Search

KAI2 receptors, classified as plant α/β hydrolase enzymes, are capable of perceiving smoke-derived butenolide signals and endogenous yet unidentified KAI2-ligands (KLs). While the number of functional KAI2 receptors varies among land plant species, rice has only one KAI2 gene. Rice, a significant crop and representative of grasses, relies on KAI2-mediated Arbuscular mycorrhiza (AM) symbioses to flourish in traditionally arid and nutrient-poor environments. This study presents the first crystal structure of an active rice (Oryza sativa, Os) KAI2 hydrolase receptor. Our structural and biochemical analyses uncover grass-unique pocket residues influencing ligand sensitivity and hydrolytic activity. Through structure-guided analysis, we identify a specific residue whose mutation enables the increase or decrease of ligand perception, catalytic activity, and signal transduction. Furthermore, we investigate OsKAI2-mediated signaling by examining its ability to form a complex with its binding partner, the F-box protein DWARF3 (D3) ubiquitin ligase and subsequent degradation of the target substrate OsSMAX1, demonstrating the significant role of hydrophobic interactions in the OsKAI2-D3 interface. This study provides new insights into the diverse and pivotal roles of the OsKAI2 signaling pathway in the plant kingdom, particularly in grasses.

Segregation distorters (SDs) are genetic elements that distort the Mendelian segregation ratio to favor their own transmission and are able to spread even when they incur fitness costs on organisms carrying them. Depending on the biology of the host organisms and the genetic architecture of the SDs, the population dynamics of SDs can be highly variable. Inbreeding is considered an effective mechanism for inhibiting the spread of SDs in populations, and can evolve as a defense mechanism against SDs in some systems. However, we show that inbreeding in the form of selfing in fact promotes the spread of SDs acting as pollen killers in a toxin-antidote system in hermaphroditic plants by two mechanisms: (i) By reducing the effective recombination rate between killer and antidote loci in the two-locus system and (ii) by increasing the proportion of SD alleles in individual flowers, rather than in the general gene-pool. We also show that in rice (Oryza sativa L.), a typical hermaphroditic plant, all molecularly characterized SDs associated with pollen killing were involved in population hybridization and have introgressed across different species. Paradoxically, these loci, which are associated with hybrid incompatibility and can be thought of as Bateson-Dobzhansky-Muller incompatibility loci are expected to reduce gene-flow between species, in fact cross species boundaries more frequently than random loci, and may act as important drivers of introgression.

Excessive nitrogen promotes the formation of nonproductive tillers in rice, which decreases nitrogen use efficiency (NUE). Developing high-NUE rice cultivars through balancing nitrogen uptake and the formation of productive tillers remains a long-standing challenge, yet how these two processes are coordinated in rice remains elusive. Here we identify the transcription factor OsGATA8 as a key coordinator of nitrogen uptake and tiller formation in rice. OsGATA8 negatively regulates nitrogen uptake by repressing transcription of the ammonium transporter gene OsAMT3.2. Meanwhile, it promotes tiller formation by repressing the transcription of OsTCP19, a negative modulator of tillering. We identify OsGATA8-H as a high-NUE haplotype with enhanced nitrogen uptake and a higher proportion of productive tillers. The geographical distribution of OsGATA8-H and its frequency change in historical accessions suggest its adaption to the fertile soil. Overall, this study provides molecular and evolutionary insights into the regulation of NUE and facilitates the breeding of rice cultivars with higher NUE.

P/TGMS (Photo/thermo-sensitive genic male sterile) lines are crucial resources for two-line hybrid rice breeding. Previous studies revealed that slow development is a general mechanism for sterility-fertility conversion of P/TGMS in Arabidopsis. However, the difference in P/TGMS genes between rice and Arabidopsis suggests the presence of a distinct P/TGMS mechanism in rice. In this study, we isolated a novel P/TGMS line, ostms19, which shows sterility under high-temperature conditions and fertility under low-temperature conditions. OsTMS19 encodes a novel pentatricopeptide repeat (PPR) protein essential for pollen formation, in which a point mutation GTA(Val) to GCA(Ala) leads to ostms19 P/TGMS phenotype. It is highly expressed in the tapetum and localized to mitochondria. Under high temperature or long-day photoperiod conditions, excessive ROS accumulation in ostms19 anthers during pollen mitosis disrupts gene expression and intine formation, causing male sterility. Conversely, under low temperature or short-day photoperiod conditions, ROS can be effectively scavenged in anthers, resulting in fertility restoration. This indicates that ROS homeostasis is critical for fertility conversion. This relationship between ROS homeostasis and fertility conversion has also been observed in other tested rice P/TGMS lines. Therefore, we propose that ROS homeostasis is a general mechanism for the sterility-fertility conversion of rice P/TGMS lines.

