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Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.

Key message: CesA proteins response to arsenic stress in rice involves structural and regulatory mechanisms, highlighting the role of BES1/BZR1 transcript levels under arsenate exposure and significant downregulation of BZR1 protein expression. Plants interact with several hazardous metalloids during their life cycle through root and soil connection. One such metalloid, is arsenic and its perilous impact on rice cultivation is a well-known threat. Cellulose synthase and cellulose synthase-like (CesA/CSL) gene family build major constituent of cell wall polysaccharides, however, their interaction and responses to arsenic stress remains enigmatic. The current study describes the structural, functional, and regulatory behavior of CesA proteins using in silico tools with datasets of 367 sequences and an in vitro germination model. Interpro analysis revealed six types of domains, further classified into two major clades: cellulose synthase and glycosyl transferase family group 2 exhibiting polyphyletic grouping. The MEME suite analysis identified the frequent occurrence of “QXXRW” among 35 identified conserved motifs. Further observation of the regulatory mechanism of CesA identified 36 types of trans-regulatory elements involved in hormone signaling, developmental regulation, stress response, etc. Among these, hormone signaling comprises of 7 types of elements, with BES1 being less studied, sequences containing BES1 sites were selected. Additionally, 56 cis-regulatory elements were identified. Arsenate exposure increased transcript level of CesA and BES1/BZR1 compared to control. Western blot analysis revealed a significant downregulation of the BZR1 protein expression in arsenate stressed seedlings. This research shed light on the regulation of CesA mediated by (BES1/BZR1) and brassinosteroid signalling. [ABSTRACT FROM AUTHOR]

Summary: Terpene synthases (TPSs) are key enzymes in terpenoids synthesis of plants and play crucial roles in regulating plant defence against pests and diseases. Here, we report the functional characterization of OsTPS19 and OsTPS20, which were upregulated by the attack of brown planthopper (BPH). BPH female adults performed concentration‐dependent behavioural responses to (S)‐limonene showing preference behaviour at low concentrations and avoidance behaviour at high concentrations. Overexpression lines of OsTPS19 and OsTPS20, which emitted higher amounts of the monoterpene (S)‐limonene, decreased the hatching rate of BPH eggs, reduced the lesion length of sheath blight caused by Rhizoctonia solani and bacterial blight caused by Xanthomonas oryzae. While knockout lines of OsTPS19 and OsTPS20, which emitted lower amounts of (S)‐limonene, were more susceptible to these pathogens. Overexpression of OsTPS19 and OsTPS20 in rice plants had adverse effects on the incidence of BPH, rice blast, and sheath blight in the field and had no significant impacts on rice yield traits. OsTPS19 and OsTPS20 were found to be involved in fine‐tuning the emission of (S)‐limonene in rice plants and play an important role in defence against both BPH and rice pathogens. [ABSTRACT FROM AUTHOR]

The virulence of Magnaporthe oryzae largely hinges on its secretory effectors. Therefore, identification and thorough understanding of the effector functionality is crucial for unravelling the pathogenicity of the pathogen. In the present study, we employed a modified computational pipeline with deep machine learning techniques with an integration of Magnaporthe effector reference datasets (MOED) that predicted 434 M. oryzae candidate secretory effector proteins (MoCSEPs) from the genomic data. The reliability of the modified CSEP prediction workflow through utilization of precise parametric filtering is considered valid as it predicted 100 functional effectors (97.08%) out of 103 previously identified effector proteins within the Magnaporthe genus. Insights into secretion patterns and subcellular localization elucidated the role of these proteins in host cell recognition. Furthermore, structural classification of MoCSEPs, based on conserved motifs, combined with an exploration of their biological functions, revealed their significance in host adaptability and localization. Experimental validation done through examining expression of the MoCSEPs revealed varied secretion patterns in the resistant (40 expressed) and susceptible (92 expressed) rice cultivars at different time intervals after pathogen inoculation owing to different degrees of resistance by the host cultivars. The present work thus provides the strategic model of canonical parametric evaluation within the MOED and deepens the understanding on the role of secretory proteins of M. oryzae in establishing successful parasitic infection in rice. The predicted MoCSEPs could be used as biomarkers for disease diagnosis and tracking evolutionary shifts in M. oryzae. [ABSTRACT FROM AUTHOR]

Main conclusion: Rhizobacteria and silicon fertilization synergism suppress leaf and panicle Blast, and mitigates biotic stress in rice plants. Association of bioagents and silicon is synergistic for mitigating leaf and panicle blast and low phosphorus (P) levels in upland rice, under greenhouse conditions. This study aimed to evaluate the potential of the bioagents and silicon interaction on blast disease severity suppression in upland rice plants, under field low P conditions. The experiment was conducted during two growing seasons (E1 and E2), in randomized block design with four replications, and consisted of five treatments, combining a mix of three rhizobacteria, BRM 32114 and BRM62523 (Serratia marcescens), and BRM32110 (Bacillus toyonensis), and three application methods (seed treatment, drenching, spraying). Calcium and magnesium silicate (2 t/ha) was applied over a low soil P, 30 days before sowing. Leaf blast (LBS) and panicle blast (PBS), area under the disease progress curve (AUDPC), activity of enzymes related to oxidative stress, pathogenesis-related (PR), biochemical indicators such as hydrogen peroxide, chlorophyll a and b, carotenoids, and grain yield (GY), were assessed. Bioagents and silicon suppressed LBS by 77.93 and PBS by 62.37%, reduced AUDPC by 77.3 (LBS) and 60.6% (PBS). The yield in E1 was 25% higher than in E2. The treatments statistically differ only in E2, the yield with bioagents and silicon (2435.72 kg ha−1) was 71.95% higher compared to the absolute control. All enzymatic activities related to oxidative stress and PR proteins were modulated by bioagents and silicon association. The association of rhizobacteria and silicon exhibited a synergistic effect, and represents a bioprotective combination to reduce the effects of different stresses and indirectly reduces the use of chemical inputs. [ABSTRACT FROM AUTHOR]

