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At least 19 recordsLinked to original sources
PubMed2025

Genome wide association study of rice agronomical traits and seed ionome with the NARO Open Rice Collection.

To meet the nutritional needs of the rising human population, genetic variants are necessary for the breeding of new cultivars. Rice (Oryza sativa L.) is a staple food for over half of the world's population. Here, we developed a new rice genetic resource, the NARO Open Rice Collection (NRC) with high-resolution genome data. NRC consists of 623 accessions, and approximately 200 accessions are categorized into three major subgroups, categorized as Indica, Japonica, and Aus. In this study, we performed genome-wide association studies (GWAS) for rice heading date, seed shape, and seed ionome using the NRC. Well-known genes related to heading date and seed shape were detected by GWAS using the NRC accessions. Therefore, we concluded that our new rice collection is suitable for GWAS. In addition, GWAS with each subgroup was advantageous for the detection of particular genes. Finally, we performed GWAS for seed ionome with the aim of improving the nutritional properties of rice, as essential minerals for humans, such as iron (Fe) and zinc (Zn), are not sufficient in rice seeds. Our study revealed that OsATL31, a likely ubiquitin E3 ligase, was involved in the control of Fe and Zn contents in seeds.

Oryza↗
PubMed2026

Metabolomic and structural signatures of pigmented and non-pigmented Himalayan rice landraces.

BACKGROUND: This study investigated the anti-oxidant properties, starch composition, pasting behavior, structural properties, textural properties and non-targeted metabolomic profiles of pigmented and non-pigmented rice landraces as potential next-generation functional food ingredients. RESULTS: Pigmented rice demonstrated 1.34 times more anti-oxidant activity as compared to non-pigmented rice. Pigmented landraces showcased superior nutritional and functional attributes, including higher total dietary fiber and starch content. Fourier-transform infrared (FTIR) analysis revealed distinct molecular signatures with enhanced peak transmittance, while X-ray diffraction (XRD) indicated greater crystallinity ranging from 36-44.3% in pigmented rice compared with 30-40% in non-pigmented rice, suggesting improved digestibility and processing versatility. Pigmented rice recorded less amylose content hence tended to possess increased adhesiveness values whereas non-pigmented rice revealed greater amylose content hence was coupled with greater hardness values. Field-emission scanning electron microscopy (FE-SEM) images revealed that pigmented rice had densely packed and polygonal starch granules whereas non-pigmented rice had loosely packed starch granules with intergranular voids. Untargeted gas chromatography-mass spectrometry (GC-MS) profiling identified 84 metabolites, including unique compounds such as 3,3-dimethylbutanol and ethanoic acid, along with shared metabolites such as sucrose and linoleic acid, highlighting notable biochemical diversity. Multivariate statistical analyses using principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping further differentiated the metabolomic landscapes, with variable importance in the projection (VIP) scores identifying key bioactive contributors. CONCLUSION: Pigmented rice landraces exhibited significant functional and nutritional advantages, making them promising candidates for functional food development and nutritional improvement programs. These findings support their potential role in advancing sustainable and health-oriented food systems. © 2026 Society of Chemical Industry.

Oryza↗
PubMed2025

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective.

Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19th century. The phylogeography of RYMV in East Africa was reconstructed from coat protein gene sequences (ORF4) of 335 isolates sampled over two million square kilometers between 1966 and 2020. Dispersal patterns obtained from ORF2a and ORF2b, and full-length sequences converged to the same scenario. The following imprints of rice cultivation on RYMV epidemiology were unveiled. RYMV emerged in the middle of the 19th century in the Eastern Arc Mountains where slash-and-burn rice cultivation was practiced. Several spillovers from wild hosts to cultivated rice occurred. RYMV was then rapidly introduced into the nearby large rice growing Kilombero valley and Morogoro region. Harvested seeds are contaminated by debris of virus infected plants that subsist after threshing and winnowing. Long-distance dispersal of RYMV is consistent (i) with rice introduction along the caravan routes from the Indian Ocean Coast to Lake Victoria in the second half of the 19th century, (ii) seed movement from East Africa to West Africa at the end of the 19th century, from Lake Victoria to the north of Ethiopia in the second half of the 20th century and to Madagascar at the end of the 20th century, (iii) and, unexpectedly, with rice transport at the end of the First World War as a troop staple food from the Kilombero valley towards the South of Lake Malawi. Overall, RYMV dispersal was associated to a broad range of human activities, some unsuspected. Consequently, RYMV has a wide dispersal capacity. Its dispersal metrics estimated from phylogeographic reconstructions are similar to those of highly mobile zoonotic viruses.

