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The study focused on the photodegradation of profoxydim, a low-toxicity cyclohexanedione herbicide commonly used in rice crops, under simulated sunlight conditions. Profoxydim's behavior in paddy field conditions is not well understood, and this research aimed to fill that gap, particularly examining the effect of commonly utilized organic amendments such as biochar (BC) on its degradation. Results indicated that profoxydim degrades rapidly, with a half-life of 2.4 ± 0.3 h in paddy water and 1.03 ± 0.1 h in paddy soil. However, when BC was introduced, the degradation slowed significantly, extending the half-lives to 3.1 ± 0.2 h in water and 3.07 ± 0.5 h in soil. The study identified five degradation products (DPs) using TOF mass accuracy measurements and MS/MS spectra fragmentation. Two of these DPs were found to be more stable than profoxydim itself. Additionally, the research proposed a novel photodegradation pathway, highlighting processes such as homolytic C-N bond cleavage, photoisomerization, and photoinduced oxidation. The study's findings contribute new insights into the environmental fate of profoxydim, offering a deeper understanding of its transformation in rice paddy fields and aiding in the assessment of potential risks associated with its residues in agricultural environments., (© 2024. The Author(s).)

An efficacious strategy to adapt to climate change involves optimizing the planting season, a technique that has been extensively utilized to enhance the use of solar radiation and temperature resources in rice cultivation. Field experiments were executed in the middle and lower reaches of the Yangtze River, China, employing three distinct rice cultivars and seven disparate sowing periods spanning 2019 to 2021. The objective of assessing the impact of sowing date on apparent radiation use efficiency (RUE A ), accumulated temperature use efficiencies (TUE), and overall rice yield. Subsequent to the delay of sowing dates, the duration of the comprehensive growth period initially exhibited a declining trajectory before subsequently escalating, with the reduction predominantly ascribed to a decrease in the number of days preceding heading. Furthermore, there was a tendency for both the mean daily and effective cumulative solar radiation to decline over the course of the growing period. The yield of the three rice varieties demonstrated an initial surge, which was then followed by a subsequent decline in reaction to the delay of sowing dates. A correlation analysis disclosed that solar radiation and effective cumulative temperature (EAT) were the predominant elements impacting grain yield. The outcomes of the path analysis indicate that EAT exerts the most substantial influence on yield, succeeded by cumulative total solar radiation (TSR), while photothermal quotient (PTQ) demonstrates the least impact on yield. There was a significant positive correlation between EAT and cumulative TSR with spikelets per panicle (0.237** and 0.218**), grain filling (0.753** and 0.576**), and grain weight (0.339** and 0.359**), respectively. The findings of this study indicate that an increase in yield is facilitated when the EAT after heading exceeds 594.9 ℃, the EAT surpasses 2016.7 ℃, the cumulative TSR before heading is above 1548.7 MJ m - 2 , the cumulative TSR after heading is over 603.0 MJ m - 2 , and the cumulative total radiation throughout the entire growth period is more than 2151.8 MJ m - 2 . Furthermore, the most optimal sowing date, as identified by this study, is June 6. This study provides key insights into boosting rice productivity in the middle and lower reaches of the Yangtze River, China by analyzing the impact of temperature and solar radiation on yield and identifying optimal growth conditions. Clinical trial number Not applicable., (© 2024. The Author(s).)

Gamma irradiation-based mutant creation is one of the most important methods for rice plant mutagenesis breeding and molecular biology research. Although median lethal dose irradiation severely damages rice seedlings, applying brassinolide (BR) can increase the survival rate of irradiated seedlings. In this study, we investigated the effects of soaking seeds in solutions containing different BR concentrations (0.001, 0.01, 0.1, 1.0, and 5.0 μmol/L) and then spraying the resulting seedlings twice with 0.1 μmol/L BR. The combined BR treatments markedly decreased the superoxide anion (O 2 •- ), hydrogen peroxide (H 2 O 2 ), and malondialdehyde contents but increased the chlorophyll content. An appropriate BR treatment of gamma-irradiated samples substantially increased the activities of the antioxidant enzymes superoxide dismutase, peroxidase, and ascorbate peroxidase as well as the proline, ascorbic acid, and glutathione contents in rice seedling shoots. The BR treatment also promoted the growth of seedlings derived from irradiated seeds and increased the shoot and root fresh and dry weights. Most notably, soaking seeds in 0.01 or 0.1 μmol/L BR solutions and then spraying seedlings twice with 0.1 μmol/L BR significantly increased the final seedling survival rate and decreased mutant loss. The study results suggest that exogenous BR treatments can protect rice seedlings from gamma irradiation stress by enhancing antioxidant metabolism.

The main aim of this work was to better understand how the low temperature signal from the leaves may affect the stress responses in the roots, and how the light conditions modify certain stress acclimation processes in rice plants. Rice plants grown at 27°C were exposed to low temperatures (12°C) with different light intensities, and in the case of some groups of plants, only the leaves received the cold, while the roots remained at control temperature. RNA sequencing focusing on the roots of plants grown under normal growth light conditions found 525 differentially expressed genes in different comparisons. Exposure to low temperature led to more down-regulated than up-regulated genes. Comparison between roots of the leaf-stressed plants and whole cold-treated or control plants revealed that nitrogen metabolism and nitric oxide-related signalling, as well as the phenylpropanoid-related processes, were specifically affected. Real-time PCR results focusing on the COLD1 and polyamine oxidase genes, as well as metabolomics targeting hormonal changes and phenolic compounds also showed that not only cold exposure of the leaves, either alone or together with the roots, but also the light conditions may influence certain stress responses in the roots of rice plants., (© 2024 Scandinavian Plant Physiology Society.)

Maharaji rice, an aromatic variety with medium slender grains, is traditionally cultivated in the central regions of India. This study aimed to identify the biochemical compounds responsible for Maharaji rice's distinctive fragrance and enhance its agro-morphological traits through mutation breeding. Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis, forty major metabolites were identified which may be responsible for its characteristic aroma. The bioactive compounds included terpenes, flavonoids, and amino acids. Maharaji brown rice extract exhibited potent radical scavenging activity. Radiation-induced mutation breeding improved the agro-morphological traits and also triggered biochemical diversification in different mutants. Maharaji Mutant-2 exhibited improved aroma due to higher abundance of aromatic compounds, improved yield and morphological characters as compared to the parent. This study, for the first time identifies the compounds associated with the characteristic aroma of Maharaji rice. Global metabolomics may, therefore, expedite the selection of mutants with suitable aroma and desirable biological properties., Competing Interests: Declaration of competing interest The authors declare that they have no known competing interests related to the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Background: UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the molecular mechanisms underlying the response to UV-B stress remain elusive in rice., Results: We perform comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal light conditions using a widely targeted metabolomics approach. Our results reveal substantial differences in metabolite accumulation between the two major rice subspecies indica and japonica, especially after UV-B treatment, implying the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response. We next conduct a transcriptome analysis from four representative rice varieties under UV-B stress, revealing genes from amino acid and flavonoid pathways involved in the UV-B response. We further perform a metabolite-based genome-wide association study (mGWAS), which reveals 3307 distinct loci under UV-B stress. Identification and functional validation of candidate genes show that OsMYB44 regulates tryptamine accumulation to mediate UV-B tolerance, while OsUVR8 interacts with OsMYB110 to promote flavonoid accumulation and UV-B tolerance in a coordinated manner. Additionally, haplotype analysis suggests that natural variation of OsUVR8 groupA contributes to UV-B resistance in rice., Conclusions: Our study reveals the complex biochemical and genetic foundations that govern the metabolite dynamics underlying the response, tolerance, and adaptive strategies of rice to UV-B stress. These findings provide new insights into the biochemical and genetic basis of the metabolome underlying the crop response, tolerance, and adaptation to UV-B stress., (© 2024. The Author(s).)

Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.

The long-term cultivation of higher plants in space plays a substantial role in investigating the effects of microgravity on plant growth and development, acquiring valuable insights for developing a self-sustaining space life supporting system. The completion of the Chinese Space Station (CSS) provides us with a new permanent space experimental platform for long-term plant research in space. Biological Culture Module (GBCM), which was installed in the Wentian experimental Module of the CSS, was constructed with the objective of growing Arabidopsis thaliana and rice plants a full life cycle in space. The techniques of LED light control, gas regulation and water recovery have been developed for GBCM in which dry seeds of Arabidopsis and rice were set in root module of four culture chambers (CCs) and launched with Wentian module on July 24, 2022. These seeds were watered and germinated from July 28 and grew new seeds until November 26 within a duration of 120 days. To this end, both Arabidopsis and rice plants completed a full life cycle in microgravity on the CSS. As we know, this is the first space experiment achieving rice complete life cycle from seed-to-seed in space. This result demonstrates the possibility to cultivate the important food crop rice throughout its entire life cycle under the spaceflight environment and the technologies of GBCM have effectively supported the success of long-term plant culture experiments in space. These results can serve as invaluable references for constructing more expansive and intricate space plant cultivation systems in the future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Committee on Space Research (COSPAR). Published by Elsevier B.V. All rights reserved.)

Plants use light as a resource and signal. Photons within the 400-700 nm waveband are considered photosynthetically active. Far-red photons (FR, 700-800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot-architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO 2 -fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR-enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end-of-day FR pulse, this prevented photosynthesis-promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy., (© 2024 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

In plants, the conserved plant-specific photoreceptor UV RESISTANCE LOCUS 8 (UVR8) perceives ultraviolet-B (UV-B) light and mediates UV-B-induced photomorphogenesis and stress acclimation. In this study, we reveal that UV-B light treatment shortens seedlings, increases stem thickness, and enhances UV-B stress tolerance in rice (Oryza sativa) via its two UV-B photoreceptors OsUVR8a and OsUVR8b. Although the rice and Arabidopsis (Arabidopsis thaliana) UVR8 (AtUVR8) photoreceptors all form monomers in response to UV-B light, OsUVR8a, and OsUVR8b function is only partially conserved with respect to AtUVR8 in UV-B-induced photomorphogenesis and stress acclimation. UV-B light and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) promote the nuclear accumulation of AtUVR8; by contrast, OsUVR8a and OsUVR8b constitutively localize to the nucleus via their own nuclear localization signals, independently of UV-B light and the RING-finger mutation of OsCOP1. We show that OsCOP1 negatively regulates UV-B responses, and shows weak interaction with OsUVR8s, which is ascribed to the N terminus of OsCOP1, which is conserved in several monocots. Furthermore, transcriptome analysis demonstrates that UV-B-responsive gene expression differs globally between Arabidopsis and rice, illuminating the evolutionary divergence of UV-B light signaling pathways between monocot and dicot plants., (© 2024. The Author(s).)

Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Plant leaves contain multiple cell types which achieve distinct characteristics whilst still coordinating development within the leaf. The bundle sheath possesses larger individual cells and lower chloroplast content than the adjacent mesophyll, but how this morphology is achieved remains unknown. To identify regulatory mechanisms determining bundle sheath cell morphology we tested the effects of perturbing environmental (light) and endogenous signals (hormones) during leaf development of Oryza sativa (rice). Total chloroplast area in bundle sheath cells was found to increase with cell size as in the mesophyll but did not maintain a 'set-point' relationship, with the longest bundle sheath cells demonstrating the lowest chloroplast content. Application of exogenous cytokinin and gibberellin significantly altered the relationship between cell size and chloroplast biosynthesis in the bundle sheath, increasing chloroplast content of the longest cells. Delayed exposure to light reduced the mean length of bundle sheath cells but increased corresponding leaf length, whereas premature light reduced final leaf length but did not affect bundle sheath cells. This suggests that the plant hormones cytokinin and gibberellin are regulators of the bundle sheath cell-chloroplast relationship and that final bundle sheath length may potentially be affected by light-mediated control of exit from the cell cycle., (© 2024 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

UV RESISTANCE LOCUS 8 (UVR8) has been identified in Arabidopsis thaliana as the receptor mediating responses to UV-B radiation. However, UVR8-mediated UV-B signaling pathways in rice, which possesses two proteins (UVR8a and UVR8b) with high identities to AtUVR8, remain largely unknown. Here, UVR8a/b were found to be predominantly expressed in rice leaves and leaf sheaths, while the levels of UVR8b transcript and UVR8b protein were both higher than those of UVR8a. Compared to wild-type (WT) plants, uvr8b and uvr8a uvr8b rice mutants exposed to UV-B showed reduced UV-B-induced growth inhibition and upregulation of CHS and HY5 transcripts alongside UV-B acclimation. However, uvr8a mutant was similar to WT plants and exhibited changes comparable with WT. Overexpressing OsUVR8a/b enhanced UV-B-induced growth inhibition and acclimation to UV-B. UV-B was able to enhance the interaction between E3 ubiquitin ligase OsCOP1 and OsUVR8a/b, whereas the interaction of the homologous protein of Arabidopsis REPRESSOR OF UV-B PHOTOMORPHOGENESIS2 (AtRUP2) in rice with OsUVR8a/b was independent of UV-B. Additionally, OsUVR8a/b proteins were also found in the nucleus and cytoplasm even in the absence of UV-B. The abundance of OsUVR8 monomer showed an invisible change in the leaves of rice seedlings transferred from white light to that supplemented with UV-B, even though UV-B was able to weaken the interactions between OsUVR8a and OsUVR8b homo and heterodimers. Therefore, both OsUVR8a and OsUVR8b, which have different localization and response patterns compared with AtUVR8, function in the response of rice to UV-B radiation, whereas OsUVR8b plays a predominant role in this process., (© 2024 Scandinavian Plant Physiology Society.)

