Search

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]

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]

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]

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]

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]

Background: Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation and harvest. WRKY transcription factors regulate many aspects of plant development including seed dormancy and germination. Both positive and negative regulators of seed germination have been reported in many plants such as rice and Arabidopsis. Using a transient expression system, we previously demonstrated that OsWRKY71 is a negative regulator of gibberellin (GA) signaling in aleurone cells and likely forms a "repressosome" complex with other transcriptional repressors. Hence, it has the potential to impact seed germination properties. Results: In this study, we demonstrate that OsWRKY71, a Group IIa WRKY gene, appeared at the same time as seed-bearing plants. Rice mutants lacking OsWRKY71 have seeds and embryos that germinate earlier than wildtype controls. In oswrky71 aleurone layers, α-amylase activity was hypersensitive to stimulation by GA3 and hyposensitive to inhibition by abscisic acid (ABA). Early germination in oswrky71 intact seeds was also hyposensitive to ABA. Transcriptomic profiling during embryo germination and early post-germination growth demonstrates that OsWRKY71 influences the expression of 9–17% of genes in dry and imbibing embryos. Compared to wildtype embryos, the mutant transcriptomes have large temporal shifts at 4, 8 and 12 h after imbibition (HAI). Importantly, many genes involved in the ABA-dependent inhibition of seed germination were downregulated in oswrky71-1. This mutant also displayed altered expression of multiple ABA receptors (OsPYLs/RCARs) that control ABA signaling and the VP1-SDR4-DOG1L branch of ABA signaling that promotes seed dormancy. Association studies reveal an OsWRKY71-containing quantitative trait locus involved in low-temperature seed germinability, qLTG-2. Indeed, oswrky71 seeds germinated early at 15 °C. Conclusions: Rice Group-IIa WRKY transcription factor OsWRKY71 is a master regulator of germination that influences the expression of 9–17% of genes in dry and imbibing embryos. It is also most likely the primary candidate of low-temperature seed germinability QTL, qLTG-2. We propose that knockouts of OsWRKY71 can generate rice varieties with improved germination properties under normal or low-temperature conditions. [ABSTRACT FROM AUTHOR]

Background: Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation and harvest. WRKY transcription factors regulate many aspects of plant development including seed dormancy and germination. Both positive and negative regulators of seed germination have been reported in many plants such as rice and Arabidopsis. Using a transient expression system, we previously demonstrated that OsWRKY71 is a negative regulator of gibberellin (GA) signaling in aleurone cells and likely forms a "repressosome" complex with other transcriptional repressors. Hence, it has the potential to impact seed germination properties. Results: In this study, we demonstrate that OsWRKY71, a Group IIa WRKY gene, appeared at the same time as seed-bearing plants. Rice mutants lacking OsWRKY71 have seeds and embryos that germinate earlier than wildtype controls. In oswrky71 aleurone layers, α-amylase activity was hypersensitive to stimulation by GA3 and hyposensitive to inhibition by abscisic acid (ABA). Early germination in oswrky71 intact seeds was also hyposensitive to ABA. Transcriptomic profiling during embryo germination and early post-germination growth demonstrates that OsWRKY71 influences the expression of 9–17% of genes in dry and imbibing embryos. Compared to wildtype embryos, the mutant transcriptomes have large temporal shifts at 4, 8 and 12 h after imbibition (HAI). Importantly, many genes involved in the ABA-dependent inhibition of seed germination were downregulated in oswrky71-1. This mutant also displayed altered expression of multiple ABA receptors (OsPYLs/RCARs) that control ABA signaling and the VP1-SDR4-DOG1L branch of ABA signaling that promotes seed dormancy. Association studies reveal an OsWRKY71-containing quantitative trait locus involved in low-temperature seed germinability, qLTG-2. Indeed, oswrky71 seeds germinated early at 15 °C. Conclusions: Rice Group-IIa WRKY transcription factor OsWRKY71 is a master regulator of germination that influences the expression of 9–17% of genes in dry and imbibing embryos. It is also most likely the primary candidate of low-temperature seed germinability QTL, qLTG-2. We propose that knockouts of OsWRKY71 can generate rice varieties with improved germination properties under normal or low-temperature conditions. [ABSTRACT FROM AUTHOR]

Neck blast is one of the most damaging fungal disease of rice, causing severe yield losses in the North‐Western region of Haryana, India. Due to the lack of resistant cultivars commonly grown in Haryana, the management of the disease has relied predominantly on the foliar application of fungicides. Therefore, this study evaluated the field efficacy of various fungicides against rice neck blast in the North‐Western region of Haryana, India, over the kharif seasons of 2020, 2021 and 2022. Fungicides were applied twice per season, at panicle emergence and 10 days later. Among the seven fungicides tested, isoprothiolane 40% EC, propineb 70% WP and difenoconazole 25% EC significantly reduced neck blast severity by 63.2%, 55.2% and 47.3% in 2020; 60.6%, 51.4% and 47.4% in 2021; and 70.0%, 64.9% and 62.5% in 2022, respectively with corresponding reductions in area under disease progress curve values compared with the untreated control. The highest grain yield was recorded for isoprothiolane 40% EC, followed by propineb 70% WP and difenoconazole 25% EC. The greatest increase in grain yield was observed in kharif 2020, whereas the lowest yield in kharif 2022 was associated with moderate total rainfall (284 mm) and high average relative humidity (94.4%) following the appearance of neck blast. These results suggest that these fungicides are effective in reducing rice neck blast and enhancing grain yield in the North‐Western region of Haryana, India. [ABSTRACT FROM AUTHOR]

