed a Pixel Color- and Coordinate-based K-Means Clustering (PCC-KMC) algorithm utilizing the Mahalanobis distance metric, aimed at accurately segmenting symptomatic and non-symptomatic regions within rice stem images. The performance of PCC-KMC, combined with manual classification of the segmented regions, was evaluated using Lin’s concordance correlation coefficient (${\rho }_c$) by comparing its results to visual measurements of ShB lesion height (cm) and to lesion/diseased area (cm₂) measured using ImageJ. Low bias (C_b) and high precision (r) were observed for absolute lesion height (C_b = 0.93, r = 0.94) and absolute symptomatic area (C_b = 0.98, r = 0.97) studies. Furthermore, to automatically classify the segmented regions produced by the PCC-KMC algorithm, we employed a convolutional neural network (CNN). Unlike conventional CNNs that require fixed-size image inputs, our CNN is designed to take the RGB histogram of each segmented region (a 1000 by 3 representation) as input and determine whether the region corresponds to ShB infection. This design effectively handles the arbitrary sizes and irregular shapes of segmentation regions generated by PCC-KMC. Our CNN was trained based on an 85%:15% composition for the training and testing dataset from a total of 168 ShB-infected stem sample images, recording 92% accuracy and 0.21 loss. PCC-KMC-CNN also showed high accuracy and precision for the absolute lesion height (C_b = 0.86, r = 0.90) and absolute diseased area (C_b = 0.99, r = 0.97) studies, indicating that PCC-KMC combined with automatic CNN-based classification performs very effectively. These results demonstrate that the potential of our methodology to serve as an alternative to the traditional visual-based ShB disease severity assessment and can be considered to be utilized for lab-scale, high-throughput phenotyping of rice ShB. Full article

Salinity is one of the primary limiting factors in the rice production system in northeast Thailand due to the presence of underground salt rocks, and the situation is expected to deteriorate further in the future since rice is particularly susceptible to salinity. In this study, 382 indigenous lowland rice germplasms were evaluated for salt tolerance under hydroponic conditions at the seedling stage. The stress condition was induced by adding NaCl from 2 dS/m to 22 dS/m. Twenty-two varieties (group 1) were selected based on low leaf salinity scores in 2019 and 2020. Ten varieties, LLR050, LLR054, LLR106, LLR216, LLR309, LLR365, LLR377, LLR402, LLR441, and LLR449, were selected from leaf salt injury scores under hydroponic conditions in 2021 and 2022. The response of ten selected varieties was investigated under both hydroponic and soil media at the seedling stage, as well as soil culture at the tillering and flowering stages. The results revealed that LLR054, LLR365, and LLR216 exhibited low leaf injury scores (less than 4.0) at both the seedling and tillering stages. At the seedling stage, most varieties demonstrated high Na+ accumulation in the root, while high accumulation in the shoot was observed at the tillering stage. Varieties LLR054 and LLR441 displayed low leaf damage scores, root sodium accumulation at the seedling stage, and shoot sodium accumulation at the tillering stage, similar to the tolerant check variety Pokkali. Additionally, LLR365 and LLR216 showed high shoot sodium accumulation but low leaf damage scores at the tillering stage. At the flowering stage, LLR050 and LLR449 maintained high yields and filled seeds per panicle under salt stress. Therefore, early-stage LLR054, LLR441, LLR365, and LLR216 had high tolerance and LLR050 and LLR449 maintained high yields, and these varieties are potential sources of salt tolerance for future rice breeding programs. Full article

Background/Objectives: Bacterial blight (BB) represents one of the most devastating diseases threatening global rice production. Exploring and characterizing disease resistance (R) genes provides an effective strategy for controlling BB and enhancing rice resilience. Common wild rice (Oryza rufipogon) serves as a valuable reservoir of genetic diversity and disease resistance resources. In this study, we identified and functionally characterized a novel NLR gene, YPR1, from common wild rice (Oryza rufipogon), which exhibited significant spatial, temporal, and tissue-specific expression patterns. Methods: Using a combination of conventional PCR, RT-PCR, bioinformatics, transgenic analysis, and CRISPR/Cas9 gene-editing approaches, the full-length YPR1 sequence was successfully cloned. Results: The gene spans 4689 bp with a coding sequence (CDS) of 2979 bp, encoding a 992-amino acid protein. Protein domain prediction revealed that YPR1 is a typical CNL-type NLR protein, comprising RX-CC_like, NB-ARC, and LRR domains. The predicted molecular weight of the protein is 112.43 kDa, and the theoretical isoelectric point (pI) is 8.36. The absence of both signal peptide and transmembrane domains suggests that YPR1 functions intracellularly. Furthermore, the presence of multiple phosphorylation sites across diverse residues implies a potential role for post-translational regulation in its signal transduction function. Sequence alignment showed that YPR1 shared 94.02% similarity with Os09g34160 and up to 96.47% identity with its closest homolog in the NCBI database, confirming that YPR1 is a previously unreported gene. To verify its role in disease resistance, an overexpression vector (Ubi–YPR1) was constructed and introduced into the BB-susceptible rice cultivar JG30 via Agrobacterium tumefaciens-mediated transformation. T₁ transgenic lines were subsequently inoculated with 15 highly virulent Xanthomonas oryzae pv. oryzae (Xoo) strains. The transgenic plants exhibited strong resistance to eight strains (YM1, YM187, C1, C5, C6, T7147, PB, and HZhj19), demonstrating a broad-spectrum resistance pattern. Conversely, CRISPR/Cas9-mediated knockout of YPR1 in common wild rice resulted in increased susceptibility to most Xoo strains. Although the resistance of knockout lines to strains C7 and YM187 was comparable to that of the wild type (YP^WT), the majority of knockout plants exhibited more severe symptoms and significantly lower YPR1 expression levels compared with YP^WT. Conclusions: Collectively, these findings demonstrate that YPR1 plays a crucial role in bacterial blight resistance in common wild rice. As a novel CNL-type NLR gene conferring specific resistance to multiple Xoo strains, YPR1 provides a promising genetic resource for the molecular breeding of BB-resistant rice varieties. Full article

Shanlan upland rice is a unique rice resource of the Li and Miao ethnic group in China and serves as a valuable gene pool adapted to tropical mountainous environments. To explore the genetic relationships of Shanlan upland rice from different geographical origins, 21 SSR markers were used to conduct genetic diversity and population structure analyses on 288 Shanlan upland rice accessions from 10 provinces (regions) in southern China. Results: The study revealed that the mean values of effective allele number (Ne), Shannon’s information index (I), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) for Shanlan upland rice were 1.616, 0.491, 0.74, 0.129, and 0.306, respectively. Genetic diversity analysis and molecular variance analysis (AMOVA) showed that the main source of variation between materials was the individual Shanlan upland rice plants. Genetic distance and differentiation results revealed the phylogenetic relationships among Shanlan upland rice populations. Both clustering and population structure analyses divided the materials into five subgroups, suggesting that the Shanlan upland rice from Qiongzhong, Hainan, might be the center of genetic diversity for the Hainan Shanlan upland rice, while rice from Dongfang, Hainan, and the inland populations exhibit genetic isolation. This study provides foundational data for the prioritized conservation and innovative utilization of Shanlan upland rice germplasm resources. Full article