Acclimation to crop niches for thousands of years has made indigenous rice cultivars better suited for stress-prone environments. Still, their response to UV-B resiliency is unknown. 38 rice landraces were grown in cemented pots in a randomised block design with three replicates under open field conditions in Sambalpur University in the wet season of 2022. Half of the plants in each of the cultivars were administered UV-B radiation at the panicle emergence stage in an adjustable UV-B chamber permitting sunlight, and the effects of the stress on various morpho-physiological features, such as spikelet sterility, flag leaf photosynthetic and flavonoid pigment contents, and lipid peroxidation activities, were estimated for calibration of stress resistance. The experiment identified Swarnaprabha and Lalkain as the most sensitive and resilient to stress respectively, and the differential response between them was further revealed in the expression of genes related to UV-B sensitivity. Subject to the stress, Swarnaprabha exhibited symptoms of injuries, like leaf burns, and a higher loss of various photosynthetic parameters, such as pigment contents, SPAD and Fv/Fm, ETR and qP values, while NPQ increased only in Lalkain. Exposure to UV-B increased the total phenolic and flavonoid contents in Lalkain while depressing them in Swarnaprabha. Such an effect amounted to a higher release of fluorescent energy in the latter. The levels of expression of gene families controlling flavonoid activation and UV-B signal transduction, such as OsWRKY, OsUGT, OsRLCK, OsBZIP, OsGLP, and CPD photolyase were similar in both the cultivars in the control condition. However, exposure to UV-B stress overexpressed them in resilient cultivars only. The magnitude of expression of the genes and the impact of the stress on photosynthetic parameters, phenolic compounds and pubescent hair structure at the panicle emergence stage could be valid indicators among indigenous rice for UV-B tolerance., (© 2024. The Author(s).)

As a physical mutagen, carbon ion beam (CIB) irradiation can induce high-frequency mutation, which is user-friendly and environment-friendly in plant breeding. In this study, we resequenced eight mutant lines which were screened out from the progeny of the CIB-irradiated dehulled rice seeds. Among these mutants, CIB induced 135,535 variations, which include single base substitutions (SBSs), and small insertion and deletion (InDels). SBSs are the most abundant mutation, and account for 88% of all variations. Single base conversion is the main type of SBS, and the average ratio of transition and transversion is 1.29, and more than half of the InDels are short-segmented mutation (1-2 bp). A total of 69.2% of the SBSs and InDels induced by CIBs occurred in intergenic regions on the genome. Surprisingly, the average mutation frequency in our study is 9.8 × 10 -5 /bp and much higher than that of the previous studies, which may result from the relatively high irradiation dosage and the dehulling of seeds for irradiation. By analyzing the mutation of every 1 Mb in the genome of each mutant strain, we found some unusual high-frequency (HF) mutation regions, where SBSs and InDels colocalized. This study revealed the mutation mechanism of dehulled rice seeds by CIB irradiation on the genome level, which will enrich our understanding of the mutation mechanism of CIB radiation and improve mutagenesis efficiency.

Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

The effect of UV-B radiation exposure on transgenerational plasticity, the phenomenon whereby the parental environment influences both the parent's and the offspring's phenotype, is poorly understood. To investigate the impact of exposing successive generations of rice plants to UV-B radiation on seed morphology and proanthocyanidin content, the local traditional rice variety 'Baijiaolaojing' was planted on terraces in Yuanyang county and subjected to enhanced UV-B radiation treatments. The radiation intensity that caused the maximum phenotypic plasticity (7.5 kJ·m -2 ) was selected for further study, and the rice crops were cultivated for four successive generations. The results show that in the same generation, enhanced UV-B radiation resulted in significant decreases in grain length, grain width, spike weight, and thousand-grain weight, as well as significant increases in empty grain percentage and proanthocyanidin content, compared with crops grown under natural light conditions. Proanthocyanidin content increased as the number of generations of rice exposed to radiation increased, but in generation G3, it decreased, along with the empty grain ratio. At the same time, biomass, tiller number, and thousand-grain weight increased, and rice growth returned to control levels. When the offspring's radiation memory and growth environment did not match, rice growth was negatively affected, and seed proanthocyanidin content was increased to maintain seed activity. The correlation analysis results show that phenylalanine ammonialyase (PAL), cinnamate-4-hydroxylase (C4H), dihydroflavonol 4-reductase (DFR), and 4-coumarate:CoA ligase (4CL) enzyme activity positively influenced proanthocyanidin content. Overall, UV-B radiation affected transgenerational plasticity in seed morphology and proanthocyanidin content, showing that rice was able to adapt to this stressor if previous generations had been continuously exposed to treatment.

Environmental variation has a significant impact on how organisms, including cyanobacteria, respond physiologically and biochemically. Salinity and ultraviolet radiation (UVR)-induced variations in the photopigments of the rice-field cyanobacterium Nostochopsis lobatus HKAR-21 and its photosynthetic performance was studied. We observed that excessive energy dissipation after UVR is mostly caused by Non-Photochemical Quenching (NPQ), whereas photochemical quenching is important for preventing photoinhibition. These findings suggest that ROS production may play an important role in the UVR-induced injury. To reduce ROS-induced oxidative stress, Nostochopsis lobatus HKAR-21 induces the effective antioxidant systems, which includes different antioxidant compounds like carotenoids and enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). The study indicates that Nostochopsis lobatus HKAR-21 exposed to photosynthetically active radiation + UV-A + UV-B (PAB) and PAB + NaCl (PABN) had significantly reduced photosynthetic efficiency. Furthermore, maximum ROS was detected in PAB exposed cyanobacterial cells. The induction of lipid peroxidation (LPO) has been investigated to evaluate the impact of UVR on the cyanobacterial membrane in addition to enzymatic defensive systems. The maximal LPO level was found in PABN treated cells. Based on the findings of this research, it was concluded that salinity and UVR had collegial effects on the major macromolecular components of the rice-field cyanobacterium Nostochopsis lobatus HKAR-21., (© 2023. The Author(s), under exclusive licence to European Photochemistry Association, European Society for Photobiology.)

Gamma radiation ( 60 Co)-induced mutagenesis offers an alternative to develop rice lines by accelerating the spontaneous mutation process and increasing the pool of allelic variants available for breeding. Ionizing radiation works by direct or indirect damage to DNA and subsequent mutations. The technique can take advantage of in vitro protocols to optimize resources and accelerate the development of traits. This is achieved by exposing mutants to a selection agent of interest in controlled conditions and evaluating large numbers of plants in reduced areas. This chapter describes the protocol for establishing gamma radiation dosimetry and in vitro protocols for optimization at the laboratory level using seeds as the starting material, followed by embryogenic cell cultures, somatic embryogenesis, and regeneration. The final product of the protocol is a genetically homogeneous population of Oryza sativa that can be evaluated for breeding against abiotic and biotic stresses., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Sensitivity to ultraviolet-B (UVB, 280-315 nm) radiation varies widely among rice (Oryza sativa) cultivars due to differences in the activity of cyclobutane pyrimidines dimer (CPD) photolyase. Interestingly, cultivars with high UVB sensitivity and low CPD photolyase activity have been domesticated in tropical areas with high UVB radiation. Here, we investigated how differences in CPD photolyase activity affect plant resistance to the rice blast fungus, Magnaporthe oryzae, which is one of the other major stresses. We used Asian and African rice cultivars and transgenic lines with different CPD photolyase activities to evaluate the interaction effects of CPD photolyase activity on resistance to M. oryzae. In UVB-resistant rice plants overexpressing CPD photolyase, 12 h of low-dose UVB (0.4 W m -2 ) pretreatment enhanced sensitivity to M. oryzae. In contrast, UVB-sensitive rice (transgenic rice with antisense CPD photolyase, A-S; and rice cultivars with low CPD photolyase activity) showed resistance to M. oryzae. Several defense-related genes were upregulated in UVB-sensitive rice compared to UVB-resistant rice. UVB-pretreated A-S plants showed decreased multicellular infection and robust accumulation of reactive oxygen species. High UVB-induced CPD accumulation promoted defense responses and cross-protection mechanisms against rice blast disease. This may indicate a trade-off between high UVB sensitivity and biotic stress tolerance in tropical rice cultivars., (© 2023. The Author(s).)