Efficient sucrose transport and metabolism are vital for seed and pollen development in plants. Cell wall invertases (CINs) hydrolyze sucrose into glucose and fructose, maintaining a sucrose gradient in the apoplast of sink tissues. In rice, two CIN isoforms, OsCIN1 and OsCIN2, were identified as being specifically expressed in the anthers but not in pollen. Functional analyses through genetic crosses and mutant characterization showed that oscin1/2 double mutants exhibit a sporophytic male-sterile phenotype and produce shrunken seeds. This suggests that CIN activity is essential for proper pollen development and seed formation in rice. Observation of the progeny genotypes and phenotypes from various genetic crosses revealed that the phenotype of oscin1/2 seeds is determined by the genotype of the maternal tissue, indicating the critical role of CIN function in the apoplast between maternal and filial tissues for sucrose transport and metabolism. The CIN activity in the anthers and seeds of wild-type rice was found to be significantly higher—over 500-fold in the anthers and 5-fold in the seeds—than in the leaves, highlighting the importance of CIN in facilitating the efficient unloading of sucrose. These findings suggest that the fine-tuning of CIN activity in the apoplast, achieved through tissue-specific expression and CIN isoform regulation, plays a key role in determining the carbohydrate distribution across different tissues. Understanding this regulatory mechanism could provide opportunities to manipulate carbohydrate allocation to sink organs, potentially enhancing crop yields. [ABSTRACT FROM AUTHOR]

Bacterial secondary metabolites have an important role in encouraging the growth of plants by influencing phytohormone production and metabolism. The effect of secondary metabolites secreted by an actinobacterium Zhihengliuella sp. ISTPL4 (Z. sp. ISTPL4) on growth promotion in the Oryza sativa plant was studied. The growth of Z. sp. ISTPL4 has been evaluated in the presence of Arsenic (As) up to the concentration range of 0.2–1.9 mM followed by observing the growth of rice in the presence of As. The present study was carried out to analyze the significant role of metabolites released by Z. sp. ISTPL4 in growth-promoting activities of plants. We have also reported various metabolites released by Oryza sativa after microbial inoculation under normal growth conditions and in the presence of As stress. It was observed that 43 metabolites were released by Z. sp. ISTPL4 under normal conditions and 34 metabolites were released in the presence of As stress. Some of these metabolites including Hexadecane, Heptadecane, Hexadecanoic acid methyl ester, Eicosane, Cyclo (L-prolyl-L-valine) were common among metabolites released by Z. sp. ISTPL4 in the presence of normal growth conditions and under As stress. The area percentage of hexadecenoic acid methyl ester, methyl stearate, octadecanoic acid, 2,3-dihydroxypropyl ester was higher in the presence of As stress than its concentration under normal growth conditions while hexadecane is released in the presence of As stress only. These metabolites are involved in antimicrobial, antiproliferative antioxidants and plant growth promotion by stimulating gibberellin synthesis. The results of our research indicate that under different biotic and abiotic stress conditions, the actinobacterium Z. sp. ISTPL4 can be deployed to improve sustainable agricultural practices. [Display omitted] • Zhihengliuella sp. ISTPL4 tolerate up to 2 mM concentration of arsenate. • Secondary metabolite production in Zhihengliuella sp. ISTPL4. • Abiotic stress-mediated secondary metabolite production in rice. [ABSTRACT FROM AUTHOR]

The rice albumin (RAG) gene family belongs to the Tryp_alpha_amyl family. RAG2, specifically expressed in 14–21 DAP (days after pollination) seeds, regulates grain yield and quality. In this study, we identified another RAG family gene, RAL6, which exhibits specific expression in developing seeds, particularly in 7, 10, and 15 DAP seeds. Employing the CRISPR/Cas9 system, we analyzed functions of RAL6 and found that the ral6 lines (ral6-1, ral6-2, ral6-3, and ral6-4) displayed thinner seeds with significantly decreased 1000-grain weight and grain thickness compared to ZH11. Additionally, the cell width of spikelet cells, total protein and glutelin contents were significantly reduced in ral6. The germination assay and 1% TTC staining revealed a significant decrease in seed vigor among the ral6 lines. The alpha-amylase activity in ral6 mutant seeds was also markedly lower than in ZH11 seeds after 2 days of imbibition. Furthermore, co-expression analysis and GO annotation showed that co-expressed genes were involved in immune response, oligopeptide transport, and the glucan biosynthetic process. Collectively, our findings suggest that RAL6 plays a coordinating role in regulating grain weight and seed germination in rice. [ABSTRACT FROM AUTHOR]

SUMMARY: Cytoplasmic male sterility (CMS) is an agronomically significant trait that causes dysfunction in pollen and anther development. It is often observed during successive backcrossing between distantly related species. Here, we show that Asian japonica cultivars (Oryza sativa) exhibit CMS when the nucleus is replaced with that of the African rice Oryza glaberrima. The CMS line produced stunted anthers and did not set any seeds. Mitochondrial orf288 RNA was detected in the anthers of CMS lines but not in fertility restorer lines. The mitochondrial genome‐edited japonica rice that was depleted of orf288 did not exhibit male sterility when backcrossed with O. glaberrima. These results demonstrate that orf288 is a CMS‐causing gene. As orf288 commonly occurs in the mitochondrial genomes of japonica rice, these results indicate that common japonica rice cultivars possess a cryptic CMS‐causing gene hidden in their mitochondrial genomes. [ABSTRACT FROM AUTHOR]