Oryza↗
PubMed2025

Lysine-rich rice enhanced muscle growth and development in young rats.

Rice is the staple food for half of the world's population but is low in lysine content. We previously developed transgenic lysine-rich rice with enhanced free lysine content in rice seeds and demonstrated that it could improve skeletal growth and development in rats. However, the effects of lysine-rich rice on muscle remain to be studied. We hypothesized that lysine-rich rice was able to improve muscle growth in weaning rats via its anabolic effects on muscle metabolism. Male weaning Sprague-Dawley rats received lysine-rich rice (HFL) diet, wild-type rice (WT) diet, or wild-type rice with various doses of lysine supplementation (WT + Lys) diet (+ 0%, + 10%, + 20%, and + 40% lysine) for 70 days. Muscle strength and quality were analyzed by biomechanical test and muscle fiber typing of the extensor digitorum longus (EDL) muscles. Molecular mechanisms of lysine on muscle growth were also explored by rat serum biochemistry and cell culture systems. Results indicated that the HFL diet improved rats' muscle growth, strength, and physiological cross-sectional area (CSA) over the WT diet group. The CSAs of fast-twitch muscle fibers (Type IIb and IIx) were also increased. In addition, the HFL increased serum insulin-like growth factor 1 (IGF-1) and decreased serum myostatin (MSTN) concentrations. The cell culture model showed that lysine deficiency reduced IGF-1 expression and inhibited myoblast differentiation associated with muscle growth. Our findings showed that lysine-rich rice improved muscle growth and development in weaning rats. Higher dietary lysine possibly inhibited MSTN and activated of IGF-1 signaling pathway for muscle growth and development.

Animals↗
PubMed2026

Identification of rice DUF1719 gene family and analysis of alkaline tolerance function of OsDUF1719.8.

Alkaline stress severely constrains the physiological metabolism and growth and development of rice through high pH and ionic toxicity. Domains of unknown function (DUF) play significant roles in plant stress responses. However, the function of the DUF1719 family (PF08224) in rice has not been reported and further research is needed. This study systematically identified the OsDUF1719 gene family in rice and investigated the function of OsDUF1719.8 under alkaline stress. The results demonstrate that the rice DUF1719 family comprises 13 protein members, all containing the PF08224 domain. It is predicted that this domain may play a role in ATPase activation. Evolutionary analysis divided DUF1719 proteins from eight grass species into six subgroups, with highly conserved gene structures, motifs, and tertiary architectures within each subgroup. Promoter analysis indicated enrichment of stress- and hormone-responsive elements, implying broad involvement in stress regulation. Expression analysis revealed that several genes, including OsDUF1719.5 and OsDUF1719.8, were upregulated under multiple abiotic stresses. Notably, OsDUF1719.8 was strongly induced during early alkaline stress. Consequently, we further analyzed the function of OsDUF1719.8 in the rice alkaline stress response. The results demonstrate that overexpression of OsDUF1719.8 enhanced rice alkaline tolerance, whereas knockout mutants exhibited stress sensitivity. OsDUF1719.8 enhances rice tolerance to alkaline stress by coordinately regulating reactive oxygen species metabolism, promoting the accumulation of osmotic adjustment compounds, and modulating ion homeostasis. This study provides the first systematic identification of the DUF1719 family and elucidates the function of OsDUF1719.8 in positively regulating rice alkaline tolerance, offering a novel gene for alkali-tolerant molecular breeding of rice.

Oryza↗
PubMed2026

Monitoring the fate of paternal mitochondria and their elimination in rice zygotes.

Mitochondria are preferentially transmitted from the maternal plant in most angiosperms, including rice, and paternal mitochondria are generally eliminated during microgametogenesis and/or in zygotes. The mechanism by which paternal mitochondria are eliminated progresses during plant reproductive processes. In the present study, we examined the distribution of paternal mitochondria in rice sperm cells and zygotes produced through the in vitro fertilization (IVF) of isolated rice gametes. Male gametes of rice possess mitochondria with nucleoids, suggesting the potential transfer of paternal mitochondria and their DNA into zygotes on fertilization and subsequent selective elimination of paternal mitochondria in the zygote. To intensively monitor the fate of rice paternal mitochondria in zygotes immediately after gamete fusion, time-lapse observations were conducted in paternal mitochondria labeled with GFP from rice zygotes produced using an IVF system. The results showed that the paternal mitochondria are progressively degraded during the early developmental stage at 1 to 3 h after fusion (HAF), leaving a small number of paternal mitochondria at 6 HAF. The remaining paternal mitochondria were considered to be degraded in later developmental-stage zygotes because paternal mitochondrial DNA-derived single-nucleotide polymorphisms were not detected in the sequencing reads of genomic DNA prepared from inter-subspecific hybrid rice. In addition, treatment with autophagy inhibitors stabilized the paternal mitochondria in zygotes. This suggests that the autophagy-dependent massive and selective elimination machinery for male mitochondria functions in rice zygotes immediately after gamete fusion and supports the strict maternal inheritance of mitochondria in rice.