Low phytate level is a desirable trait because it promotes mineral bioavailability and thus offers a solution to tackle mineral deficiencies. The objectives of the present study were to characterize low phytate (lpa) Basmati rice mutants for the identification of novel mutations in target gene(s) and to develop a PCR-based CAPS (cleaved amplified polymorphic sequence) marker for low phytate Basmati rice. For this purpose, cultivar Super Basmati (Q4) was irradiated with gamma rays (60Co source) and three mutants named Q1 (lpa-5-9), Q2 (lpa-9-13), and Q3 (lpa-59-14) were isolated. Four genes previously been reported for the low phytic acid trait in rice were sequenced in these mutants and no mutation was observed in Q1 and Q2. However, in Q3 (lpa14) mutant a novel mutation in OsMRP5 gene (LOC_Os03g04920') was detected. Sequence analysis displayed a substitution in the first exon of OsMRP5 at position 1142 bp resulting in the amino acid change from glycine (Gly) to alanine (Ala) at position 381a.a. To facilitate low-phytate breeding program, CAPS marker was developed to confirm this mutation site using the restriction digestion by Alu I restriction enzyme. After enzyme digestion, Q3 produces four bands (32, 220, 154, and 32 bp) while Q4 (parent cultivar Super Basmati) produces only 3 bands (32, 374, and 32 bp). These results showed that this CAPS marker is 100% linked with this mutation and can be used for future breeding programs. Present findings provided insights in molecular basis of low phytate trait in rice paving the way for developing low-phytate rice varieties through marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Enhancing crops productivity to ensure food security is one of the major challenges encountering agriculture today. A promising solution is the use of biostimulants, which encompass molecules that enhance plant fitness, growth, and productivity. The regulatory metabolite zaxinone and its mimics (MiZax3 and MiZax5) showed promising results in improving the growth and yield of several crops. Here, the impact of their exogenous application on soil and rice root microbiota was investigated. Plants grown in native paddy soil were treated with zaxinone, MiZax3, and MiZax5 and the composition of bacterial and fungal communities in soil, rhizosphere, and endosphere at the tillering and the milky stage was assessed. Furthermore, shoot metabolome profile and nutrient content of the seeds were evaluated. Results show that treatment with zaxinone and its mimics predominantly influenced the root endosphere prokaryotic community, causing a partial depletion of plant-beneficial microbes at the tillering stage, followed by a recovery of the prokaryotic community structure during the milky stage. Our study provides new insights into the role of zaxinone and MiZax in the interplay between rice and its root-associated microbiota and paves the way for their practical application in the field as ecologically friendly biostimulants to enhance crop productivity. [ABSTRACT FROM AUTHOR]

Plants known as obligate aerobes developed different mechanisms to overcome the damage incurred under oxygen limitation. One of the survival strategies to have commonly appeared in hydrophytic plants is the escape strategy, which accelerates plant axial organs' growth in order to escape hypoxic conditions as soon as possible. The present study aimed to distinguish the alterations in coleoptile elongation, viability and metabolic profiles in coleoptiles of slow- and fast-growing rice varieties. All the parameters were tested at 3, 5 and 7 days after sowing, to highlight changes during seedling development in normal and submerged conditions. The obtained results indicated that coleoptile elongation correlated with higher resistance to oxygen deprivation. GS-MS-based metabolic profiling indicated that coleoptiles of the fast-growing cultivar accumulated higher amounts of sugar phosphates, disaccharides, fatty acid derivatives and sterols, which are important for maintaining growth, membrane stability and viability. The slow-growing variety was characterized by a greater abundance of carboxylates, including lactate and phosphoric acid, indicating an energy crisis and cytosol acidification, leading to cell damage and low tolerance. Therefore, a metabolomics approach could be used for phenotyping (chemotyping) in the large-scale screening of newly developed varieties with higher tolerance to oxygen deprivation. [ABSTRACT FROM AUTHOR]

SUMMARY: Arsenic (As) is extremely toxic to plants, posing a serious concern for food safety. Identification of genes responsive to As is significative for figuring out this issue. Here, we identified a bHLH transcription factor OsbHLH6 that was involved in mediating the processes of As tolerance, uptake, and root‐to‐shoot translocation in rice. The expression of OsbHLH6 gene was strongly induced after 3 and 48 h of arsenite [As(III)] treatment. The OsbHLH6‐overexpressed transgenic rice (OE‐OsbHLH6) was sensitive to, while the knockout mutant of OsbHLH6 gene (Osbhlh6) was tolerant to As(III) stress by affecting the contents of reactive oxygen species (ROS) and non‐protein thiols (NPT), etc. Knockout of OsbHLH6 gene increased significantly the As concentration in roots, but decreased extensively As accumulation in shoots, compared to that in OE‐OsbHLH6 and WT plants. The transcripts of phytochelatins (PCs) synthetase encoding genes OsPCS1 and OsPCS2, as well as As(III) transporter encoding genes OsLsi1 and OsABCC1 were greatly abundant in Osbhlh6 mutants than in OE‐OsbHLH6 and WT plants under As(III) stress. In contrast, the expression of OsLsi2 gene was extensively suppressed by As(III) in Osbhlh6 mutants. OsbHLH6 acted as a transcriptional activator to bind directly to the promoter and regulate the expression of OsPrx2 gene that encodes a peroxidase precursor. Moreover, overexpression of OsbHLH6 gene resulted in significant change of expression of amounts of abiotic stress‐related genes, which might partially contribute to the As sensitivity of OE‐OsbHLH6 plants. These findings may broaden our understanding of the molecular mechanism of OsbHLH6‐mediated As response in rice and provide novel useful genes for rice As stress‐resistant breeding. Significance Statement: Arsenic (As) contamination in rice highlights serious concerns for food safety, and identification of As‐responsive genes and further clarification the underlying molecular mechanisms are significative for solving this issue. Here, we establish that loss‐of‐function of OsbHLH6 gene strongly enhanced rice plants tolerance to As stress by modulating ROS scavenging and NPT synthesis as well as regulating the expression of genes involved in As uptake, translocation, and detoxification, providing potential genes for rice As stress‐resistant breeding. [ABSTRACT FROM AUTHOR]