Investigating soil properties and yield variability in farming systems is crucial for delineating Management Zones (MZs). The objectives of study were to investigate the spatiotemporal variability of soil properties, identify spatial and temporal yield-limiting factors of soil and delineate MZs based on these factors. This study was conducted at the Xinghua Rice Smart Farm (33.08°E, 119.98°N) in Jiangsu Province, China, and the experiment covered five consecutive years of soil and rice yield testing from 2017 to 2021, with 933 geo-referenced soil samples and 140 rice yield samples collected annually. Soil samples were analyzed for pH, soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and apparent soil conductivity (ECa). Spatial and temporal variability of soil properties and RY were analyzed using statistical and geostatistical methods. Ordinary Kriging (OK) interpolation characterized these distributions, and the random forest (RF) algorithm identified key yield-limiting factors. Subsequently, the effectiveness of using all variables to delineate the MZ was compared against the approach of defining MZs based solely on the identified yield-limiting factors. The study also compared Fuzzy C Means (FCM) and Spatial Fuzzy C-Means (sFCM) clustering to evaluate MZs and their temporal stability. Results showed that the coefficients of variation for soil properties ranged from low to medium (7.7-77.4%), with semi-variational function analyses showing moderate to high spatial dependence for most properties. Temporally, soil nutrients and ECa exhibited a slow increase, whereas pH decreased, showing the highest temporal stability for pH and the lowest for AP. RF analysis identified SOM, TN, and ECa as primary influencers of spatial variability of RY, and SOM, pH, and TN as main contributors to its temporal variability. The integration of yield-limiting factors with the sFCM method improves performance of MZ delineation, maintaining stability over the five-year period. [ABSTRACT FROM AUTHOR]

Summary: Measurements of stable isotope ratios in organic compounds are widely used tools for plant ecophysiological studies. However, the complexity of the processes involved in shaping hydrogen isotope values (δ2H) in plant carbohydrates has limited its broader application.To investigate the underlying biochemical processes responsible for 2H fractionation among water, sugars, and cellulose in leaves, we studied the three main CO2 fixation pathways (C3, C4, and CAM) and their response to changes in temperature and vapor pressure deficit (VPD).We show significant differences in autotrophic 2H fractionation (εA) from water to sugar among the pathways and their response to changes in air temperature and VPD. The strong 2H depleting εA in C3 plants is likely driven by the photosynthetic H+ production within the thylakoids, a reaction that is spatially separated in C4 and strongly reduced in CAM plants, leading to the absence of 2H depletion in the latter two types. By contrast, we found that the heterotrophic 2H‐fractionation (εH) from sugar to cellulose was very similar among the three pathways and is likely driven by the plant's metabolism, rather than by isotopic exchange with leaf water.Our study offers new insights into the biochemical drivers of 2H fractionation in plant carbohydrates. [ABSTRACT FROM AUTHOR]

Maintenance of ion homeostasis in plant cells is an essential physiological requirement for sustainable growth, development, and yield of crops. Plants respond to high levels of heavy metals such as copper (Cu) and cadmium (Cd) to avoid irreversible damage at the structural, physiological and molecular levels. Our previous study found that rice germin-like proteins (OsGLPs) are a type of Cu-responsive proteins. The deletion of 10 tandem OsGLP genes on chromosome 8 led to more severe heavy metal toxicity in rice. In this study, we show that rice WRKY transcription factor OsWRKY72 negatively regulates OsGLP8-7 transcription. Overexpression of OsWRKY72 weakens the Cu/Cd tolerance of rice when exposed to Cu and Cd. OsWRKY72 suppressed expression of OsGLP8-7 and lignin synthesis genes, resulting in reduced lignin polymerization and consequently lower lignin accumulation in cell walls, thereby increasing the Cu and Cd accumulation. In addition, OsWRKY53 bound to OsWRKY72 to alleviate the transcriptional inhibition of OsGLP8-7. These results revealed that OsWRKY72-OsGLP8-7 is an important module response of rice to heavy metal stress, and that transcription factor OsWRKY72 acts upstream of OsGLP8-7 to regulate Cu/Cd toxicity. [ABSTRACT FROM AUTHOR]

Rice stripe necrosis virus (RSNV) is the causal agent of the disease 'rice crinkling' and is transmitted by the protozoan Polymyxa graminis. Although genetic resistance has been explored, no resistant commercial cultivars are currently available. Oryza glaberrima has been identified as a promising source of resistance. However, it remains unclear whether this resistance is effective against the virus, the vector, or both, as well as whether it can be transferred to Oryza sativa cultivars. Disease‐resistant genotypes are primarily selected through visual observations of symptom expression. The absence of a severity scale for RSNV makes this process difficult, and relying solely on visual assessments can introduce subjectivity. We developed a severity scale and a reverse transcripiton‐quantitative PCR (RT‐qPCR) assay for screening resistance levels in rice genotypes against RSNV and its vector and to analyse the genetic variability of RSNV isolates. To achieve absolute quantification, experiments were conducted using O. glaberrima and three O. sativa cultivars. Inoculation occurred naturally using soil from an area with a history of the disease. Visual symptoms were recorded and disease intensity was evaluated. Subsequently, total nucleic acid extraction was performed on the samples and viral and vector loads were quantified through RT‐qPCR and qPCR, respectively. To characterize the virus variability, symptomatic rice samples were collected in the 2021/2022 crop season. RT‐PCR was conducted to amplify the coat protein gene of RSNV, and molecular variability descriptors were analysed. [ABSTRACT FROM AUTHOR]

