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At least 19 recordsLinked to original sources
PubMed2026

Transmission dynamics and driving mechanisms of antibiotic resistance genes through a chronosequence of saline-sodic rice cultivation.

Rice cultivation reclaims saline-sodic soils and improves fertility, but may also promote antibiotic resistance genes (ARGs) accumulation and horizontal transfer, posing ecological risks. This study investigated long-term co-evolution of soil properties, microbial communities, ARGs, and mobile genetic elements (MGEs) across a 1-78 year cultivation chronosequence in saline-sodic fields. Results indicated that prolonged cultivation effectively alleviated soil salinization and increased fertility. Microbial communities shifted directionally, with functional taxa enriched, while opportunistic pathogen-containing genera peaked during 5-20 years. ARGs abundance and diversity increased markedly after five years and peaked at 10-20 years. Multidrug efflux pump genes persisted throughout the chronosequence, whereas aminoglycoside resistance genes declined after 30 years. MGEs activity increased over time and was significantly correlated with key ARGs. Path analysis identified improved soil properties as the primary direct driver of ARGs accumulation, while cultivation-induced declines in microbial diversity indirectly promoted ARGs dissemination by weakening the community's suppression of MGEs-mediated horizontal transfer. Collectively, long-term rice cultivation not only ameliorated saline-sodic soils but also created a dynamic, stage-specific resistome, with the 5-20 year period representing a critical risk window for ARGs propagation. These findings highlight the need to integrate ARGs monitoring into soil health assessments for sustainable management of reclaimed saline-sodic lands.

Oryza↗
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↗
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↗
PubMed2026

Alternatively spliced killer-protector system confers S19-mediated hybrid male sterility in rice.

Hybrid sterility limits the use of strong interspecific heterosis and S19 is a major locus that confers hybrid sterility between Oryza sativa (Asian cultivated rice) and Oryza glaberrima (African cultivated rice). However, the S19 is not yet cloned and its underlying mechanism remains elusive. In this study, we identify two closely linked genes (S19A1 and S19A7) specific to African rice allele that encode a killer-protector module at the S19 locus. Two alternatively spliced transcripts expressed from the killer gene S19A1 (S19A1.1 and S19A1.2) encode mitochondria-targeted cytotoxic proteins that cause toxicity diversity for somatic and/or gametic cell death, respectively. However, S19A7 interacts with S19A1.1 and S19A1.2, blocking their cytotoxic effect. Because the Asian rice S19 allele lacks S19A1 and S19A7, male gametes that carry this allele are selectively aborted in Asian-African F1 hybrids. Knockout of S19A1 can overcome S19-mediated hybrid sterility. Haplotype analysis reveals that the functional S19 allele is absent in non-AA-genome Oryza species and likely emerged in the O. barthii-O. glaberrima lineage through a multi-step evolutionary process. Our findings provide insight into the genetic mechanisms responsible for hybrid sterility between Asian and African rice and suggest genetic and biotechnological strategies for the use of interspecific heterosis in rice.

Oryza↗
PubMed2026

Multi-locus allelic architecture underlying natural variation in leaf rolling in japonica rice.