Oryza↗
PubMed2026

DNA hypermethylation of abscisic-acid-related genes helps enhance the cold tolerance of tetraploid rice.

Polyploid plants exhibit enhanced stress resistance and superior adaptability to extreme environments, but the underlying molecular mechanisms remain incompletely understood. Here we confirm that tetraploid rice exhibits stronger cold tolerance than diploid rice. This improved tolerance is mediated by reduced malondialdehyde accumulation, elevated antioxidant enzyme activity, and epigenetic regulation of genes involved in abscisic acid (ABA) biosynthesis and signaling. Under cold stress, tetraploid rice induces stress-responsive genes (especially in the ABA pathway) more rapidly and to higher levels than diploid rice. This enhanced gene expression coincides with increased endogenous ABA accumulation. Furthermore, polyploidization and cold stress synergistically induce high methylation at CG, CHG, and CHH sites in genes and transposons (TEs). Notably, the methylation level of class II TEs in tetraploid rice is significantly higher than in diploid rice under low temperatures. To suppress TE activation in gene promoter regions under cold stress, tetraploid rice enhances the methylation level of ABA pathway-related gene promoters, thereby silencing TEs and maintaining genome stability. Collectively, these results enrich the theoretical understanding of the strong stress tolerance in polyploid plants and provide theoretical support for breeding cold-tolerant polyploid rice varieties.

ABA↗
PubMed2026

Strigolactones constrain rice drought acclimation by suppressing ROS scavenging through the D53-OsWRKY31-ZFP36 module.

Strigolactones (SLs) are a class of plant hormones essential for tiller development and yield under diverse environmental conditions. Drought is a major limiting factor for rice yields. Although SLs contribute to drought resistance, mechanisms and practical applications of SL pathway in drought acclimation of rice remain poorly understood. Our study shows that short-term dehydration represses SL biosynthesis in rice roots. Genetic assays indicate that disruption of SL biosynthesis or signaling elevates rice drought resistance, whereas SL signaling activation or supplementation with the SL analog GR244DO impairs drought resistance. SLs negatively regulate drought acclimation by promoting degradation of the repressor protein DWARF53 (D53). D53 interacts with the transcription factor OsWRKY31 via its N-terminal domain and suppresses the protein level of OsWRKY31, which binds to and represses transcription of the ZFP36 promoter. ZFP36 encodes a zinc-finger transcription factor that promotes H2O2 scavenging to sustain reactive oxygen species (ROS) homeostasis during drought stress. Notably, the drought-resistant upland rice variety IRAT109 exhibits lower SL levels in root exudates than the lowland rice variety Nipponbare (NP). Genome editing of key components in SL pathway enhances drought resistance in NP, Huazhan (HZ), and IRAT109. The agronomic potential of tuning SL biosynthesis is further supported by the elite D17/HTD1 allele, which weakens SL biosynthesis and improves drought resistance and grain yield in Nekken 2 (NK2) under field conditions. These findings uncover a key mechanism underlying SL-repressed drought acclimation in rice and provide an effective strategy to improve drought resistance in diverse rice varieties amid ongoing climate change.

D53↗
PubMed2026

Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region.

Journal Article↗
PubMed2026

Establishment of a CRISPR-Cas9 Library for Indica Rice and Identification of OsOPR5 (LOC_Os06g11210) as a Regulator of Root Architecture.

Functional characterization of a large number of rice genes remains a major challenge despite the availability of genome sequences and large-scale transcriptomic datasets. CRISPR-Cas9 library is a powerful approach for high-throughput targeted mutagenesis; however, its application in indica rice cultivars remains limited due to low transformation and regeneration efficiencies. In this study, we developed a CRISPR-Cas9 library targeting 12,000 rice genes and evaluated its utility for functional genomics in the indica cultivar MTU-1010. Sanger sequencing and NGS analysis of the plasmid library revealed high sgRNA coverage and more than 80% accuracy. Transformation of the developed library into the indica cultivar MTU-1010 resulted in a high target editing efficiency, with 90% of analyzed transgenic plants carrying mutations at the intended target site. Functional analysis of one homozygous mutant identified a previously uncharacterized role for OsOPR5 (LOC_Os06g11210), a member of the 12-oxophytodienoate reductase family in root architecture. The opr5 mutants exhibited significant reductions in lateral root number, seminal and crown root number, and root length, demonstrating that OsOPR5 positively regulates root system architecture in rice. Notably, endogenous jasmonic acid (JA) and JA-isoleucine levels were not significantly altered in the mutant, suggesting potential functional specialization or redundancy among rice OPR family members for JA accumulation. The root system architecture is a key determinant of water and nutrient acquisition; our results suggest that OsOPR5 may play an important role in adaptation under adverse environmental conditions. Collectively, this study establishes an efficient genome-editing platform for indica rice and identifies OsOPR5 as a novel regulator of root development.