The study investigates the impact of polyethylene glycol (PEG), sodium nitroprusside (SNP), and different carbon sources on the in vitro callus induction and regeneration of drought-tolerant and drought-sensitive rice (Oryza sativa L.) genotypes. PEG, a known osmotic agent, mimics drought conditions, thus providing insights into the plant's response mechanisms under stress. SNP, a nitric oxide donor, is evaluated for its role in modulating stress responses and promoting growth under adverse conditions. Various carbon sources are evaluated to determine their efficacy in supporting callus induction and subsequent regeneration. Results indicate differential responses between drought-tolerant and drought-sensitive rice genotypes, highlighting the potential for optimizing tissue culture protocols to enhance the resilience and regenerative capacity of rice under drought stress. While moderate PEG (5%) stimulated callus induction and regeneration, higher concentrations resulted in adverse effects, including reduced callus mass and regeneration potential. Morphological changes were also observed in response to PEG concentrations, highlighting genotype-specific responses. Meanwhile, combined effect of carbon sources such as maltose and sorbitol along with nitrogen sources "SNP" enhanced callus induction (> 90%) and regeneration (> 90%) under 20% PEG stress in both drought-tolerant and drought-sensitive rice. [ABSTRACT FROM AUTHOR]

The fall armyworm (FAW), Spodoptera frugiperda, is a serious pest that threatens a range of important crops worldwide. It originated in America and rapidly dispersed throughout Africa and Asia in 2018. There are two subtypes, corn-strain (C-strain) and rice-strain (R-strain), that have different host plant preferences, and the individuals damaging maize in China were identified as C-strain. In the present study, we found FAW individuals damaging rice plants in the field of Guangdong Province, China. FAW larvae and male adults were collected, and the majority of FAWs were characterized as CO I R-strain Tpi C-strain, which is similar to the FAWs damaging maize in China. The FAW adults preferred laying eggs on maize plants more than on rice plants. Compared to those that were fed maize leaves, the FAW larvae were unable to survive when fed 4-week-old rice plants, whereas they could complete their life cycle on 2-week-old rice plants, for which the total survival rate was 8%. The pre-adult- and pupal-stage durations were prolonged, and the fecundity of adult females decreased. Thus, the FAWs found in paddy fields showed better fitness on maize than on rice in the laboratory. Owing to their low survival rate on rice plants, they were unlikely to damage paddy fields in large areas, but populations of FAWs in paddy fields should be monitored. [ABSTRACT FROM AUTHOR]

Decreasing nitrogen (N) supply affected the normal growth of Oryza sativa (O. sativa) seedlings, reducing CO2 assimilation, stomatal conductance (gs), the contents of chlorophylls (Chl) and the ratio of Chl a/Chl b, but increasing the intercellular CO2 concentration. Polyphasic chlorophyll a fluorescence transient and relative fluorescence parameters (JIP test) results indicated that N deficiency increased Fo, but decreased the maximum quantum yield of primary photochemistry (Fv/Fm) and the maximum of the IPphase, implying that N-limiting condition impaired the whole photo electron transport chain from the donor side of photosystem II (PSII) to the end acceptor side of PSI in O. sativa. N deficiency enhanced the activities of the antioxidant enzymes, such as ascorbate peroxidase (APX), guaiacol peroxidase (GuPX), dehydro–ascorbate reductase (DHAR), superoxide dismutase (SOD), glutathione peroxidase (GlPX), glutathione reductase (GR), glutathione S-transferase (GST) and O-acetylserine (thiol) lyase (OASTL), and the contents of antioxidant compounds including reduced glutathione (GSH), total glutathione (GSH+GSSG) and non-protein thiol compounds in O. sativa leaves. In contrast, the enhanced activities of catalase (CAT), DHAR, GR, GST and OASTL, the enhanced ASC–GSH cycle and content of sulfur-containing compounds might provide protective roles against oxidative stress in O. sativa roots under N-limiting conditions. Quantitative real-time PCR (qRT-PCR) analysis indicated that 70% of the enzymes have a consistence between the gene expression pattern and the dynamic of enzyme activity in O. sativa leaves under different N supplies, whereas only 60% of the enzymes have a consistence in O. sativa roots. Our results suggested that the antioxidant system and sulfur metabolism take part in the response of N limiting condition in O. sativa, and this response was different between leaves and roots. Future work should focus on the responsive mechanisms underlying the metabolism of sulfur-containing compounds in O. sativa under nutrient deficient especially N-limiting conditions. [ABSTRACT FROM AUTHOR]