Leaf rolling is a key component of rice canopy architecture that affects light interception, microclimate formation, and planting density. The contribution of naturally occurring allelic variation to quantitative variation in leaf rolling within cultivated rice remains poorly understood, while extreme leaf rolling caused by loss-of-function mutations often results in detrimental pleiotropic effects. Herein, we examined how multi-locus allelic variation contributes to natural variation in leaf rolling within japonica rice. Leaf rolling was quantified based on the leaf rolling index (LRI) using a panel of 201 japonica accessions. The phenotype was transformed using the Yeo-Johnson method to reduce strong right skewness and improve the distributional properties of the data, thereby facilitating subsequent regression modeling. Haplotype analyses were performed for previously reported leaf rolling-associated genes and genome-wide association study (GWAS) lead loci, leading to the identification of five loci exhibiting substantial haplotype-dependent phenotypic variation. Phenotypically defined allelic groups represented these loci were subsequently evaluated using multiple linear regression (MLR), with the first two principal components derived from genome-wide SNP data included as covariates to account for population structure. The final MLR model identified four loci (qALR1, OsYABBY1, OsSLL2, and OsSRL10) as the independent contributors to leaf rolling variation, collectively explaining 21% of the variance in the transformed phenotype after accounting for population structure. Model diagnostics and ten-fold cross-validation supported the statistical validity of the framework and indicated stable model performance across validation folds. Analysis of multi-locus allelic combinations showed 13 distinct configurations that clustered into three phenotypically differentiated groups. This reflected the cumulative dosage of high-leaf rolling alleles. Thus, the natural variation in leaf rolling in japonica rice is governed by the additive effects of multiple moderate-impact loci. The multi-locus allelic framework established here provides a statistically sound and biologically interpretable basis for dissecting polygenic canopy traits and practical guidance for developing genetic materials aimed at optimizing rice plant architecture.

cross-validation↗
PubMed2026

Uncovering hub genes and key pathways responsive to drought stress in rice via meta-analysis of transcriptomic data.

Drought stress presents a formidable threat to global rice cultivation, triggering complex molecular responses that impact plant growth and productivity. To decipher the underlying gene expression dynamics, we performed a comprehensive meta-analysis of transcriptomic datasets derived from drought-tolerant rice genotypes. Via microarray data from three independent studies, we identified a set of consistently expressed differentially expressed genes (DEGs) under drought conditions. Integration of functional annotation tools, including GO and KEGG pathway enrichment, revealed key biological processes and signaling cascades involved in stress mitigation, such as ABA signaling, protein folding, and photosynthesis suppression. Protein-protein interaction (PPI) network construction, followed by hub gene identification via maximal clique centrality (MCC), highlighted pivotal regulators including LEA proteins, dehydrins, HSP70, and several transcription factors. Machine learning approaches further prioritize potential biomarkers, with Random Forest models achieving high classification accuracy and pinpointing key predictive genes. Chromosomal localization analysis provided spatial insights into the distribution of these hub genes, whose expression patterns were further compared against qRT-PCR data from previously published studies. This integrative approach identifies candidate genomic markers and mechanistic insights that may support future breeding strategies for drought-tolerant rice, pending experimental validation.

Cytoscape↗
PubMed2026

Comparative analysis of DDR-related genes and microRNA expression during rice germination: Implications for salinity susceptibility screening.

Soil salinity poses a significant threat to the agri-food sector and particularly to rice cultivation. High salinity during germination induces overproduction of reactive oxygen species (ROS) that cause lesions in the DNA resulting in reduced vigor. MicroRNAs (miRNAs) are known to modulate stress response in plants, however, studies focusing on its relation with the expression of the DNA damage response (DDR)-related genes are not thoroughly explored. In this regard, the aim of this work was to investigate the link between the expression of miRNAs and putative targeted DDR-related genes in response to salinity stress during germination. Eight varieties representative of indica and japonica rice subspecies were categorized into clusters through a principal component analysis (PCA) based on their germination performance and stress tolerance index under varying concentrations of NaCl. Subsequently, the expression patterns of six miRNAs and their putative targeted DDR genes were measured in two contrastive cultivars through quantitative real-time PCR (qRT-PCR) while correlations were examined through Pearson's analysis. Results showed distinct expression profiles between halotolerant and sensitive cultivars. Two miRNAs were further investigated in mature dry seeds of all the cultivars to verify their earliest, seed-specific discriminative potential. The distinct miR414 expression pattern may represent a potential biomarker for identifying salinity-susceptible cultivars during early-stage breeding screening.

Oryza↗
PubMed2025

Beyond parental lines: multi-omics analyses reveal epigenetic and transcriptional mechanisms underlying heterosis in Oryza sativa × Oryza rufipogon hybrids.

Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the Oryza genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific Oryza hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using Oryza sativa L. ssp. japonica cv. Nipponbare (NIP), Oryza rufipogon Griff. acc. CWR, and their resulting F1 hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.