Mutation breeding is a significant means of increasing breeding efficiency and accelerating breeding process. In present study, we explored a new method for mutations inducing in rice (Oryza sativa L.) by using direct current electrophoresis bath (DCEB). The results showed that 20 mM NaCl solution is the optimal buffer, and the mortality of rice seeds followed an upward trend with increasing voltage and processing time of DCEB. By exploring the mutagenic effects of γ-irradiation and DCEB on seed vigor and physiological damages, we found that the physiological damages induced by DCEB on seed vigor were significant compared with that by γ-irradiation. We screened two mutants with low filled grain percentage and one mutant with abnormal hull from the M 2 generations. These three mutants were confirmed to be authentic mutants based on 48 SSR markers followed by the protocol NY/T 1433-2014. Whole-genome resequencing detected a total of 503 and 537 polymorphisms in the two mutants, respectively, and the DCEB mutagenesis induced mainly InDel variants, while the exon region of mutant genes occupied a large proportion, especially the SNP variants, which occupied about 20% of the mutation sites in the exon region., (© 2023. The Author(s).)

Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO ( LUX ) and EARLY FLOWERING3 ( ELF3 ) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7 . We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.

Ligands plays an important role in the extraction procedures for the determination of cadmium in rice samples by using flame atomic absorption spectrometry (FAAS). In the present study, comparative evaluation of 10 commercially available ligands for formation of Cd(II)-ligand complex and determination of cadmium in rice samples by ultrasound-assisted dispersive liquid-liquid microextraction (UADLLME) combined with FAAS was developed. Sodium diethyldithiocarbamate (DDTC) provided a high distribution coefficient as well as a good absorbance signal, therefore DDTC was used as a ligand in UADLLME. A low density and less toxic solvent, 1-heptanol, was used as the extraction solvent and ethanol was used as the disperser solvent. In addition, the experimental conditions of UADLLME were optimized in standard solution first and then applied in rice, such as the type and volume of extractant and dispersant, pH, extraction time, and temperature. Under the optimal experimental conditions, the detection limit (3σ) was 0.69 μg/L for Cd(II). The proposed method was applied for the determination of Cd(II) in three different rice samples (polished rice, brown rice, and glutinous rice), the recovery test was carried out, and the results ranged between 96.7 to 113.6%. The proposed method has the advantages of simplicity, low cost, and accurate and was successfully applied to analyze Cd(II) in rice.

The prebiotic properties of xylooligosaccharides (XOS) and arabino-xylooligosaccharides (AXOS) produced from rice husk (RH) using microwave treatment combined with enzymatic hydrolysis were evaluated. The RH was subjected to microwave pretreatment at 140, 160 and 180 °C for 5, 10 and 15 min to obtain crude arabinoxylan (AX). Increasing microwave pretreatment time increased sugar content. Crude AX was extracted with 2% (w/v) sodium hydroxide at 25 °C for 24 h and used as a substrate for XOS production by commercial xylanases. Results showed that oligosaccharides produced by Pentopan Mono BG and Ultraflo Max provided xylobiose and xylotriose as the main products. AXOS was also present in the oligosaccharides that promoted growth of Lactobacillus spp. and resisted degradation by over 70% after exposure to simulated human digestion., (© 2022. The Author(s).)

Purpose: Rice is a prime staple crop for more than half of the world population. Improved White Ponni (IWP) is a premium quality grain rice variety that is fetching a good price and is increasingly popular among the consumers of Tamil Nadu. Tall plant stature of IWP makes them susceptible to lodging and medium duration are two undesirable traits in the variety increases yield losses in the field and also productivity. In this context, we aimed to generate a large mutant population of IWP irradiated with various doses of gamma irradiation to recover putative mutants for semi-dwarfism and earliness., Materials and Methods: Totally, 34 putative mutants ( 22 early, 11 semi-dwarf and early and 1 Narrow-leaf dwarf mutant) were phenotyped for nine morphological traits and genotyped using 34 microsatellite markers linked to a trait of interest of earliness and semi-dwarfism. Trait variability, allelic variations, genetic structure and marker-trait associations in gamma-irradiated putative mutants of Improved White Ponni (IWP) rice were investigated in this study., Results: The hierarchical clustering of morphological data produced five clusters with a dissimilarity coefficient of 1.39. A minimum dissimilarity coefficient of 0.23 was observed between the mutants IWPM9 and IWPM20 and a maximum dissimilarity coefficient of 2.55 was observed between IWPM1 and IWPM25. In cluster analysis with molecular marker data, five clusters with a similarity coefficient of 0.67 were observed. The mutant IWPM29 exhibited the most divergence from the wild type at the genotype level. The first principal component explained 50.99% of the total variability and the majority of the traits were contributed positively. The single-marker analysis revealed the strong association of SSR marker RM3912 with the traits plant height, panicle length and number of grains per panicle with an R 2 value of 0.235, 0.235 and 0.250 respectively., Conclusions: The study identified semi-dwarf and short-duration rice mutants of IWP that can be utilized as potential breeding stocks. The trait-linked SSR markers can improve selection cycles in advanced breeding programs.

Cryptochrome 1 and 2 (CRY1 and CRY2) are blue light receptors involved in the regulation of hypocotyl elongation, cotyledon expansion, and flowering time in Arabidopsis thaliana . Two cryptochrome-interacting proteins, Blue-light Inhibitor of Cryptochrome 1 and 2 (BIC1 and BIC2), have been found in Arabidopsis . BIC1 plays critical roles in suppressing the physiological activities of CRY2, which include the blue light-dependent dimerization, phosphorylation, photobody formation, and degradation process, but the functional characterization of BIC protein in other crops has not yet been performed. To investigate the function of BIC protein in rice ( Oryza sativa ), two homologous genes of Arabidopsis   BIC1 and BIC2 , namely OsBIC1 and OsBIC2  ( OsBICs ), were identified. The overexpression of OsBIC1 and OsBIC2 led to increased leaf sheath length, whereas mutations in OsBIC1 displayed shorter leaf sheath in a blue light intensity-dependent manner. OsBIC1 regulated blue light-induced leaf sheath elongation through direct interaction with OsCRY1a, OsCRY1b, and OsCRY2 (OsCRYs). Longitudinal sections of the second leaf sheath demonstrated that OsBIC1 and OsCRYs controlled leaf sheath length by influencing the ratio of epidermal cells with different lengths. RNA-sequencing (RNA-seq) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) analysis further proved that OsBIC1 and OsCRYs regulated similar transcriptome changes in regulating Gibberellic Acids (GA)-responsive pathway. Taken together, these results suggested that OsBIC1 and OsCRYs worked together to regulate epidermal cell elongation and control blue light-induced leaf sheath elongation through the GA-responsive pathway.

Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the "replication and repair" pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.

Background: Glycolate oxidase (GLO) is not only a key enzyme in photorespiration but also a major engine for H 2 O 2 production in plants. Catalase (CAT)-dependent H 2 O 2 decomposition has been previously reported to be involved in the regulation of IAA biosynthesis. However, it is still not known which mechanism contributed to the H 2 O 2 production in IAA regulation., Results: In this study, we found that in glo mutants of rice, as H 2 O 2 levels decreased IAA contents significantly increased, whereas high CO 2 abolished the difference in H 2 O 2 and IAA contents between glo mutants and WT. Further analyses showed that tryptophan (Trp, the precursor for IAA biosynthesis in the Trp-dependent biosynthetic pathway) also accumulated due to increased tryptophan synthetase β (TSB) activity. Moreover, expression of the genes involved in Trp-dependent IAA biosynthesis and IBA to IAA conversion were correspondingly up-regulated, further implicating that both pathways contribute to IAA biosynthesis as mediated by the GLO-dependent production of H 2 O 2 ., Conclusion: We investigated the function of GLO in IAA signaling in different levels from transcription, enzyme activities to metabolic levels. The results suggest that GLO-dependent H 2 O 2 signaling, essentially via photorespiration, confers regulation over IAA biosynthesis in rice plants.

Background: Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy., Results: A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts., Conclusion: The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.

High energy ion beams are effective physical mutagens for mutation induction in plants. Due to their high linear energy transfer (LET) property, they are known to generate single nucleotide variations (SNVs) and insertion/deletions (InDels, <50 bp) as well as structural variations (SVs). However, due to the technical difficulties to identify SVs, studies on ion beam induced SVs by genome sequencing have so far been limited in numbers and inadequate in nature, and knowledge of SVs is scarce with regards to their characteristics. In the present study, we identified and validated SVs in six M 4 plants (designated as Ar&#95;50, Ar&#95;100, C&#95;150, C&#95;200, Ne&#95;50 and Ne&#95;100 according to ion beam types and irradiation doses), two each induced by argon ( 40 Ar 18+ ), carbon ( 12 C 6+ ) and neon ( 20 Ne 10+ ) ion beams and performed in depth analyses of their characteristics. In total, 22 SVs were identified and validated, consisting of 11 deletions, 1 duplication, and 4 intra-chromosomal and 6 inter-chromosomal translocations. There were several SVs larger than 1 kbp. The SVs were distributed across the whole genome with an aggregation with SNVs and InDels only in the Ne&#95;50 mutants. An enrichment of a 11-bp wide G-rich DNA motif 'GAAGGWGGRGG' was identified around the SV breakpoints. Three mechanisms might be involved in the SV formation, i.e., the expansion of tandem repeats, transposable element insertion, and non-allelic homologous recombination. Put together, the present study provides a preliminary view of SVs induced by Ar, C and Ne ion beam radiations, and as a pilot study, it contributes to our understanding of how SVs might form after ion beam irradiation in rice., (Copyright © 2021 Elsevier B.V. All rights reserved.)

When exposed to high light, plants produce reactive oxygen species (ROS). In Arabidopsis thaliana , local stress such as excess heat or light initiates a systemic ROS wave in phloem and xylem cells dependent on NADPH oxidase/respiratory burst oxidase homolog (RBOH) proteins. In the case of excess light, although the initial local accumulation of ROS preferentially takes place in bundle-sheath strands, little is known about how this response takes place. Using rice and the ROS probes diaminobenzidine and 2',7'-dichlorodihydrofluorescein diacetate, we found that, after exposure to high light, ROS were produced more rapidly in bundle-sheath strands than mesophyll cells. This response was not affected either by CO 2 supply or photorespiration. Consistent with these findings, deep sequencing of messenger RNA (mRNA) isolated from mesophyll or bundle-sheath strands indicated balanced accumulation of transcripts encoding all major components of the photosynthetic apparatus. However, transcripts encoding several isoforms of the superoxide/H 2 O 2 -producing enzyme NADPH oxidase were more abundant in bundle-sheath strands than mesophyll cells. ROS production in bundle-sheath strands was decreased in mutant alleles of the bundle-sheath strand preferential isoform of OsRBOHA and increased when it was overexpressed. Despite the plethora of pathways able to generate ROS in response to excess light, NADPH oxidase-mediated accumulation of ROS in the rice bundle-sheath strand was detected in etiolated leaves lacking chlorophyll. We conclude that photosynthesis is not necessary for the local ROS response to high light but is in part mediated by NADPH oxidase activity., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Exposure to ultraviolet B radiation (UV-B) stress can have serious effects on the growth and development of plants. Germin-like proteins (GLPs) may be involved in different abiotic and biotic stress responses in different plants, but little is known about the role of GLPs in UV-B stress response and acclimation in plants. In the present study, knockout of GLP 8-14 (OsGLP1) using the CRISPR/Cas9 system resulted in mutant rice (Oryza sativa L.) plants (herein called glp1) that exhibited UV-B-dependent formation of lesion mimic in leaves. Moreover, glp1 grown under solar radiation (including UV-B) showed decreased plant height and increased leaf angle, but we observed no significant differences in phenotypes between wild-type (WT) plants and glp1 grown under artificial light lacking UV-B. Fv/Fm, Y (II) and the expression of many genes, based on RNA-seq analysis, related to photosynthesis were also only reduced in glp1, but not in WT, after transfer from a growth cabinet illuminated with artificial white light lacking UV-B to growth under natural sunlight. The genes-associated with flavonoid metabolism as well as UV resistance locus 8 (OsUVR8), phytochrome interacting factor-like 15-like (OsPIF3), pyridoxal 5'-phosphate synthase subunit PDX1.2 (OsPDX1.2), deoxyribodipyrimidine photolyase (OsPHR), and deoxyribodipyrimidine photolyase family protein-like (OsPHRL) exhibited lower expression levels, while higher expression levels of mitogen-activated protein kinase 5-like (OsMPK3), mitogen-activated protein kinase 13-like (OsMPK13), and transcription factor MYB4-like (OsMYB4) were observed in glp1 than in WT after transfer from a growth cabinet illuminated with artificial white light to growth under natural sunlight. Therefore, mutations in OsGLP1 resulted in rice plants more sensitive to UV-B and reduced expression of some genes for UV-B protection, suggesting that OsGLP1 is involved in acclimation to UV-B radiation., (© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Responses of rice seedlings to UV-B radiation (UV-B) were investigated, aiming to establish rice as a model plant for UV-B signalling studies. The growth of japonica rice coleoptiles, grown under red light, was inhibited by brief irradiation with UV-B, but not with blue light. The effective UV-B fluences (10 -1 -10 3 μmol m -2 ) were much lower than those reported in Arabidopsis. The response was much less in indica rice cultivars and its extent varied among Oryza species. We next identified UV-B-specific anthocyanin accumulation in the first leaf of purple rice and used this visible phenotype to isolate mutants. Some isolated mutants were further characterized, and one was found to have a defect in the growth response. Using microarrays, we identified a number of genes that are regulated by low-fluence-rate UV-B in japonica coleoptiles. Some up-regulated genes were analysed by real-time PCR for UV-B specificity and the difference between japonica and indica. More than 70% of UV-B-regulated rice genes had no homologs in UV-B-regulated Arabidopsis genes. Many UV-B-regulated rice genes are related to plant hormones and especially to jasmonate biosynthetic and responsive genes in apparent agreement with the growth response. Possible involvement of two rice homologs of UVR8, a UV-B photoreceptor, is discussed., (© 2020 John Wiley & Sons Ltd.)