Disease outbreaks are shaped by the 'disease triangle,' comprising a virulent pathogen, a susceptible plant, and appropriate environmental conditions. Recent advances have shed light on the intricate environment–plant–pathogen interactions. Rice resistance is manipulated by cytoplasmic and apoplastic effectors secreted by Magnaporthe oryzae. Environmental factors play a significant role in both blast disease epidemics and the regulation of host (or rice) resistance. Strategies such as protein engineering, genome editing, and host-induced gene silencing have been employed effectively to engineer blast-resistant rice plants. Rice blast is a highly destructive crop disease that requires the interplay of three essential factors: the virulent blast fungus, the susceptible rice plant, and favorable environmental conditions. Although previous studies have focused mainly on the pathogen and rice, recent research has shed light on the molecular mechanisms by which the blast fungus and environmental conditions regulate host resistance and contribute to blast disease outbreaks. This review summarizes significant achievements in understanding the sophisticated modulation of blast resistance by Magnaporthe oryzae effectors and the dual regulatory mechanisms by which environmental conditions influence rice resistance and virulence of the blast fungus. Furthermore, it emphasizes potential strategies for developing blast-resistant rice varieties to effectively control blast disease. [ABSTRACT FROM AUTHOR]

SUMMARY: Soil salinity significantly limits rice productivity, but it is poorly understood how excess sodium (Na+) is delivered to the grains at the reproductive stage. Here, we functionally characterized OsHAK4, a member of the clade IV HAK/KUP/KT transporter subfamily in rice. OsHAK4 was localized to the plasma membrane and exhibited influx transport activity for Na+, but not for K+. Analysis of organ‐ and growth stage‐dependent expression patterns showed that very low expression levels of OsHAK4 were detected at the vegetative growth stage, but its high expression in uppermost node I, peduncle, and rachis was found at the reproductive stage. Immunostaining indicated OsHAK4 localization in the phloem region of node I, peduncle, and rachis. Knockout of OsHAK4 did not affect the growth and Na+ accumulation at the vegetative stage. However, at the reproductive stage, the hak4 mutants accumulated higher Na+ in the peduncle, rachis, husk, and brown rice compared to the wild‐type rice. Element imaging revealed higher Na+ accumulation at the phloem region of the peduncle in the mutants. These results indicate that OsHAK4 plays a crucial role in retrieving Na+ from the phloem in the upper nodes, peduncle, and rachis, thereby preventing Na+ distribution to the grains at the reproductive stage of rice. [ABSTRACT FROM AUTHOR]

Heat and drought stress, which often co-occur due to water evaporation, are two major abiotic factors limiting the production of rice (Oryza sativa L.) It is crucial to enhance understanding of the effects of these abiotic stresses in rice, particularly for rice-producing countries like Malaysia, which has yet to achieve rice selfsufficiency. This greenhouse study was conducted to evaluate the morphological changes of two important Malaysian cultivars (‘MR219’ and ‘MR303’) at vegetative, reproductive, and ripening stages, as well as their physiological response and yield components under normal (control), heat, drought, and combined heatdrought stress conditions. Individual heat stress greatly influenced rice growth and yield, with significant differences (p < 0.01) observed across all examined parameters except the grain to leaf area index ratio (GtoLAI). Conversely, individual drought stress mostly affected yield-related parameters, with significant differences (p < 0.01) in grain weight (GW), harvest index (HI), and percentage of filled grain (%FG). Interestingly, the combined stresses in this study did not significantly affect plant height (PH) for all growth stages and most yield-related traits (HI, GW, and GtoLAI). The majority of the significant changes (p < 0.01) were observed on physiological traits, including chlorophyll a (Chl A) and b (Chl B). We found a positive correlation between HI and %FG (R² = 0.3974**) under heat and drought stress, indicating that improving either of these traits can boost rice production. Collectively, our study revealed that the individual effects of heat and drought on rice growth and yield can differ from the effects of combined stress. [ABSTRACT FROM AUTHOR]

Fossil fuels, particularly oil, face sustainability challenges due to depletion and their role in increasing atmospheric CO2 levels, contributing to climate change and impacting global agriculture. Renewable energy sources like solar power offer a viable alternative. This study explores the feasibility of agro-photovoltaic (APV) systems, which integrate solar panels with agricultural land to generate electricity while cultivating crops. Specifically, the impact of APV systems on rice production and quality was investigated. Solar modules with a total capacity of 99.84 kW were installed on a 2580 m² site, with two module configurations tested. Two rice (Oryza sativa L.) cultivars, Woonkwang and Saenuri, were transplanted and monitored for growth characteristics, chlorophyll content, and fluorescence, as well as yield and quality. Growth analysis of rice under APV systems showed minimal impact on plant height and tiller numbers, though chlorophyll content analysis indicated delayed leaf aging and extended maturation time. Rice yield decreased due to altered panicle and spikelet numbers. Quality analysis revealed changes in head rice rate and broken rice, stressing optimal harvest timing in APV systems. Shading conditions also affected physicochemical properties and taste profiles. Yields dropped by about 20% under APV systems, but the financial returns from electricity generation significantly outweighed the crop revenue loss. Despite the high initial installation costs and regulatory challenges, APV systems present a promising dual-use approach for enhancing farm income and promoting renewable energy. Continued research and investment are essential for optimizing APV systems and expanding their adoption. [ABSTRACT FROM AUTHOR]