Oryza↗
PubMed1978

Epidemiological studies on Japanese encephalitis in Kyoto City area, Japan. I. Evidence for decrease of vector mosquitoes.

Mosquito collections by using light traps have been carried out at 10 to 11 stations in Kyoto City area at intervals of about 10 days every year. Mean percent indexes (MPI), being calculated from the data of mosquito collections, were used for comparison of the annual abundance of mosquitoes. It is no doubt that Culex tritaeniorhynchus summorosus has decreased recently and this decrease is correlated with the reduction of human patients of Japanese encephalitis. Wide use of two herbicides, CNP and nitrofen, for rice plant cultivation, may probably be one of the reasons for the decrease of the mosquitoes.

Animals↗
PubMed2026

Beyond the salt barrier: CRISPR-mediated DNA reprogramming to uncouple yield from tolerance in Rice: A review.

Rice (Oryza sativa L.) feeds half of humanity, yet its cultivation is increasingly threatened by soil salinization, which now affects 1.4 billion hectares globally. Decades of breeding and engineering have focused on Na+ exclusion, principally through the Saltol QTL and the xylem-unloading transporter OsHKT1;5, yet this strategy has reached a physiological ceiling. Excluder genotypes survive salinity but fail to fill grain, because the ATP-intensive cost of continuous ion extrusion starves reproductive sinks, while ABA-mediated stomatal closure imposes chronic carbon limitation. The resulting "survival-yield gap" exposes a fundamental flaw in single-trait approaches to a polygenic stress. In this review, we argue that durable, yield-stable salt tolerance requires a coordinated systems-level intervention spanning five mechanistic tiers: (i) CRISPR/Cas9-mediated removal of negative regulatory brakes (OsRR22, RST1, PC1) that suppress plant's latent stress-adaptive capacity; (ii) reinforcement of actin-myosin cytoskeletal transport to sustain SOS1, NHX1, and HKT1;5 delivery under ionic stress; (iii) importation of halophyte design principles from Oryza coarctata, including salt gland architecture and superior Na+ compartmentalization; (iv) recalibration of the ROS-photosynthesis axis via the DHHC09-STRK1-CatC molecular switch and stomatal density engineering; and (v) pyramiding these modules into a "Salt-Shield Rice" genotype through multiplex editing, marker-assisted introgression, speed breeding, and genomic selection. We propose a phased ten-year roadmap that integrates synthetic biology circuit design with conventional breeding to deliver field-ready, multi-module varieties with greater than 70% yield stability at 8-10 dS m-1. This remains an aspirational design target rather than a demonstrated outcome, as three of the five tiers-halophyte-derived structural traits, cytoskeletal reinforcement, and full multi-module pyramiding-remain unvalidated in rice.

CRISPR/Cas9↗
PubMedDate not supplied

[Effect of the composition of the medium and the conditions of Aspergillus foetidus cultivation on the biosynthesis of glucoamylase].

The optimal conditions for biosynthesis of exocellular glucoamylase were found in the course of submerged cultivation of Aspergillus foetidus ATCC 14916: pH 4.5 at the beginning of cultivation, cultivation for four days, a temperature of 30 degrees C, and an aeration in the fermenter of 1.5 volumes of the air per 1 volume of the medium with a stirring of 280 rpm. The material can be inoculated either as spores (1 X 10(7) spores per 100 ml of the medium) or a material germinated from spores (5% by volume). The composition of the medium was improved by using waste products of the agricultural industry (wheat and rice bran, yellow maize, etc.). The maximum biosynthesis of glucoamylase under the optimum conditions of cultivation was observed on crushed yellow maize (10--15%): up to 6.8--8.0 units of GIA (g of glucose per hour) per 1 ml of the cultural filtrate which was 3.4--4.0 times higher than on the original medium and 5--10 times higher than for Endomycopsis bispora, Endomycopsis sp. 20--9, Aspergillus niger and other cultures producing glucoamylase.