Rice commercial production is seriously threatened by various pathogens. Generally, the susceptibility (S) genes in plants are exploited by phytopathogens to promote infection. Dysfunction of S genes may result in recessively inheritable durable and broad-spectrum disease resistance. In this review, we summarize the latest research on S genes that encode proteins contributing to pathogen infection in rice. The S genes in rice are prospective targets of genome engineering to create resistance germplasms. However, the potential pleiotropic effects resulting from the deletion of S genes limit their application in resistance breeding. The newly developed CRISPR/Cas9-mediated genome editing system offers a promising approach for developing transgene-free rice varieties with durable disease resistance. [ABSTRACT FROM AUTHOR]

Hydropriming rice seeds effectively improve the germination percentage, shortens the germination period, and promotes seedling growth. The impact of seed hydropriming is to speed up growth under dry soil conditions, thereby avoiding drought damage. This study analyzes the effect of hydropriming on morpho-physiological changes in the water uptake of rice seeds using "Kasalath" and "Nipponbare" under water-deficit conditions. Upon exposure to osmotic stress, both varieties showed delays in the time to reach germination. In addition, all germination phases exhibited reductions in the activity of alpha-amylase and total soluble sugar by osmotic stress; however, in all germination phases of the hydroprimed seeds, the activity and contents of those were significantly increased, resulting in increased size of the coleoptile, plumule, and radicle. In hydroprimed seeds, "Kasalath" was superior to "Nipponbare" in the ratio of the water-deficit-to-well-watered conditions for all traits related to germination, which may have been attributable to hydropriming having a greater effect on "Kasalath". Interestingly, Primed "Kasalath" had a lower level of α-amylase, despite the having a higher content of total soluble sugars than primed "Nipponbare". [ABSTRACT FROM AUTHOR]

The X-ray method, together with image analysis tools, has been used to evaluate the internal structures of seeds and correlate them with the physical, physiological and sanitary quality, providing significant and accurate results. The objective of this study was to analyze radiographic images of rice seeds infested by the rice weevil Sitophilus oryzae (Linnaeus, 1763) (Coleoptera: Curculionidae). Rice seed samples from three different cultivars were infested with S. oryzae for 90 days. Next, seed samples collected at random were analyzed by X-ray testing. The radiographic images were analyzed by ImageJ® software to extract color and shape features. Scanning electron microscopy analyses were also performed. The results showed that X-ray testing was effective in detecting infestation. The gray distribution histograms revealed differences between healthy seeds and those infested by adult insects or empty seeds, confirmed by the significant differences obtained for the area and relative and integrated density variables. The study demonstrated that the analysis of radiographic images can provide quantitative information on insect infestation of rice seeds, which is useful in the evaluation of seed quality and for detecting the presence of pests in rice seeds. [ABSTRACT FROM AUTHOR]

Rice is considered to be moderately salt-tolerant during germination, development, and ripening stages, and environmentally sensitive during seedling and reproductive stages, which affects seedling emergence and growth, resulting in significant yield losses. Seed conditioning with chitosan has been employed as a useful tool in high-salinity environments with the aim of increasing crop productivity and quality, as well as promoting more sustainable agricultural practices. Therefore, this study aimed to examine the effect of seed conditioning with chitosan on seed germination and rice seedling growth under salinity stress. The experiment consisted of three seeds conditioning and 4 salinity levels, arranged in a completely randomized design with 4 replications. Seeds were sown on germitest paper, and the rolls were placed in a germination chamber (25 ± 2°C and 12 hr photoperiod). Germination and seedling growth parameters were determined. The high salt concentration resulted in reduced growth of rice seedlings, and exogenous application of chitosan at different concentrations and soaking times exerted no apparent adverse effect on germination and growth variables. The attenuating effect of chitosan was observed in the length of the seedlings at all the concentrations utilized. Therefore, evidence indicates that conditioning rice seeds with chitosan might serve as an alternative to mitigate the adverse effects of exposure to stress induced by high salt concentrations. [ABSTRACT FROM AUTHOR]