Soil salinization, a rising issue globally, is a negative effect of the ever-changing climate, which has drawn attention to, and exacerbated problems related to soil degradation and the decline in wetland rice (Oryza sativa L.) production, leading to an unstable national economy. The use of rhizosphere inhabiting microorganisms (plant growth-promoting rhizobacteria, PGPR) is a viable method for boosting agricultural production on saline soils and reduce salt stress in rice crops. The objective of this studywas to support the development of rice under salt stress by using a consortium of bacterial strains. ‘Pokkali’ rice plants inoculated with single Bacillus tequilensis and B. aryabhattai isolates were compared with consortium and non-inoculated plants while salinity was increased and by irrigation with tap water (control), 30 mM (5 dS m-1 ) and 60 mM (10 dS m-1 ) NaCl. The present study exhibited that inoculation of a mixed inoculum at 5 dS m-1 resulted in significantly higher dry weight of the shoots and roots of seedlings (9.29 and 1.24 g, respectively)which was due to the increased SPAD value, proline content (7.55 µmol g-1 FW), and antioxidant enzyme activity in the inoculated plants. The higher accumulation of osmoprotectants such as proline supported Na+ ion reduction and antioxidant enzymes such as ascorbate peroxidase and reduced polyphenol oxidase content protect against higher cellular damage, eventually leading to increase plant growth performance in saline soil. This study demonstrates some positive effects of the locally isolated salt tolerant consortium PGPR strains on the growth of rice plants under salt stress conditions. [ABSTRACT FROM AUTHOR]

Rice root system plays a crucial role in plant adaptation under adverse conditions, particularly drought stress. However, the regulatory gene networks that govern rice root development during stress exposure remain largely unexplored. In this study, we applied a QTL sequencing method to identify QTL/gene controlling the crown root development under Jasmonic acid simulation using the Bulk-segregant analysis. Two rice cultivars with contrasting phenotypes from the Vietnamese traditional rice collection were used as parent pairs for crossing. The single-seed descent method was employed to generate an F2 population of progenies. This F2/3 population was further segregated based on root count under JA stress. Pooled DNA from the two extreme groups in this population was sequenced, and SNP indexes across all loci in these pools were calculated. We detected a significant genomic region on chromosome 10, spanned from 20.39–20.50 Mb, where two rice RLKs were located, OsPUB54 and OsPUB58. Receptor-like kinases (RLKs) are pivotal in regulating various aspects of root development in plants, and the U-box E3 ubiquitination ligase class was generally known for its degradation of some protein complexes. Notably, OsPUB54 was strongly induced by JA treatment, suggesting its involvement in the degradation of the Aux/IAA protein complex, thereby influencing crown root initiation. Besides, the Eukaryotic translation initiation of factor 3 subunit L (eIF3l) and the Mitogen-activated protein kinase kinase kinase 37 (MAPKKK 37) proteins identified from SNPs with high score index which suggests their significant roles in the translation initiation process and cellular signaling pathways, respectively. This information suggests several clues of how these candidates are involved in modifying the rice root system under stress conditions. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa) is a staple food for billions of people across the globe, that feeds nearly three-quarters of the human population on Earth, particularly in Asian countries. Rice yield has been drastically reduced and severely affected by various biotic and abiotic stresses, especially pathogens. Controlling the attack of such pathogens is a matter of immediate concern as yield losses in rice crops could deprive millions of lives of nourishment worldwide. Pyricularia oryzae is one such pathogen that has been considered the major disease of rice because of its worldwide geographic distribution. P. oryzae belongs to the kingdom fungi, that causes rice blast ultimately adversely affecting the yield of the rice crop. Keeping in view this alarming scenario, the present study was designed so that the identifications of genome-encoded miRNAs of Oryza sativa were employed to target and silence the genome of P. oryzae. This study accomplished the computational analysis of algorithms related to miRNA target prediction. Four computational target prediction algorithms i.e., psRNATarget, RNA22, miRanda, and RNAhybrid were utilized in this investigation. The consensus among target prediction algorithms was created to discover six miRNAs from the O. sativa genome with the conservation of the target site fully evaluated on the genome of P. oryzae. The discovery of these novel six miRNAs in Oryza sativa paved a strong way toward the control of this disease in rice. It will open doors for further research in the field of gene silencing in rice. These miRNAs can be designed and employed in the future as experimentation to create constructs regarding the silencing of P. oryzae in rice crops. In the future, this research would be surely helpful for the development of P. oryzae resistant rice varieties. [ABSTRACT FROM AUTHOR]

This study demonstrated the plant growth-promoting capabilities of native actinobacterial strains obtained from different regions of the rice plant, including the rhizosphere (FT1, FTSA2, FB2, and FH7) and endosphere (EB6). We delved into the molecular mechanisms underlying the beneficial effects of these plant-microbe interactions by conducting a transcriptional analysis of a select group of key genes involved in phytohormone pathways. Through in vitro screening for various plant growth-promoting (PGP) traits, all tested isolates exhibited positive traits for indole-3-acetic acid synthesis and siderophore production, with FT1 being the sole producer of hydrogen cyanide (HCN). All isolates were identified as members of the Streptomyces genus through 16S rRNA amplification. In pot culture experiments, rice seeds inoculated with strains FB2 and FTSA2 exhibited significant increases in shoot dry mass by 7% and 34%, respectively, and total biomass by 8% and 30%, respectively. All strains led to increased leaf nitrogen levels, with FTSA2 demonstrating the highest increase (4.3%). On the contrary, strains FB2 and FT1 increased root length, root weight ratio, root volume, and root surface area, leading to higher root nitrogen content. All isolates, except for FB2, enhanced total chlorophyll and carotenoid levels. Additionally, qRT-PCR analysis supported these findings, revealing differential gene expression in auxin (OsAUX1, OsIAA1, OsYUCCA1, OsYUCCA3), gibberellin (OsGID1, OsGA20ox-1), and cytokinin (OsIPT3, OsIPT5) pathways in response to specific actinobacterial treatments. These actinobacterial strains, which enhance both aboveground and belowground crop characteristics, warrant further evaluation in field trials, either as individual strains or in consortia. This could lead to the development of commercial bioinoculants for use in integrated nutrient management practices. [ABSTRACT FROM AUTHOR]

