Publications by authors named "Binying Fu"

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice and the associated epigenetic responses (DNA methylation). Abiotic stress factors, including high temperature, drought, cold, heavy metal pollution, and high salinity, have a negative impact on crop productivity.

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Hydrogen peroxide-based Fenton reaction can effectively degrade many small-molecule fluorescent dyes, leading to notable alterations in fluorescence signals. Additionally, the two-dimensional black phosphorus/platinum nanocomposite (BP/Pt) demonstrates exceptional catalase (CAT) characteristics. Based on these, a colorimetric-fluorescence dual-mode signal output pattern based on BP/Pt-Fenton reaction-rhodamine B tandem reaction system is reported.

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Background: Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.

Results: In this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments.

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Introduction: Drought and submergence are contrasting abiotic stresses that often occur in the same rice crop season and cause complete crop failure in many rain-fed lowland areas of Asia.

Methods: To develop rice varieties with good tolerances to drought and submergence, 260 introgression lines (ILs) selected for drought tolerance (DT) from nine BC populations were screened for submergence tolerance (ST), resulting in 124 ILs with significantly improved ST.

Results: Genetic characterization of the 260 ILs with DNA markers identified 59 DT quantitative trait loci (QTLs) and 68 ST QTLs with an average 55% of the identified QTLs associated with both DT and ST.

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The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination.

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Allantoin is crucial for plant growth and development as well as adaptations to abiotic stresses, but the underlying molecular mechanisms remain unclear. In this study, we comprehensively analyzed the physiological indices, transcriptomes, and metabolomes of rice seedlings following salt, allantoin, and salt + allantoin treatments. The results revealed that exogenous allantoin positively affects the salt tolerance by increasing the contents of endogenous allantoin with antioxidant activities, increasing the reactive oxygen species (ROS)-scavenging capacity, and maintaining sodium and potassium homeostasis.

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Introduction: Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding.

Objectives: How rice was domesticated and impacted by modern breeding.

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Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions () and (), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured.

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N-methyladenosine (mA) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of mA on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in mA methylation and gene expression in rice under salt stress conditions.

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Gibberellin 2-oxidase (GA2ox) plays an important role in the GA catabolic pathway and the molecular function of the genes in plant abiotic stress tolerance remains largely unknown. In this study, we functionally characterized the rice () gene. The protein was localized in the nucleus, cell membrane, and cytoplasm, and was induced in response to various abiotic stresses and phytohormones.

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A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones.

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Integration of transcriptomics and metabolomics data can provide detailed information for better understanding the molecular mechanisms underlying salt tolerance in rice. In the present study, we report a comprehensive analysis of the transcriptome and metabolome of rice overexpressing the OsDRAP1 gene, which encodes an ERF transcription factor and was previously identified to be conferring drought tolerance. Phenotypic analysis showed that OsDRAP1 overexpression (OE) improved salt tolerance by increasing the survival rate under salt stress.

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High salinity is one of the major abiotic stresses limiting rice production. Melatonin has been implicated in the salt tolerance of rice. However, the molecular basis of melatonin-mediated salt tolerance in rice remains unclear.

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Background: High soil salinity can cause significant losses in rice productivity worldwide, mainly because salt inhibits plant growth and reduces grain yield. To cope with environmental changes, plants have evolved several adaptive mechanisms that involve the regulation of many stress-responsive genes.

Results: In this study, we identified OsSTAP1, which encodes an AP2/ERF-type transcription factor, was rapidly induced by ABA, ACC, salt, cold, and PEG treatments.

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OsPUB67, a U-box E3 ubiquitin ligase, may interact with two drought tolerance negative regulators (OsRZFP34 and OsDIS1) and improve drought tolerance by enhancing the reactive oxygen scavenging ability and stomatal closure. E3 ubiquitin ligases are major components of the ubiquitination cascade and contribute to the biotic and abiotic stress response in plants. In the present study, we show that a rice drought responsive gene, OsPUB67, encoding the U-box E3 ubiquitin ligase was significantly induced by drought, salt, cold, JA, and ABA, and was expressed in nuclei, cytoplasm, and membrane systems.

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A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development.

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Improving the performance of rice () under drought stress has the potential to significantly affect rice productivity. Here, we report that the ERF family transcription factor OsLG3 positively regulates drought tolerance in rice. In our previous work, we found that has a positive effect on rice grain length without affecting grain quality.

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Genomic diversity within a species genome is the genetic basis of its phenotypic diversity essential for its adaptation to environments. The big picture of the total genetic diversity within Asian cultivated rice has been uncovered since the sequencing of 3,000 rice genomes, including the SNP data publicly available in the SNP-Seek database. Here we report other aspects of the genetic diversity, including rice sequences assembled from over 3,000 accessions but absent in the Nipponbare reference genome, structural variations (SVs) and gene presence/absence variations (PAVs) in 453 accessions with sequencing depth over 20x.

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Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location.

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Overexpressing and RNA interfering transgenic rice plants exhibited significantly improved and reduced drought tolerance, but accompanied with negative effects on development and yield. The dehydration responsive element binding (DREBs) genes are important transcription factors which play a crucial role in plant abiotic stress tolerances. In this study, we functionally characterized a DREB2-like gene, conferring drought tolerance (DT) in rice.

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Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O.

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In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant BCF IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F progeny and 318 random F plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F progenies of four rice populations in a single generation; (2) ∼25% of the stress-induced ES loci were transgenerational and inherited from their salt- and drought- selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance.

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Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions.

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Semidwarfism is an important agronomic trait in rice breeding programs. The semidwarf mutant gene Sdt97 was previously described. However, the molecular mechanism underlying the mutant is yet to be elucidated.

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