SUMMARY Establishing reciprocal symbiosis with arbuscular mycorrhizal (AM) fungi is an important evolutionary strategy of most terrestrial plants to adapt to environmental stresses, especially phosphate (Pi) deficiencies. Identifying the key genes essential for AM symbiosis in plants and dissecting their functional mechanisms will be helpful for the breeding of new crop varieties with enhanced nutrient uptake efficiency. Here, we report a nuclear factor YC subunit‐encoding gene, OsNF‐YC3, whose expression is specifically induced in arbuscule‐containing cells, plays an essential role in AM symbiosis. Knockout of OsNF‐YC3 resulted in stunted arbuscule morphology and substantially decreased P accumulation, while overexpressing OsNF‐YC3 enhanced mycorrhization and Pi uptake efficiency. OsNF‐YC3 is directly regulated by OsPHRs, the major regulators of Pi starvation responses. Chromatin immunoprecipitation sequencing analysis uncovered multiple genes with crucial roles in arbuscule development as its potential downstream targets, including the AM‐specific Pi transporter gene OsPT11. OsNF‐YC3 can form a heterotrimer with the other two NF‐Y subunits, OsNF‐YA11 and OsNF‐YB11, in yeast. Loss of OsNF‐YA11 function also severely impaired arbuscule development in its mutants. Overall, our results highlight an essential role of OsNF‐YC3 and its potential interacting NF‐Y subunit, OsNF‐YA11, in regulating AM symbiosis and arbuscule development. [ABSTRACT FROM AUTHOR]

Serratia marcescens, isolated from the rhizosphere of rice crops, has the potential to improve the acquisition of scarce minerals and provide plant growth. Rice seeds microbiolized with S. marcescens and non-microbiolized seeds were sown in a culture medium enriched with non-labile phosphorus, and the roots were analyzed in WinRhizo. The plant segments were documented by scanning electron microscopy (SEM) and incubated in an NBRIP culture medium. DNAs from endophytic colonies were extracted and analyzed by PCR. The genome of S. marcescens was annotated using subsystem technology to detect genes involved in phosphorus solubilization, biofilm production, and growth promotion. The root system increased in area, volume, and length by 61.5, 31.5, and 101%, respectively. Halos were formed around segments of microbiolized plants, indicating the solubilization of non-labile phosphorus. SEM detected the presence of biofilms and microcolonies, identified as S. marcescens by the molecular markers. Genome annotation found genes with potential functions in plant growth promotion, including genes involved in the biosynthesis of indole-3-acetic acid, phosphate solubilization, and biofilm production. In the low phosphorus crop, the treated plants showed a 181% increase in total biomass. S. marcescens solubilizes non-labile phosphorus, colonizes endophytes, modifies the architecture of the root system, and promotes the growth of rice plants, and can be considered a biofertilizer for growing upland rice. [ABSTRACT FROM AUTHOR]

Amino acid transporters (AATs) have been shown to be involved in immune responses during plant–pathogen interactions; however, the molecular mechanism by which they function in this process remains unclear. Here, we used a joint analysis of a genome-wide association study and quantitative trait locus (QTL) mapping to identify MEMBRANE PROTEIN 1 , which acts as a QTL in rice against blast fungus. Heterogeneous expression of OsMP1 in yeast supported its function in transporting a wide range of amino acids, including Thr, Ser, Phe, His, and Glu. OsMP1 could also mediate 15N-Glu efflux and influx in Xenopus oocyte cells. The expression of OsMP1 was significantly induced by Magnaporthe oryzae in the resistant rice landrace Heikezijing, whereas no such induction was observed in the susceptible landrace Suyunuo. Overexpressing OsMP1 in Suyunuo enhanced disease resistance to blast fungus and leaf blight bacterium without resulting in a yield penalty. In addition, the overexpression of OsMP1 led to increased accumulation of Thr, Ser, Phe, and His in the leaves and this contributed to the reduced disease susceptibility, which was associated with up-regulation of the jasmonic acid pathway. Our results demonstrate the important role of OsMP1 in disease resistance in rice and provide a potential target for breeding more resistant cultivars without reducing yield. [ABSTRACT FROM AUTHOR]

Seed vigour and longevity are intricate yet indispensable physiological traits for agricultural crops, as they play a crucial role in facilitating the successful emergence of seedlings and exert a substantial influence on crop productivity. Transcriptional regulation plays an important role in seed development, maturation, and desiccation tolerance, which are important attributes for seed vigour and longevity. Here, we have investigated the regulatory role of the seed-specific DNA-binding with One Finger (DOF) transcription factor and the rice prolamin box binding factor (RPBF) in seed vigour. RPBF modulates the transcription of galactinol synthase (GolS) and improves seed vigour. The promoter region of GolS-encoding genes from different species was enriched with DOF-binding sites, and the expression levels of both RPBF ; OsGolS were found to enhance during seed development. Furthermore, direct interaction of RPBF with the OsGolS promoter has been demonstrated through multiple approaches: yeast one-hybrid assays, in planta promoter–GUS assays, dual luciferase assay, and in silico molecular docking. To assess functionality, Agrobacterium-mediated genetic transformation of rice was performed to generate the RNAi lines with reduced RPBF expression. In these RNAi lines, a reduction in both galactinol and raffinose content was observed. Since galactinol and raffinose are known contributors to seed vigour, the T2-transgenic lines were assessed for vigour and viability. For this, RNAi seeds were subjected to accelerated ageing by exposing them to high relative humidity and temperature, followed by scoring the germination and viability potential. Tetrazolium and seed germination assay revealed that the RNAi seeds were more sensitive to ageing compared to their wild-type and vector control counterparts. Collectively, this is the first report demonstrating that the DOF transcription factor RPBF controls the seed vigour through transcriptional regulation of GolS. [ABSTRACT FROM AUTHOR]