Oryza↗
PubMed2025

Pan-analysis of intra- and inter-species diversity reveals a group of highly variable immune receptor genes in rice.

Plant immune receptors and their natural variations play a central role in combating disease-causing pathogens. These immune receptors include intracellular nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) and cell-surface pattern recognition receptors (PRRs) that can be further classified as receptor-like proteins (RLPs) and receptor-like kinases (RLKs). Although the NLRome has been characterized, the repertoire and extent of diversity of PRRome remain undetermined in rice. In this study, we examined the diversity of immune receptor genes using high-quality genomes of 309 rice accessions from 8 species within the genus Oryza. A total of 376 310 immune receptor genes were identified, including 149 592 NLR-coding genes and 226 718 PRR coding genes. Shannon entropy analysis revealed a set of immune receptors that display significant intra-species and inter-species diversity in rice. In general, RLPs are more variable than RLKs, while NLRs and LRR-RLPs are more variable than LRR-RLKs. Additionally, NLR and PRR genes exhibit contrasting shoot/root expression patterns, with NLRs generally skewed towards root expression. Furthermore, we found that the size of the LRR-RLK gene families correlates with local annual precipitation, suggesting a stronger selection pressure on LRR-RLK genes in rice accessions grown under wet conditions than dry conditions. In sum, this pan-genomic analysis not only reveals the extensive diversity of the immune receptor repertoires in rice but also provides potential target genes for improving disease resistance in rice.

Oryza↗
PubMedDate not supplied

On the nature of rheumatoid rice bodies: an immunologic, histochemical, and electron microscope study.

The nature of rice bodies was studied, utilizing histochemistry, immunofluorescence, and scanning and transmission electron microscopy. Rice bodies were found to consist primarily of fibrous material, most of which was fibrin with small amounts of collagen. Channels containing a variety of viable cells permeated the rice bodies. Blood vessels occurred in a few rice bodies indicating a former connection with the synovial membrane. Nonvascularized rice bodies might represent a further degeneration of the vascular type. Rice bodies seem to be a nonspecific response to inflammation.

Arthritis, Rheumatoid↗
PubMed2026

Mapping the Molecular Evolution and Role of Wild Rice GLYIII Protein-Encoding Genes in Abiotic Stress Response.

To address the need for sustainable food production amid rapid global climate change, developing rice varieties that grow optimally even under harsh conditions is essential. An effective approach in this direction would be to harness the stress resilience traits of the crop wild relatives (CWRs) of rice. Among the various crucial stress-responsive genes, the Glyoxalase III (GLYIII) gene family is of utmost importance for its ability to detoxify the toxic glycolytic byproduct, methylglyoxal (MG), in a less energy-intensive, single-step process, as well as for its multifaceted cytoprotective role. In our study, a comprehensive genome-wide search across the Oryza genus revealed that GLYIII genes are conserved across wild rice genotypes. Their number has expanded during domestication, driven by gene duplications. Interestingly, only a few orthologous pairs showed positive selection, suggesting that the functions of most others need to be constrained and or conserved.We found that higher GLYIII activity, Total Antioxidant Capacity, endogenous glutathione (GSH) levels, and free radical scavenging activity contributes to the stress resilience of wild rices O. punctata, O. meridionalis, and O. nivara, in addition to other factors. , , . , . Our qRT-PCR analysis revealed differential expression of the OpGLYIII, OmGLYIII, and OnGLYIII genes across different developmental stages and in response to various abiotic stresses. Furthermore, we report that wild rice GLYIII proteins, specifically OpGLYIII-3, OmGLYIII-3, and OnGLYIII-5, exhibit high catalytic efficiency over a broad pH range and at higher temperatures under in vitro assay conditions. Overexpression of these proteins was found to impart substantial stress resilience to the transformed E. coli cells. These findings collectively suggest that GLYIII proteins constitute a key component of the abiotic stress response machinery in wild rice.

Oryza↗
PubMed2024

Transfer of antibiotic resistance genes from soil to rice in paddy field.

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Oryza↗