In response to various stressors, the calmodulin-binding transcription activator (CAMTA) can regulate downstream genes involved in calcium (Ca2+)/calmodulin signaling after binding to calmodulin (CAM) or calmodulin-like (CML) proteins. We previously reported seven OsCAMTA genes available throughout the rice (Oryza sativa) genome and their docking with the best probable interactors. This refined study demonstrated the evolutionary conservation of OsCAMTA motif structure and its correlation with 41 different plant species through phylogenetic tree construction along with the detailed molecular docking study focusing specifically on the calmodulin-binding domain (CaMBD) of each CAMTA protein with all available CAM/CML proteins across the rice genome. More insights regarding these were obtained from gene duplication studies through synteny analysis. Protein–protein interactions by STRING database analysis were conducted to know the involvement of OsCAMTA proteins in various development and stress-dependent pathways by identifying probable interactors. Tissue-specific expression analysis through qRT-PCR revealed that all the OsCAMTA genes except OsCAMTA7a and OsCAMTA7b were abundantly expressed in the roots of rice plants. Transcript expressions of rice CAMTAs under differential salt concentrations have depicted their participation in salt stress activity. Gene expression analysis in various temperatures indicated the most up-regulation of OsCAMTA7b, OsCAMTA4 and OsCAMTA3b at 4 ºC, 37 ºC and 42 ºC, respectively. In comparison to earlier research on OsCAMTA genes, this study is the most comprehensive fine-tuned and well-honed research conducted through tissue-specific expression study, followed by spatio-temporal expression analysis under different stresses with protein–protein interaction studies, molecular docking and prediction of microRNA to target each of the OsCAMTAs. [ABSTRACT FROM AUTHOR]

Interspecific F1 hybrids between Asian (Oryza sativa) and African rice (Oryza glaberrima) exhibit severe sterility caused by the accumulation of hybrid sterility genes/loci at 15 or more loci. The mechanisms underlying the hybrid sterility genes are largely unknown; however, a few genes associated with the killer–protector system, which is the system most frequently associated with hybrid sterility genes, have been identified. We previously produced fertile plants as tetraploids derived from diploid interspecific F1 hybrids through anther culture; therefore, it was suggested that hybrid sterility could be overcome following tetraploidization. We investigated whether tetraploid interspecific plants produced by crossing are fertile and tested the involvement of hybrid sterility genes in the process. Fertile tetraploid interspecific F1 hybrid plants were obtained by crossing 2 tetraploids of O. sativa and O. glaberrima. To elucidate the relationships between pollen fertility and the hybrid sterility loci in the tetraploid F1 microspores, we performed genetic analyses of the tetraploid F2 hybrids and diploid plants obtained from the microspores of tetraploid interspecific hybrids by anther culture. The result suggested that the tetraploid interspecific hybrids overcame pollen and seed infertility based on the proportion of loci with the killer–protector system present in the tetraploids. The heterozygous hybrid sterility loci with the killer–protector system in the tetraploid segregate the homozygous killed allele (16.7–21.4%), with more than three-quarters of the gametes surviving. We theoretically and experimentally demonstrated that fertile rice progenies can be grown from tetraploid interspecific hybrids. [ABSTRACT FROM AUTHOR]

Profiled metabolites from 5-donor plants; Mucuna pruriens, L. (Mc), Cymbopogon nardus L. (C), Desmodium uncinatum Jacq. DC. (D), (Zea mays, L. (Mz) and New Rice for Africa 1 (NERICA 1) were Terpenoids and Phenols. NERICA 1 (R) is a cross of Oryza sativa and Oryza glaberrima. C produced 10 terpenoids + 1 ester, R and D each released 6 Terpenoids + 3 Phenols. Mc produced 2 Terpenoids + 4 Phenols and 5 Terpenoids + 4 Phenols were profiled from Mz. We adopted a completely randomised block design with 3 replicates and eight combinations of 3 leaf+ stem+root powders namely; Mc+D+C, Mz+Mc+C, RDC, Mc+D+C, Mz+R+Mc, Mz+D+Mc, R+Mc+C and Mz+R+C, mixed with 1.5 kg soil (15, 30 and 45 %, w/w). Controls had no powders. Mixtures were placed in plastic pots and 20 seeds of Biden pilosa L. were sown in each pot. Every 2 days, 200 ml of water was applied to all treatments for 60 days. Mz+Mc controlled B. pilosa and volunteer weeds relative to R+C and C+D. Weed germination and biomass reduced with increased powder doses. Volunteer monocot weeds were more inhibited than dicots. High potential exists for functional allelopathy using allelochemicals in the donor plants to develop bio-herbicides. [ABSTRACT FROM AUTHOR]