The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model photosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosynthetic parameters using concurrent gas exchange and chlorophyll fluorescence measurements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, K m , that is, Michaelis constant for CO 2 by Rubisco, prefixed. Additionally, we show that including detailed low CO 2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement protocols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided., (© 2021 John Wiley & Sons Ltd.)

We identified a rapid cell death 2 ( rcd2 ) mutant from an indica cultivar Zhongjian100 mutant bank. The red-brown lesions appeared firstly on young seedling leaves, then gradually merged and the leaves completely withered at the late tillering stage. rcd2 displayed apparent cell death at/around the lesions, accumulation of superoxide anion (O 2 - ) and disturbed ROS scavenging system, impaired photosynthetic capacity with significantly reduced chlorophyll content. The lesion formation was controlled by a single recessive nuclear gene and induced by natural light as well as mechanical wounding. A single base mutation (A1726T) at the 6th exon of OsMH&#95;03G0040800 resulted in I576F substitution in the encoding protein, pheophorbide a oxygenase (PAO). Functional complementation could rescue the mutant phenotype and PAO- knockout lines exhibited the similar phenotype to rcd2 . The activity of PAO decreased significantly while the content of PAO substrate, pheophorbide a, increased apparently in rcd2 . The expression of chlorophyll synthesis/degradation-related genes and the contents of metabolic intermediates were largely changed. Furthermore, the level of chlorophyllide a, the product of chlorophyllase, increased significantly, indicating chlorophyllase might play a role in chlorophyll degradation in rice. Our results suggested that the I576F substitution disrupted PAO function, leading to O 2 - accumulation and chlorophyll degradation breakdown in rice.

Long-term fluctuating light (FL) conditions are very common in natural environments. The physiological and biochemical mechanisms for acclimation to FL differ between species. However, most of the current conclusions regarding acclimation to FL were made based on studies in algae or Arabidopsis thaliana. It is still unclear how rice (Oryza sativa L.) integrate multiple physiological changes to acclimate to long-term FL. In this study, we found that rice growth was repressed under long-term FL. By systematically measuring phenotypes and physiological parameters, we revealed that: (a) under short-term FL, photosystem I (PSI) was inhibited, while after 1-7 days of long-term FL, both PSI and PSII were inhibited. Higher acceptor-side limitation in electron transport and higher overall nonphotochemical quenching (NPQ) explained the lower efficiencies of PSI and PSII, respectively. (b) An increase in pH differences across the thylakoid membrane and a decrease in thylakoid proton conductivity revealed a reduction of ATP synthase activity. (c) Using electron microscopy, we showed a decrease in membrane stacking and stomatal opening after 7 days of FL treatment. Taken together, our results show that electron flow, ATP synthase activity and NPQ regulation are the major processes determining the growth performance of rice under long-term FL conditions., (© 2020 John Wiley & Sons Ltd.)

The formation of fungal colonies, mycotoxins, phenolic compounds, cooking quality and color properties were evaluated in freshly-harvested brown, black, and red rice grains and then subjected to ultraviolet radiation (UV-C) for 1 and 3 h. Assessments were made after 6 months of storage. The exposure of black and red rice at 1 h of UV-C was enough to decrease the presence of fungal colonies by 22% and 79%, respectively, without any changes in cooking and coloring properties. In brown rice, only 3 h of UV-C irradiation was able to reduce the formation of fungal colonies. The release of phenolic compounds associated with cell wall was observed only in black and red rice subjected to UV-C radiation. The levels of mycotoxins gradually decreased with the increase in the time of exposure to UV-C radiation, demonstrating UV-C irradiation to be an effective method in fungal control and reduction of mycotoxins in stored rice., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Senescence in plants is induced by endogenous physiological changes and exogenous stresses. In this study, we isolated two alleles of a novel rice (Oryza sativa) mutant, yellow and premature dwarf 1 (ypd1). The ypd1 mutants exhibited a yellow and dwarf phenotype from germination, and premature senescence starting at tillering. Moreover, the ypd1 mutants were sensitive to high light, which accelerated cell death and senescence. Consistent with their yellow phenotype, the ypd1 mutants had abnormal chloroplasts and lower levels of photosynthetic pigments. TUNEL assays together with histochemical staining demonstrated that ypd1 mutants showed cell death and that they accumulated reactive oxygen species. The ypd1 mutants also showed increased expression of genes associated with senescence. Map-based cloning revealed a G→A substitution in exon 6 (ypd1-1) and exon 13 (ypd1-2) of LOC&#95;Os06g13050 that affected splicing and caused premature termination of the encoded protein. YPD1 was found to be preferentially expressed in the leaf and it encodes a LRR-like1 protein. Complementation, overexpression, and targeted deletion confirmed that the mutations in YPD1 caused the ypd1 phenotype. YPD1 was localized on the chloroplast membrane. Our results thus demonstrate that the novel rice LRR-like1 protein YPD1 affects chloroplast development and leaf senescence., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: Methyl-CpG-binding domain (MBD) proteins play important roles in epigenetic gene regulation, and have diverse molecular, cellular, and biological functions in plants. MBD proteins have been functionally characterized in various plant species, including Arabidopsis, wheat, maize, and tomato. In rice, 17 sequences were bioinformatically predicted as putative MBD proteins. However, very little is known regarding the function of MBD proteins in rice., Results: We explored the expression patterns of the rice OsMBD family genes and identified 13 OsMBDs with active expression in various rice tissues. We further characterized the function of a rice class I MBD protein OsMBD707, and demonstrated that OsMBD707 is constitutively expressed and localized in the nucleus. Transgenic rice overexpressing OsMBD707 displayed larger tiller angles and reduced photoperiod sensitivity-delayed flowering under short day (SD) and early flowering under long day (LD). RNA-seq analysis revealed that overexpression of OsMBD707 led to reduced photoperiod sensitivity in rice and to expression changes in flowering regulator genes in the Ehd1-Hd3a/RFT1 pathway., Conclusion: The results of this study suggested that OsMBD707 plays important roles in rice growth and development, and should lead to further studies on the functions of OsMBD proteins in growth, development, or other molecular, cellular, and biological processes in rice.