Aerobiosis↗
PubMed1977

The cultivation of the rumen ciliate Entodinium bursa in the presence of Entodinium caudatum.

The rumen ciliate protozoon Entodinium bursa has been grown in vitro in the presence of bacteria and Entodinium caudatum for over a year at population densities of 100 to 200 ml-1. The medium contained potassium phosphate, prepared fresh rumen fluid, cysteine, wholemeal flour (or rice starch), dried grass and a culture of the spineless form of Entodinium caudatum. Entodinium bursa has an obligate requirement for this protozoon and died within 48 h in its absence. During growth from a 2% inoculum, the mean generation time of E. bursa was 6 h. Entodinium bursa engulfed 1-5 to 2-5 E. caudatum organisms h-1, and when E. caudatum was in excess it developed caudal spines for the first time in 17 years; these spined forms were engulfed much less readily than the spineless organisms.

Animals↗
PubMed2026

Seed shattering habit in millets and the secrets of the abscission layer - a comprehensive review.

Though seed shattering continues to be a significant barrier affecting yield stability and harvesting efficiency in millets and other grasses, millets are increasingly acknowledged as climate-resilient, nutrient-rich 2007cereal crops with the potential to strengthen global nutritional and food security under the combined pressures of climate change, population growth, and limited natural resources. Since strong artificial selection favoured non-shattering phenotypes during domestication, seed shattering, an adaptive trait in wild species that promotes seed dispersal through the formation and activation of specialised abscission layers, became a distinguishing feature of cultivated cereals. With a focus on the morphological, physiological, hormonal, and genetic modulation of the abscission zone, this article summarizes the state of the art regarding seed shattering in millets. Abscission layer morphology, location, and lignification vary greatly among grasses, from well-defined lignified zones in rice and sorghum to non-lignified and anatomically subtle zones in Setaria and Panicum species. Cell wall-modifying enzymes like polygalacturonases, cellulases, expansins, and pectin methylesterases that mediate middle lamella degradation are modulated by coordinated hormonal signalling involving auxin, ethylene, and abscisic acid, which controls the timing and progression of cell separation at the physiological level. Domestication-related genes, including SH1, qSH1, SH4, and LES1, demonstrate convergent evolutionary mechanisms controlling abscission layer development in a variety of grass lineages at the molecular level. Understanding these regulatory networks has been greatly enhanced by recent developments in transcriptomics, functional genomics, and genome sequencing in both model species and underused millets. The role of millets as climate-smart cereals for sustainable future agriculture is reinforced by the integration of anatomical, physiological, and genetic insights, which offer a solid basis for targeted breeding and genome-editing strategies intended to improve seed retention, enhance yield stability, and increase harvest efficiency.

Abscission Layer↗
PubMed1978

Establishment of a persistent measles virus infection in HEp-2 cells.

A productive measles virus persistent infection has been established in HEp-2 cells. Greater than 90% of the persistently infected HEp-2 cells (H2MV) exhibited measles specific immunofluorescence and haemadsorption. Although most of the H2MV cells contained measles specific antigens, only a small percentage (less than 1%) actually produced infectious measles virus as determined by infectious centre assays. The measles virus produced by H2MV cells exhibited properties different from the initiating parent Edmonston strain virus, being reduced in virulence and also temperature sensitive for replication at 39 degrees C. The role of these altered virus properties in the establishment of persistence is considered.

Antigens, Viral↗
PubMedDate not supplied

Japanese encephalitis surveillance in China (Province of Taiwan) during 1968-1971. I. Geographical and seasonal features of case outbreaks.