Recent studies in the rice genome-wide have established that de novo genes, evolving from noncoding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over time remain unclear. Here, we addressed these issues within a surprisingly short evolutionary timescale (

The co-occurrence of cadmium (Cd) pollution and selenium (Se) deficiency commonly exists in global soils, especially in China. As a result, there is great interest in developing practical agronomic strategies to simultaneously achieve Cd remediation and Se mobilization in paddy soils, thereby enhancing food quality/safety. To this end, we conducted a field-plot trial on soils having high geological background levels of Cd (0.67 mg kg-1) and Se (0.50 mg kg-1). We explored 12 contrasting fertilizers (urea, potassium sulfate (K2SO4), calcium-magnesium-phosphate (CMP)), amendments (manure and biochar) and their combinations on Cd/Se bioavailability. Soil pH, total organic carbon (TOC), soil available Cd/Se, Cd/Se fractions and Cd/Se accumulation in different rice components were determined. No significant differences existed in mean grain yield among treatments. Results showed that application of urea and K2SO4 decreased soil pH, whereas the CMP fertilizer and biochar treatments increased soil pH. There were no significant changes in TOC concentrations. Three treatments (CMP, manure, biochar) significantly decreased soil available Cd, whereas no treatment affected soil available Se at the maturity stage. Four treatments (CMP, manure, biochar and manure＋urea＋CMP＋K2SO4) achieved our dual goal of Cd reduction and Se enrichment in rice grain. Structural equation modeling (SEM) demonstrated that soil available Cd and root Cd were negatively affected by pH and organic matter (OM), whereas soil available Se was positively affected by pH. Moreover, redundancy analysis (RDA) showed strong positive correlations between soil available Cd, exchangeable Cd and reducible Cd with grain Cd concentration, as well as between pH and soil available Se with grain Se concentration. Further, there was a strong negative correlation between residual Cd/Se (non-available fraction) and grain Cd/Se concentrations. Overall, this study identified the primary factors affecting Cd/Se bioavailability, thereby providing new guidance for achieving safe production of Se-enriched rice through fertilizer/amendment management of Cd-enriched soils.

Reproductive phasiRNAs (phased, small interfering RNAs) are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt (nucleotides) phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at the premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 (Dicer-like 5) for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely i) not triggered by microRNAs, ii) not loaded by AGO18 proteins, and iii) not capable of mediating PHAS precursor cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.

BACKGROUND: Sulfur (S) is a mineral nutrient essential for plant growth and development, which is incorporated into diverse molecules fundamental for primary and secondary metabolism, plant defense, signaling, and maintaining cellular homeostasis. Although, S starvation response is well documented in the dicot model Arabidopsis thaliana, it is not clear if the same transcriptional networks control the response also in the monocots. RESULTS: We performed series of physiological, expression, and metabolite analyses in two model monocot species, one representing the C3 plants, Oryza sativa cv. kitaake, and second representing the C4 plants, Setaria viridis. Our comprehensive transcriptomic analysis revealed twice as many differentially expressed genes (DEGs) in S. viridis than in O. sativa under S-deficiency, consistent with a greater loss of sulfur and S-containing metabolites under these conditions. Surprisingly, most of the DEGs and enriched gene ontology terms were species-specific, with an intersect of only 58 common DEGs. The transcriptional networks were different in roots and shoots of both species, in particular no genes were down-regulated by S-deficiency in the roots of both species. CONCLUSIONS: Our analysis shows that S-deficiency seems to have different physiological consequences in the two monocot species and their nutrient homeostasis might be under distinct control mechanisms.

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

Autophagy in eukaryotes functions to maintain homeostasis by degradation and recycling of long-lived and unwanted cellular materials. Autophagy plays important roles in pathogenicity of various fungal pathogens, suggesting that autophagy is a novel target for development of antifungal compounds. Here, we describe bioluminescence resonance energy transfer (BRET)-based high-throughput screening (HTS) strategy to identify compounds that inhibit fungal ATG4 cysteine protease-mediated cleavage of ATG8 that is critical for autophagosome formation. We identified ebselen (EB) and its analogs ebselen oxide (EO) and 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PT) as inhibitors of fungal pathogens Botrytis cinerea and Magnaporthe oryzae ATG4-mediated ATG8 processing. The EB and its analogs inhibit spore germination, hyphal development, and appressorium formation in Ascomycota pathogens, B. cinerea, M. oryzae, Sclerotinia sclerotiorum and Monilinia fructicola. Treatment with EB and its analogs significantly reduced fungal pathogenicity. Our findings provide molecular insights to develop the next generation of antifungal compounds by targeting autophagy in important fungal pathogens.