Oryza sativa (rice) is a major staple food targeted for increased production to achieve food security. However, increased production is threatened by several biotic and abiotic factors, of which bacterial blight disease caused by Xanthomonas oryzae pathovar oryzae is severe. Developing effective control strategies requires an up-to-date understanding of its pathogenomics. This study analyzes the genomes of 30 X. oryzae strains collected from rice-producing regions across five continents to identify genetic elements critical for its pathogenicity and adaptability and for an intraspecific diversity assessment using advanced genomics and bioinformatics tools. Resistome analysis revealed 28 distinct types of antibiotic resistance genes (ARGs), both innate and acquired, indicating a growing threat from multidrug-resistant X. oryzae strains. Sixteen virulent genes, including type III and VI secretion systems, motility genes, and effector proteins, were identified. A unique 'MexCD-OprJ' multidrug efflux system was detected in the Tanzanian strains, conferring resistance to multiple antibiotic classes. To curb further ARG emergence, there is a need to regulate the use of antibiotics for X. oryzae control and adopt resistant rice varieties. Transposable elements were also discovered to contribute to X. oryzae pathogenicity, facilitating the horizontal transfer of virulence genes. Pangenome analysis revealed intraspecific variation among the population, with 112 unique CDS having diverse functional roles. Strains registered in the Philippines had the most unique genes. Phylogenetic analysis confirmed the divergent evolution of X. oryzae. This study's results will aid in identifying more effective management strategies and biocontrol alternatives for sustainable rice production. [ABSTRACT FROM AUTHOR]

SUMMARY: Plasmodesmata (PD) are nanochannels that facilitate cell‐to‐cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)‐bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein‐tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M‐BS wall interface than rice while the difference in M‐M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co‐expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD‐associated genes and photosynthesis‐related genes. PD‐associated genes identified from our co‐expression network analysis are related to cell wall expansion, translation and chloroplast signalling. Significance Statement: The important roles of plasmodesmata (PD) in plant biology present opportunity to improve crop performance but need more knowledge on the genetic control of PD formation to be realised. Here, we use unique bioimaging tools to understand PD formation during monocot leaf development in the context of photosynthesis, and identify potential genes involved. [ABSTRACT FROM AUTHOR]

Background: Fe toxicity often inhibits rice growth on acid sulfate soils in tropical coastal lowlands. Previous studies in plant physiology and breeding have focused on high‐Fe stress, but not on growth recovery after stress alleviation. Aims: The objective of this study was to elucidate the morphophysiological characteristics in rice growth recovery from high‐Fe stress. Methods: We evaluated the seedling growths of Taichung65 (T65) (Fe toxicity‐tolerant) and Ciherang (susceptible) in hydroponic culture, during the period of high‐Fe stress (250 mg Fe2+ L−1 for 12 or 18 days) and after stress alleviation. Results: The plant growth rate during recovery was negatively correlated with the leaf bronzing score (damage symptoms due to Fe toxicity) at the end of high‐Fe stress, which in turn was negatively correlated with the shoot Fe concentration. After 18‐day stress, T65 showed greater growth recovery than Ciherang, attributable to its higher net assimilation rate, higher transpiration rate (water uptake/green leaf area), and greater increase in total root length during recovery. In particular, T65 showed vigorous lateral root development in nodal roots that emerged during the stress period and vigorous growth of nodal roots that emerged during recovery. Conclusions: Our results suggest that tolerance to high‐Fe stress confers an advantage in growth recovery. It is likely that tolerance to Fe toxicity contributes not only to the maintenance of green leaf area at the end of stress but also to quick root growth recovery, leading to vigorous water uptake and high photoassimilation capacity after stress alleviation. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa) is a staple food worldwide, yet faces significant threats from over 100 insect species, including 20 economic pests that are causing serious yield loss to rice plants. In many Asian nations, stink bugs belonging to the genus Scotinophara coarctata (Fabricius, Entomolgia systematica emendata et aucta, secundum classes, ordines, genera, species adjectis synonymis, locis, observationibus, descriptionibus, Suppl.: 1–572. Proft, Hafniae, 1798), Pentatomidae, Hemiptera are a common pest of rice. Black bug sucks the sap from the rice plants, and heavily infested rice plants turn yellowish brown and further die causing "bug burned" symptoms. Excessive sucking by more number of bugs causes maximum damage to rice crop in all affected areas. This review is focused on the nature of damage, taxonomy, alternate host, biology, light trap studies, influence of host varieties on the population development of black bug, EIL, ETL, yield loss, sustainable integrated BB management including cultural practices, exploiting the pest diversionary approaches for the management of black bug, biological control by parasites, predators and entomogenous fungi, efficacy of insecticides and botanicals in the management. This review is focused on the sustainable pest management practices for black bug in rice. [ABSTRACT FROM AUTHOR]

The 'RD6' glutinous rice (Oryza sativa L.), developed from the popular aromatic rice 'KDML105' through gamma irradiation, is a key economic cultivar widely consumed in Thailand and exported throughout Asia. However, cultivation of the 'RD6' faces challenges due to its low grain yield and growth performance. The objective of this study was to use biostimulant chitosan and brassinosteroids to promote growth performance, nutrition, and yield of the 'RD6' rice. Chitosan (2.5, 5.0, 7.5, and 10.0 mg L-1) and brassinosteroids (0.00005, 0.0005, 0.001, and 0.002 mg L-1) were sprayed twice at 40- and 75-d-old rice plants in paddy fields. The results demonstrated that foliar spraying with 7.5 mg L-1 chitosan can promote leaf growth of 'RD6' and improve grain yield by 24% as compared with the control. More pronounced effects were observed with 0.002 mg L-1 brassinosteroid, improving not only growth but also 'RD6' yield by 41.8% compared to the control. Moreover, 0.002 mg L-1 brassinosteroids can enhance antioxidant capacities (total phenolic contents), elemental K and Ca contents, and the aroma compound 2-acetyl-1-pyrroline (2AP) contents in the rice grains. Furthermore, the use of 0.002 mg L-1 brassinosteroids proved to be a financially sound investment, yielding superior net returns and an advantageous benefit-cost ratio compared with 7.5 mg L-1 chitosan. Therefore, the use of exogenous brassinosteroids on glutinous rice in this study offers promising advantages for promoting the growth and physiological performance of rice plants. [ABSTRACT FROM AUTHOR]