During 1968-1971 Japanese encephalitis (JE) surveillance was conducted with WHO-assisted programs in Taiwan area. Emphasis was placed on: (1) active case-finding by hospital visits; (2) blood collection from every patient at the suitable time; and (3) the enforcement of standard diagnostic criteria on the results of hemagglutination-inhibition tests. Each year, approximately 90% of reported patients were etiologically examined. JE virus etiology was established in 277 (1968), 279 (1969), 269 (1970) and 158 (1971) cases. Despite the apparent concentration of cases in several cities, practically all the cultivated plains and basins were established as potentially endemic for JE. JE outbreak is found to have been clearly associated with season, not only in subtropical but also in tropical Taiwan. Each year it occurred consistently in mid-July in the southernmost county, 2-3 weeks after the peak of rice transplantation and its duration was a few weeks. On the western side of the island, although less consistently, JE outbreak seems to occur one to three weeks later than in the south. Outbreak in eastern Taiwan was a mid-September phenomenon for 3 years. Observed seasonal lag, which was significant between two neighboring localities on same latitude, suggests that paddy water management is more directly related to date of outbreak than local climate. Seasonal characteristics further suggests that the area may be separated into eight ecologic subdivisions. JE-virus transmission to a man during April at temperatures below the average of 20 C was discussed.

Climate↗
PubMed2026

Genome-Wide Identification of NLP Family Genes in Cultivated Strawberry (Fragaria × ananassa Duch.) and Analysis of Their Expression Under Heat and Botrytis cinerea Stresses.

Nodule inception (NIN)-like proteins (NLPs) are plant-specific transcription factors regulating nutrient absorption, growth, and stress tolerance; however, their roles in stress responses remain largely uncharacterized. Cultivated strawberry (Fragaria × ananassa 'Camarosa') serves as an ideal model for dissecting the evolution and function of NLP genes. In this study, 37 FaNLP genes were identified genome-wide. Phylogenetic analysis classified them into three subfamilies, which are evenly distributed across seven chromosomes. Divergent exon-intron structures and conserved motif compositions suggest functional differentiation among FaNLPs. Quantitative real-time PCR (qRT-PCR) revealed distinct expression profiles under heat stress and Botrytis cinerea infection. Notably, FaNLPs were significantly more upregulated in the cultivar 'Shuxing' than in 'Benihoppe'. Heat stress inhibited photosynthesis and altered catalase activity (CAT), superoxide dismutase activities (SOD) and peroxidase activities (POD), whereas fungal infection enhanced chitinase activity in both cultivars. Comparative genomics with Arabidopsis and rice revealed strawberry-specific evolutionary patterns of NLPs. Subcellular localization prediction indicates that FaNLP proteins primarily localize to the nucleus, implying their potential roles as transcriptional regulators. This study links FaNLP sequence characteristics with stress response phenotypes, providing a foundation for elucidating NLP-mediated regulatory networks in strawberry. Future functional assays, including overexpression and knockout analyses, will further clarify the biological roles of FaNLPs.

Fragaria↗
PubMed2025

Characterization of phosphorylation variants for identifying adaptive alleles in Zea.

Large-scale genome sequencing of maize wild species (teosinte) has uncovered thousands of genetic mutations, but distinguishing causal alleles from neutral variations remains a significant challenge. In this study, we conducted a comprehensive analysis of phosphorylation-associated single-nucleotide variations (pSNVs) to enhance our understanding of adaptive variations in the Zea genus. We collected 234 teosinte genomes from seven different taxa and 507 cultivated maize genomes to identify single-nucleotide variants that target phosphorylation machinery, which is crucial for plant development and environmental adaptation. Our analysis identified 33 687 pSNVs within the Zea genus and revealed a reduction in genetic conservation along with an increase in protein abundance and expression for genes harboring pSNVs. Additionally, pSNVs present stronger purifying selection pressures compared with other missense mutations. We found that maize possesses fewer pSNVs than teosinte, likely due to the effects of selection and hitchhiking. By examining the role of pSNVs related to kinase-substrate rewriting events and exhibiting evolutionary divergence jointly, our results suggest that pSNVs impact multiple traits, particularly flowering time variation between teosinte and maize. Furthermore, we documented the widespread presence of pSNVs in Arabidopsis thaliana, rice, and wheat, identifying 46 pSNVs that have convergently evolved between maize and other species. Our study provides another insight into uncovering adaptive alleles in wild species by incorporating protein signaling sites and emphasizes the potential of utilizing wild species for future crop improvement.

Zea mays↗