Aluminum (Al) is known to inhibit plant growth and limit crop yields in acid areas. This study aimed to investigate the effect of endophytic fungus Glomerella sp. JP4 infection on the growth, photosynthetic pigments, antioxidant enzyme activities, organic acids contents, and Al content of endophyte-infected rice seedlings (EI) and endophyte-uninfected rice seedlings (EF) exposed to Al stress for 9 days. Al stress decreased shoot height, root length, and dry weight of EF plants. Endophyte infection increased the growth parameters except for root length. Compared to EF plants, the chlorophyll a+b content and carotenoid content were significantly enhanced in the EI plants. Antioxidant enzyme activity was also increased in the EI plants compared to the EF plants subjected to Al stress, while malondialdehyde (MDA) content was remarkably reduced. Endophytic infection significantly increased the contents of citrate and succinate in leaves, as well as that of lactate, malate, fumarate, and succinate in roots under Al stress. Endophyte infection decreased the Al content in the shoots and the roots and restricted the Al transfer from the roots to the shoots in the EI plants compared to the EF plants. Our results indicated that infection with endophytic fungus JP4 in the roots had an active role in promoting plant growth, alleviating the phytotoxic effects caused by Al exposure. [ABSTRACT FROM AUTHOR]

The development of the embryo sac is an important factor that affects seed setting in rice. Numerous genes associated with embryo sac (ES) development have been identified in plants; however, the function of the DEAD-box RNA helicase family genes is poorly known in rice. Here, we characterized a rice DEAD-box protein, RH52A, which is localized in the nucleus and cytoplasm and highly expressed in the floral organs. The knockout mutant rh52a displayed partial ES sterility, including degeneration of the ES (21%) and the presence of a double-female-gametophyte (DFG) structure (11.8%). The DFG developed from two functional megaspores near the chalazal end in one ovule, and 3.4% of DFGs were able to fertilize via the sac near the micropylar pole in rh52a. RH52A was found to interact with MFS1 and ZIP4, both of which play a role in homologous recombination in rice meiosis. RNA-sequencing identified 234 down-regulated differentially expressed genes associated with reproductive development, including two, MSP1 and HSA1b , required for female germline cell specification. Taken together, our study demonstrates that RH52A is essential for the development of the rice embryo sac and provides cytological details regarding the formation of DFGs. [ABSTRACT FROM AUTHOR]

Asian rice (Oryza sativa L.) was domesticated from wild rice (O. rufipogon Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice O. rufipogon, but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication. [ABSTRACT FROM AUTHOR]

Seed priming enhances crop seed performance, even under stress conditions, by increasing seed vigour. There is a notable discrepancy in priming duration observed by different researchers for the same priming agent and crop. This study examined the priming efficiency during various imbibition phases under high (Ψ = 0 MPa water) and low water potential (Ψ = –1.2 MPa polyethylene glycol) conditions in rice (Oryza sativa L.). The third-degree polynomial equations facilitated the identification of three distinct imbibition phases under different water potentials. A low water potential caused a threefold extension in the imbibition duration, enhancing the priming effect. The comparative analysis of the three phases, along with two dry back temperatures (26 and 30°C), demonstrated the superiority of imbibition up to Phase II and a lower dry back temperature (26°C). We also determined that rice seeds possess desiccation tolerance, even during the lemma rupture and embryo swelling stages. Rice seeds primed up to Phase II of imbibition under two different water potential conditions with the same moisture content demonstrated that priming at a low water potential enhanced seed vigour, germination speed, and uniformity. Standardizing priming based on imbibition phases rather than soaking periods is recommended to improve efficacy and accuracy. [ABSTRACT FROM AUTHOR]

As the global climate environment continues to change, the frequency of extreme temperature events is expected to increase. The temperature stress environments of low and high temperatures can directly or indirectly affect the growth of rice (Oryza sativa L.), affecting its normal metabolism, which in turn can have an impact on yields and threaten global food security. Agriculture needs new technologies to mitigate temperature stress and improve grain yield and quality. In this study, two iron (Fe)-based nanoparticles (NPs), Fe2O3 NPs and Fe3O4 NPs, as well as groups of Fe ions corresponding to the Fe concentration, were selected for hydroponic experiments on rice under normal (25°C), low (20°C), and high (38°C) temperature conditions, respectively. It was found that low and high temperature stresses reduced stem length (3 and 7.02%), root length (49.53 and 26.01%), and aboveground (52.49 and 26.04%) and belowground biomass (53.94 and 35.22%) in rice. Both Fe2O3 NPs and Fe3O4 NPs could promote root development by nutrient uptake, transferring to the aboveground to enhance photosynthesis, and promoting the activity of antioxidant enzymes to eliminate oxidative stress to alleviate the stress of low and high temperatures. The Fe3O4 NPs were more stable and had obvious effects at both high and low temperatures. [ABSTRACT FROM AUTHOR]

Hybridization generates biodiversity, and wide hybridization plays a pivotal role in enhancing and broadening the useful attributes of crops. The hybridization barrier between wheat and rice, the two most important cereals, was recently overcome by in vitro production of allopolyploid wheat–rice hybrid zygotes, which can develop and grow into mature plants. In the study, genomic sequences and compositions of the possible hybrid plants were investigated through short- and long-read sequencing analyses and fluorescence in situ hybridization (FISH)-based visualization. The possible hybrid possessed whole wheat nuclear and cytoplasmic DNAs and rice mitochondrial (mt) DNA, along with variable retention rates of rice mtDNA ranging from 11% to 47%. The rice mtDNA retained in the wheat cybrid, termed Oryzawheat, can be transmitted across generations. In addition to mitochondrial hybridization, translocation of rice chromosome 1 into wheat chromosome 6A was detected in a F1 hybrid individual. OryzaWheat can provide a new horizon for utilizing inter-subfamily genetic resources among wheat and rice belonging to different subfamilies, Pooideae and Ehrhartoideae, respectively. [ABSTRACT FROM AUTHOR]