Salinity stress immensely inhibits rice (Oryza sativa L.) growth, development, and productivity. Hence, two rice introgression lines, Morkho60-2 and BC4F4 132-12-61, were previously developed from 'RD6' rice via markerassisted backcrossing and their adaptive salt-tolerant mechanisms were characterized in this study. Their seedling physiological and transcriptional responses to salinity stress were observed in comparison to the parental 'RD6' and 'Pokkali'. The salt stress responses were assessed under 150 mM NaCl treatment for 9 d. Interestingly, like 'Pokkali', salinity did not affect the growth parameters of the new rice genotypes. 'Pokkali', Morkho60-2, and BC4F4 132-12-61 also showed lower shoot Na+ content (0.91-1.05 vs. 2.83 mg g-1 DW), and higher selective transport of K+ over Na+ (i.e., ST value of 6.57-10.98 vs. 2.65) than RD6 genotype under salinity stress. Accordingly, the partial least squares-discriminant analysis of all physiological parameters suggested shoot Na+ accumulation and ST value as the key discriminating parameters between 'RD6' and the new genotypes. Transcriptional responses of Na+ homeostasis-related genes further supported the findings. In comparison to the salt susceptible 'RD6' rice, Na+ vacuolar compartmentalization was suggested in Morkho60-2 roots due to the higher abundance of OsNHX1 (i.e., relative expression of 2.65 vs. 1.59) and OsNHX2 (2.42 vs. 1.29) transcripts. Morkho60-2 also displayed a significant upregulation of root OsSOS1 (2.02 vs. 1.18), which may contribute to root Na+ exclusion. Therefore, we suggest that selective transport of K+ over Na+ and Na+ exclusion enhanced ion homeostasis in the newly improved rice genotypes, allowing the seedlings to adapt to the saline condition. [ABSTRACT FROM AUTHOR]

Proline is widely distributed in higher plants. In this study, the function of proline as an osmoprotectant in maintaining cell osmotic stability and structural integrity during drought was analyzed in rice roots. The cultivar of Boawae Seratus Malam(BSM), Gogo Jak(GJ), Kisol(KM), Situ Bagendit(SB) and Ciherang(CH) were exposed to the fraction of transpirable soil water (FTSW) method with FTSW 1 level (control), and FTSW 0.2 (drought) with a combination of exogenous osmoprotectant from Casuarina equisetifola leaves extract in three levels: 0%(low), 50%(moderate), and 100%(high). The root anatomical characteristics were analyzed using the paraffin embedding method. Plants undergo root structural changes when exposed to drought. In plants without exogenous osmoprotectant, the epidermal width was in the range of 20 to 30 μm. GJ and SB cultivars showed shrinking in size by 10 to 20 μm in epidermis when exposed to moderate osmoprotectants and increased by 15 to 30 μm in high osmoprotectants. Under drought and exogenous osmoprotectants, the root diameter, root area, cortex radius, vascular cylinder area, number of metaxylem, and diameter and width area of metaxylem showed a significant positive correlation. The epidermal and sclerenchyma thickness and the amount of xylem tend to show non-significant response under drought and osmoprotectants. These changes in root anatomical structure are presumed caused by amino acid compounds, particularly proline in exogenous osmoprotectants acting as a signaling molecule and cell wall protein hydrolysate as well as an inducer for the activation of genes in the biosynthesis of hormones and proteins included in the formation of the cell wall and cytoskeleton during root vegetative growth. [ABSTRACT FROM AUTHOR]

Low crop Nitrogen Use Efficiency (NUE) is an economic and environmental burden. Rice is an attractive target for NUE improvement in India, due to its highest N-fertilizer consumption and the availability of a vast germplasm. We screened 12 Indica rice genotypes (Oryza sativa ssp. Indica) on modified Arnon-Hoagland (AH) media containing graded urea doses from 0 to 7.5 mM (U0, U10, U50, or U100). We identified six genotypes with contrasting crop duration and germination rate for their life-long evaluation of 46 morpho-physiological parameters, including NUE, using at least 30 potted plants per genotype/treatment grown on nutrient-free soil supplemented with AH media containing urea as the sole N-source (U10, U50, or U100). We found significant genotype and N-dose-dependent effects of urea that correlated positively for 28 of the phenotypic parameters including five for NUE, whereas three parameters showed a negative correlation for urea dose. We also found a significant positive correlation with genotype and urea dose–response for eight physiological parameters, including one for NUE, while seven parameters showed a negative correlation, including two for NUE. A ranking of all 6 genotypes by N-responsive yield and NUE revealed that the late-germinating, long-duration genotypes had better yield and NUE than the early germinating, short-duration genotypes. The only exception was Dhala Heera from the latter group, which had the preferred combination of early (short) duration and high NUE across all urea doses. This makes it a promising donor genotype for further field evaluation and crop improvement toward higher NUE. [ABSTRACT FROM AUTHOR]