Chloroplast gene expression is controlled by both plastid-encoded RNA polymerase (PEP) and nuclear-encoded RNA polymerase and is crucial for chloroplast development and photosynthesis. Environmental factors such as light and temperature can influence transcription in chloroplasts. In this study, we showed that mutation in DUA1, which encodes a pentatricopeptide repeat (PPR) protein in rice (Oryza sativa), led to deficiency in chloroplast development and chlorophyll biosynthesis, impaired photosystems, and reduced expression of PEP-dependent transcripts at low temperature especially under low-light conditions. Furthermore, we demonstrated that sigma factor OsSIG1 interacted with DUA1 in vitro and in vivo. Moreover, the levels of chlorophyll and PEP-dependent gene expression were significantly decreased in the Ossig1 mutants at low-temperature and low-light conditions. Our study reveals that the PPR protein DUA1 plays an important role in regulating PEP-mediated chloroplast gene expression through interacting with OsSIG1, thus modulates chloroplast development in response to environmental signals.

Electromagnetic energy is the "backbone" of wireless communication systems, and its progressive use is considered to have a low but measurable impact on a wide range of biological systems. Even though a growing amount of data has reported electromagnetic energy absorption in humans along with subsequent biological effects, the consequences of electromagnetic energy absorption on plants have been insufficiently addressed. The higher surface to volume ratio along with the enormous water-ion concentrations makes the plant an ideal model to interact with non-ionizing electromagnetic radiation. In this study, controlled and periodic electromagnetic exposure of 1837.50 MHz, 2.75 W/m 2 for 6 h a day on a popular rice variety (var. Satabdi) reduced the seed germination rate. The same dose of periodic electromagnetic exposure upregulated phytochrome B and phytochrome C gene transcripts in 12-day-old seedlings, whereas, in 32-day-old plants, the dose upregulated calmodulin and phytochrome C while the bZIP1 gene showed repression. However, the transcript abundance of bZIP1, phytochrome B, and phytochrome C genes was enhanced even in 12-day-old Satabdi seedlings following instantaneous short-duration (2 h 30 min) controlled electromagnetic exposure to 1837.50 MHz, 2.75 W/m 2 . The reported responses in rice were observed below the international electromagnetic regulatory limits. Thus, rice plants perceived electromagnetic energy emitted by the wireless communication system as abiotic stress as per its response by upregulation or repression of known stress-sensing genes. Bioelectromagnetics. © 2020 Bioelectromagnetics Society., (© 2021 Bioelectromagnetics Society.)

The growth and development of plants are dependent on the interaction between carbon and nitrogen metabolism. Essential information about the metabolic regulation of carbon-nitrogen metabolism is still lacking, such as possible interactions among nitrogen metabolism, photosynthesis, and photorespiration. This study shows that higher photorespiration consumes more CO 2 fixed by photosynthesis, making the high photosynthetic efficiency mutant fail to increase production. In order to clarify the effects of photosynthesis and photorespiration on carbon and nitrogen metabolism in high photosynthetic efficiency mutant, a yellow-green leaf mutant ( ygl53 ) was isolated from rice ( Oryza sativa L.). Its chlorophyll (Chl) content decreased, but chloroplast development was not affected. Genetic analysis demonstrated that YGL53 encodes the magnesium chelatase D subunit (ChlD). The ygl53 mutant showed an increased net assimilation rate (An) and electron transport flux efficiency and catalase (CAT) activity, and it also had a higher photorespiration rate (Pr), lower H 2 O 2 , and reduced nitrogen uptake efficiency (NUpE); however, there was no loss in yield. The higher activities of glutamate synthase (GOGAT) and glutamine synthetase (GS) ensure the α-ketoglutaric acid (2-OG) and ammonia (NH 3 ) availabilities, which are produced from photorespiration in the ygl53 mutant. These have an important function for carbon and nitrogen metabolism homeostasis in ygl53 . Further analysis indicated that the energy and substances derived from carbon metabolism supplemented nitrogen metabolism in the form of photorespiration to ensure its normal development when the An of photosynthesis was increased in the ygl53 mutant with reduced NUpE.

The ultraviolet B (UVB) sensitivity of rice cultivated in Asia and Africa varies greatly, with African rice cultivars ( Oryza glaberrima Steud. and O. barthii A. Chev.) being more sensitive to UVB because of their low cyclobutane pyrimidine dimer (CPD) photolyase activity, which is a CPD repair enzyme, relative to Asian rice cultivars ( O. sativa L.). Hence, the production of UVB-resistant African rice with augmented CPD photolyase activity is of great importance, although difficulty in transforming the African rice cultivars to this end has been reported. Here, we successfully produced overexpressing transgenic African rice with higher CPD photolyase activity by modifying media conditions for callus induction and regeneration using the parental line (PL), UVB-sensitive African rice TOG12380 ( O. glaberrima ). The overexpressing transgenic African rice carried a single copy of the CPD photolyase enzyme, with a 4.4-fold higher level of CPD photolyase transcripts and 2.6-fold higher activity than its PL counterpart. When the plants were grown for 21 days in a growth chamber under visible radiation or with supplementary various UVB radiation, the overexpressing transgenic plants have a significantly increased UVB resistance index compared to PL plants. These results strongly suggest that CPD photolyase remains an essential factor for tolerating UVB radiation stress in African rice. As a result, African rice cultivars with overexpressed CPD photolyase may survive better in tropical areas more prone to UVB radiation stress, including Africa. Collectively, our results provide strong evidence that CPD photolyase is a useful biotechnological tool for reducing UVB-induced growth inhibition in African rice crops of O. glaberrima .

Several photorespiratory bypasses have been introduced into plants and shown to improve photosynthesis by increasing chloroplastic CO 2 concentrations or optimizing energy balance. We recently reported that an engineered GOC bypass could increase photosynthesis and productivity in rice. However, the grain yield of GOC plants was unstable, fluctuating in different cultivation seasons because of varying seed setting rates. In this study, we designed a synthetic photorespiratory shortcut (the GCGT bypass) consisting of genes encoding Oryza sativa glycolate oxidase and Escherichia coli catalase, glyoxylate carboligase, and tartronic semialdehyde reductase. The GCGT bypass was guided by an optimized chloroplast transit peptide that targeted rice chloroplasts and redirected 75% of carbon from glycolate metabolism to the Calvin cycle, identical to the native photorespiration pathway. GCGT transgenic plants exhibited significantly increased biomass production and grain yield, which were mainly attributed to enhanced photosynthesis due to increased chloroplastic CO 2 concentrations. Despite the increases in biomass production and grain yield, GCGT transgenic plants showed a reduced seed setting rate, a phenotype previously reported for the GOC plants. Integrative transcriptomic, physiological, and biochemical assays revealed that photosynthetic carbohydrates were not transported to grains in an efficient manner, thereby reducing the seed setting rate. Taken together, our results demonstrate that the GCGT photorespiratory shortcut confers higher yield by promoting photosynthesis in rice, mainly through increasing chloroplastic CO 2 concentrations., (Copyright © 2020 The Author. Published by Elsevier Inc. All rights reserved.)

Rooting ability of rice seedling for mechanical transplanting has a large impact on grain yield. This study explored the relationship between endogenous soluble sugar content and rooting ability of rice seedlings. We placed 15-day-old rice seedlings in controlled environment cabinets with stable light and sampled after 0, 3, 6, 9, 12, and 24 hours of light to measure their soluble sugar content, nitrate content, starch content, soluble protein content and rooting ability. The soluble sugar content of the rice seedlings before rooting increased rapidly from 65.1 mg g-1 to 126.3 mg g-1 in the first 9 hours of light and then tended to stabilize; however, few significant changes in the other physiological indices were detected. With the light exposure time increasing from 3 hours to 12 hours, the rooting ability measured with fresh weight, dry weight, total length, and number of new roots increased by 91.7%, 120.0%, 60.6% and 30.3%, respectively. Rooting ability was related more closely to soluble sugar content than to nitrate-nitrogen content of rice seedlings before rooting and their correlation coefficients were 0.8582-0.8684 and 0.7045-0.7882, respectively. The stepwise regression analysis revealed that the soluble sugar content before rooting explained 73.6%-75.4% of the variance, and the nitrate-nitrogen content explained an additional 7.3%-14.2% of the variance in rooting ability, indicating that compared with nitrate-nitrogen content, soluble sugar content of rice seedlings before rooting was more dominant in affecting rooting ability. This study provides direct evidence of the relationship between the rooting ability and endogenous soluble sugar content of rice seedlings., Competing Interests: The authors have declared that no competing interests exist.

The effect of light and water on aromatic rice remain largely unclear. A pot experiment was conducted to investigate the influences of light-water treatments (CK: natural light and well-watered conditions, WS: natural light and water-stressed conditions, LL: low light and well-watered conditions, LL-WS: low light and water-stressed treatment) on yield and 2-acetyl-1-pyrroline (2AP) formation in aromatic rice. Compared with CK, the light-water treatments decreased grain yield (10.32-39.19%) due to reductions in the filled grain percentage and total dry weight, in the regulation of biomass distribution, and in the attributes of gas exchange and antioxidant response parameters. The 2AP content in grains increased in the LL treatment (5.08-16.32%) but decreased in the WS treatment compared with that in CK. The changes in 2AP were associated with changes in 2AP formation-related traits and element content. Low light and water stress led to yield declines in aromatic rice, but low light alleviated the decrease in 2AP content caused by water stress.

Key Message: A simple and rapid speed breeding system was developed for short-day crops that enables up to five generations per year using LED lighting systems that allow very specific adjustments regarding light intensity and quality. Plant breeding is a key element for future agricultural production that needs to cope with a growing human population and climate change. However, the process of developing suitable cultivars is time-consuming, not least because of the long generation times of crops. Recently, speed breeding has been introduced for long-day crops, but a similar protocol for short-day crops is lacking to date. In this study, we present a speed breeding protocol based on light-emitting diodes (LEDs) that allow to modify light quality, and exemplarily demonstrate its effectiveness for the short-day crops soybean (Glycine max), rice (Oryza sativa) and amaranth (Amaranthus spp.). Adjusting the photoperiod to 10 h and using a blue-light enriched, far-red-deprived light spectrum facilitated the growth of short and sturdy soybean plants that flowered ~ 23 days after sowing and matured within 77 days, thus allowing up to five generations per year. In rice and amaranth, flowering was achieved ~ 60 and ~ 35 days after sowing, respectively. Interestingly, the use of far-red light advanced flowering by 10 and 20 days in some amaranth and rice genotypes, respectively, but had no impact on flowering in soybeans, highlighting the importance of light quality for speed breeding protocols. Taken together, our short-day crops' speed breeding protocol enables several generations per year using crop-specific LED-based lighting regimes, without the need of tissue culture tools such as embryo rescue. Moreover, this approach can be readily applied to a multi-storey 96-cell tray-based system to integrate speed breeding with genomics, toward a higher improvement rate in breeding.

Lignin is the most abundant aromatic biopolymer in nature and is a major byproduct from the paper industry. The unlocking of lignin's potential for high-value applications has gained increasing attention in recent years. In this study, alkali lignin (AL), with a rigid conjugated structure and amphiphilic property, was used as a sustainable and eco-friendly encapsulation material for the protection and controlled release of photosensitive abscisic acid (ABA), an important and widely used plant growth regulator. Cetyltrimethylammonium bromide (CTAB) was used to induce the formation of AL-CTAB nanomicroparticles by self-assembly. The size and morphology of AL-CTAB particles were modified by changing the AL concentration and the dispersion agent. AL (0.3 M) dissolved in tetrahydrofuran could form a uniform size (300 nm) of particles with a regular spherical structure. Subsequently, ABA was loaded on the prepared nanomicroparticles to synthesize the capsule formulation of ABA@AL-CTAB. The controlled-release behavior and the antiphotolysis performance as well as the thermal stability of ABA@AL-CTAB were proved to be superior. Lasting inhibition of Arabidopsis and rice seed germination by ABA@AL-CTAB under light irradiations implied protection of ABA from photolysis. In addition, ABA@AL-CTAB could effectively regulate plant stomata, thereby increasing plant drought resistance. Overall, lignin is suitable for the preparation of agrochemical formulations with excellent controlled release and antiphotolysis performances.

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration ( R d ) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice ( Oryza sativa L.) to determine candidate loci associated with R d . This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that R d shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. R d also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of R d collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high R d . Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1 , was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% R d of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of R d in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Chloroplast-to-nucleus retrograde signalling (RS) is known to impact plant growth and development. In Arabidopsis , we and others have shown that RS affects seedling establishment by inhibiting deetiolation. In the presence of lincomycin, a chloroplast protein synthesis inhibitor that triggers RS, Arabidopsis light-grown seedlings display partial skotomorphogenesis with undeveloped plastids and closed cotyledons. By contrast, RS in monocotyledonous has been much less studied. Here, we show that emerging rice seedlings exposed to lincomycin do not accumulate chlorophyll but otherwise remain remarkably unaffected. However, by using high red (R) and blue (B) monochromatic lights in combination with lincomycin, we have uncovered a RS inhibition of length and a reduction in the B light-induced declination of the second leaf. Furthermore, we present data showing that seedlings grown in high B and R light display different non-photochemical quenching capacity. Our findings support the view that excess B and R light impact seedling photomorphogenesis differently to photoprotect and optimize the response to high-light stress. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.