Citrus reticulata Blanco shows substantial fruit drop due to diverse environmental factors leading to agricultural waste. However, such waste can be utilized as a safe and cheape source of botanical fungicide. The present work aimed to evaluate the antifungal potential of C. reticulata fruits dropped in June against Fusarium fujikuroi Nirenberg causing foot rot disease in rice as a natural and eco-friendly fungicide. The methanol extract of dropped citrus fruits was prepared by Soxhlet extraction and was further fractionated by column chromatography using petroleum ether, dichloromethane, ethyl acetate, methanol, ethanol and distilled water as solvents. Among all the treatments, the ethyl acetate fraction exhibited the maximum antifungal potential against F. fujikuroi having the least median effective dose at 650 µg/ml. The fraction (1500 µg/ml) showed significantly less disease incidence than the untreated plants in the nursery and transplanted plants of basmati rice cultivar Pusa Basmati 1121 during the kharif seasons 2021 and 2022. The fraction also caused a significant increase in cell constituents release in F. fujikuroi as compared to the control. Scanning electron microscopy analysis also showed that the treated hyphae were shrunken and broken at several points. This finding suggests that the ethyl acetate fraction might act on the fungal cell membrane leading to loss of cell membrane permeability that ultimately leads to cell death. GC–MS analysis of the fraction showed the presence of 3',4',5,6,7,8–hexamethoxyflavone (29.58%), 2-methoxy-4-vinylphenol (22.41%) and 4',5,6,7,8–pentamethoxyflavone (16.78%) as major compounds. Molecular docking of these major compounds with α-β-tubulin (PDB Code: 4FFB) revealed a binding score in the range of -6.1 to -5.3 kcal/mol respectively. Hence, the dropped citrus fruits which are generally discarded as waste may be used as botanical fungicides to control foot rot disease in rice. [ABSTRACT FROM AUTHOR]

Antioxidant complex enzymes have a significant role in cellular homeostasis control in plants, and they inhibit the toxic action of reactive oxygen species when they are in excess. There are many antioxidant enzymes executing this role; among these, superoxide dismutase, catalase, and ascorbate peroxidase are reported as the most studied in this process, as they prevent free radicals from becoming more reactive and toxic to cells. Thus, this research was conducted to evaluate antioxidant enzyme expression in response to hydric stress at the reproductive stage in upland rice genotypes. Three genotypes from the upland rice breeding program on agreement between UFLA, EPAMIG, and EMBRAPA, CMG2093, CMG2172, and BRSMG Relâmpago, were used as controls. Genotypes were grown under field conditions with supplementary irrigation during the whole crop cycle, and hydric stress was induced in the reproductive phase before panicle emission. Seedlings were used in enzyme analyses from the emergence test and IVE on substrate (soil + sand at a 2:1 rate) at 70% and 10% field capacity. Significant differences were observed among genotypes for vigor tests. In biochemical tests, the CMG2093 genotype had lower damage on hydric deficit, with the best performance under hydric restriction conditions, being considered tolerant for this stress type. [ABSTRACT FROM AUTHOR]

Calcium (Ca) and cadmium (Cd) are transition metals coexisting in the ecosystem. Ca is indispensable for the growth and development of plants as well as animals, while Cd is regarded as a toxic heavy metal for the living system. The transportation of Cd in the biological systems often used the pathways of Ca because of chemical similarities. High concentrations of cadmium replace Ca, Mn, and Zn from their respective metalloprotein sites and strongly associated with them. Replaced minerals from their metalloprotein sites are often released as an oxidative ion that is detrimental to it. The common transportation mechanism of Ca and Cd is implicit in the role of common and similar transporters for transporting them in plants. Thus, our study was done to identify the transporters for Ca and Cd and characterize them for similarity in terms of cotransportation system. A profile-based search program identified 44 transporters genes for Ca transportation and 70 genes for cadmium transportation. They were categorized into different groups based on the presence of signature motifs and domains. Identified transporters were characterized for genomic distribution, gene structure, annotation, conserved signature motifs, and domain. Further, cis motif analysis, heat map, gene ontology, and protein–protein interaction were conducted for Ca and Cd transporter genes. In silico expression showed Os05g0319800-1304 and Os0319800-6065 transporter genes were overexpressed for Ca and Os07g00232800-40298 and Os07g00384500-25924 transporter genes overexpressed for Cd transporter. These genes could be used as a candidate genes for enhancing the Ca concentration with reduced Cd content in rice using biotechnological approaches. Twenty-seven genes were found as the common transporters for Ca and Cd. Both active and passive transporter mechanisms act as cotransporters for Ca and Cd. The common signature motifs and domains can be targeted for the characterization of cotransporters of different minerals. [ABSTRACT FROM AUTHOR]

The rice brittle culm is a cell wall composition changed mutant suitable for studying mechanical strength in rice. However, a thorough investigation of brittle culm has been limited due to the lack of diverse brittle mutants on similar genetic backgrounds in cell walls. In this study, we obtained 45 various brittle mutant lines (BMLs) from the IR64 mutant pool induced by sodium azide mutagenesis using the finger-bending method and texture profile analysis. The first scoring method was established to differentiate the levels of brittleness in rice tissues. The variation of cell wall compositions of BMLs showed that the brittleness in rice primarily correlated with cellulose content supported by high correlation coefficients (R = −0.78) and principal component analysis (PCA = 81.7%). As demonstrated using PCA, lower correlation with brittleness, hemicellulose, lignin, and silica were identified as minor contributors to the overall balance of cell wall compositions and brittleness. The analysis of hydrolysis and feeding indexes highlighted the importance of diversities of brittleness and cell wall compositions of BMLs and their potential applications in ruminant animals and making bioenergy. These results contributed to the comprehension of brittleness and mechanical strength in rice and also extended the applications of rice straw. [ABSTRACT FROM AUTHOR]

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a typical silicon-accumulating plant that positively benefits from silicon nutrition. Silicon (Si) has been demonstrated to have various advantages for plant growth, development, and stress responses. In this study, a genome-wide association analysis (GWAS) was performed for a large-scale study using genetic information from 180 Vietnamese rice landrace in the control condition and saturated supplementation of Si to elucidate related quantitative trait loci (QTL) and potential novel genes associated to Si content and morphological changes in rice under the two conditions. The obtained results indicate a wide range of physiological traits and Si accumulation of rice varieties in response to Si supplementation. Most Vietnamese rice accessions in this panel enhanced their height, biomass, and Si content under Si supplementation. After conducting the association, 133 single nucleotide polymorphisms (SNP) were found, and most significant markers were located on chromosomes 1, 2, 3, and 12. Five significant QTLs were identified after analyzing the Linkage Disequilibrium and the haplotype. Interestingly, qSi1.3 represents the most promising QTL since it possesses three nitrate transporters and three ABC transporters inside its confident interval. Other transporters were also detected such as OsPT2 in qSi3.1, PHT4;6 in qSi12.1. Besides, several proteins such as Cinnamoyl CoA Reductase CCRs in qSi2.3 and OsCYPs in qSi1.3, ONACs in qSi2.3 might also relate to the transport of heavy metals, Si, nutrients, and plant development. These results provide new insight into new genes associated with Si transportation and serve as a premise for further in-depth investigation. [ABSTRACT FROM AUTHOR]

Ovate family proteins (OFPs) are plant-specific, transcriptional repressors characterized by an OVATE domain. The OFP family has been analyzed only from a handful and functionally characterized from even fewer species. There is a gap in cataloging the complete compendium of OFP family across Gramineae although the complete genome sequence for several species are now available. In the present study, we identified and cataloged homologs of OFPs across ten Gramineae members to analyze gene and protein structure and properties, evolutionary relationship, expression pattern, and predict interacting partners. A positive correlation was found between genome-size and OFP family size, with Triticum genome harboring the maximum number; most of the Gramineae OFPs are intronless. Comparative analysis revealed variation in gene sizes, physico-chemical properties of proteins, and their structures including motifs. Phylogenetic reconstruction reflected homolog-based clustering. Expression analysis in Oryza revealed spatio-temporal variation with maximum expression in reproductive tissues. Prediction of interactome showed homeobox domain containing proteins as major interacting partners. The study thus form foundation for future functional analysis of role of OFPs in regulating economically important traits. [ABSTRACT FROM AUTHOR]

Main conclusion: SUMOylation of SLR1 at K2 protects productivity under salt stress, possibly by modulation of SLR1 interactome. DELLA proteins modulate GA signaling and are major regulators of plant plasticity to endure stress. DELLAs are mostly regulated at the post-translational level, and their activity relies on the interaction with upstream regulators and transcription factors (TFs). SUMOylation is a post-translational modification (PTM) capable of changing protein interaction and has been found to influence DELLA activity in Arabidopsis. We determined that SUMOylation of the single rice DELLA, SLENDER RICE1 (SLR1), occurs in a lysine residue different from the one identified in Arabidopsis REPRESSOR OF GA (RGA). Artificially increasing the SUMOylated SLR1 levels attenuated the penalty of salt stress on rice yield. Gene expression analysis revealed that the overexpression of SUMOylated SLR1 can regulate GA biosynthesis, which could partially explain the sustained productivity upon salt stress imposition. Furthermore, SLR1 SUMOylation blocked the interaction with the growth regulator YAB4, which may fine-tune GA20ox2 expression. We also identified novel SLR1 interactors: bZIP23, bHLH089, bHLH094, and OSH1. All those interactions were impaired in the presence of SUMOylated SLR1. Mechanistically, we propose that SUMOylation of SLR1 disrupts its interaction with several transcription factors implicated in GA-dependent growth and ABA-dependent salinity tolerance to modulate downstream gene expression. We found that SLR1 SUMOylation represents a novel mechanism modulating DELLA activity, which attenuates the impact of stress on plant performance. [ABSTRACT FROM AUTHOR]

SUMMARY Plant roots are essential for water and nutrient uptake, as well as resistance to abiotic stresses. While measuring root systems under field conditions is labor‐intensive, most quantitative trait loci (QTLs) related to root traits have been detected under artificial conditions. However, QTLs identified under artificial conditions may not always manifest the expected effects that are observed under field conditions. To address this issue, we developed RSApaddy3D, a rapid phenotyping method for rice root systems, using X‐ray computed tomography (CT) volumes of soil blocks collected from paddies. RSApaddy3D employs 2‐dimensional kernel filters tailored to extract disk‐shaped fragments from the CT volumes. Tubular root fragments are expected to exhibit disk‐shaped cross‐sections along the x‐, y‐, or z‐axes. By applying these filters along all three axes and integrating the results, 3‐dimensional root fragments can be accurately extracted. Furthermore, vectorizing the root system enables geometrical removal of the roots of neighboring individuals. We conducted a genome‐wide association study (GWAS) of root diameter, number, and growth angle in 133 Japanese rice varieties and detected three QTLs (qNCR1, qNCR2, and qRGA1) that were associated with each trait. This process was completed within 10 person‐days from soil monolith collection in the paddy to the GWAS. Without RSApaddy3D, roots would need to be washed from the soil monolith and measured, which is estimated to require >500 person‐days. Therefore, RSApaddy3D was approximately 50× more labor‐saving. In summary, we have demonstrated that RSApaddy3D is an efficient method for phenotyping rice root systems under field conditions. [ABSTRACT FROM AUTHOR]