The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.

Weedy rice is a notorious weed in the rice agroecosystem. Its infestation has caused significant economic loss in many rice-production countries, including Malaysia. In Malaysia, weedy rice consists of a genetic admixture of cultivated and wild traits, resulting in a highly competitive ability against cultivated rice for resources. The morphology and genetic plasticity of weedy rice provide several adaptive advantages, enabling it to thrive in rice agroecosystems and become a serious weed infesting Malaysian rice granaries. Previous strategies in combating weedy rice have often been less effective since weedy rice is easily adapted to a wide range of environments. In this review, we address the weedy rice issue in Malaysia and the progress of weedy rice studies. A future direction on weedy rice research via omics study is also discussed to propose solutions for improvement in weed control, good agronomic practices, and food security. [ABSTRACT FROM AUTHOR]

Background: The cold tolerance of rice is closely related to its production and geographic distribution. The identification of cold tolerance-related genes is of important significance for developing cold-tolerant rice. Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is well-adapted to the cold climate of northernmost-latitude habitats ever found in the world, and is one of the most valuable rice germplasms for cold tolerance improvement. Results: Transcriptome analysis revealed genes differentially expressed between Xieqingzao B (XB; a cold sensitive variety) and 19H19 (derived from an interspecific cross between DXWR and XB) in the room temperature (RT), low temperature (LT), and recovery treatments. The results demonstrated that chloroplast genes might be involved in the regulation of cold tolerance in rice. A high-resolution SNP genetic map was constructed using 120 BC5F2 lines derived from a cross between 19H19 and XB based on the genotyping-by-sequencing (GBS) technique. Two quantitative trait loci (QTLs) for cold tolerance at the early seedling stage (CTS), qCTS12 and qCTS8, were detected. Moreover, a total of 112 candidate genes associated with cold tolerance were identified based on bulked segregant analysis sequencing (BSA-seq). These candidate genes were divided into eight functional categories, and the expression trend of candidate genes related to 'oxidation-reduction process' and 'response to stress' differed between XB and 19H19 in the RT, LT and recovery treatments. Among these candidate genes, the expression level of LOC_Os12g18729 in 19H19 (related to 'response to stress') decreased in the LT treatment but restored and enhanced during the recovery treatment whereas the expression level of LOC_Os12g18729 in XB declined during recovery treatment. Additionally, XB contained a 42-bp deletion in the third exon of LOC_Os12g18729, and the genotype of BC5F2 individuals with a survival percentage (SP) lower than 15% was consistent with that of XB. Weighted gene coexpression network analysis (WGCNA) and modular regulatory network learning with per gene information (MERLIN) algorithm revealed a gene interaction/coexpression network regulating cold tolerance in rice. In the network, differentially expressed genes (DEGs) related to 'oxidation-reduction process', 'response to stress' and 'protein phosphorylation' interacted with LOC_Os12g18729. Moreover, the knockout mutant of LOC_Os12g18729 decreased cold tolerance in early rice seedling stage signifcantly compared with that of wild type. Conclusions: In general, study of the genetic basis of cold tolerance of rice is important for the development of cold-tolerant rice varieties. In the present study, QTL mapping, BSA-seq and RNA-seq were integrated to identify two CTS QTLs qCTS8 and qCTS12. Furthermore, qRT-PCR, genotype sequencing and knockout analysis indicated that LOC_Os12g18729 could be the candidate gene of qCTS12. These results are expected to further exploration of the genetic mechanism of CTS in rice and improve cold tolerance of cultivated rice by introducing the cold tolerant genes from DXWR through marker-assisted selection. [ABSTRACT FROM AUTHOR]

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes' expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Crop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice. Summary: O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction.Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection.The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north.Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance. [ABSTRACT FROM AUTHOR]

Summary Soil salinity has negative impacts on food security and sustainable agriculture. Ion homeostasis, osmotic adjustment and reactive oxygen species scavenging are the main approaches utilized by rice to resist salt stress. Breeding rice cultivars with high salt tolerance (ST) and yield is a significant challenge due to the lack of elite alleles conferring ST. Here, we report that the elite allele LEA12OR, which encodes a late embryogenesis abundant (LEA) protein from the wild rice Oryza rufipogon Griff., improves osmotic adjustment and increases yield under salt stress. Mechanistically, LEA12OR, as the early regulator of the LEA12OR‐OsSAPK10‐OsbZIP86‐OsNCED3 functional module, maintains the kinase stability of OsSAPK10 under salt stress, thereby conferring ST by promoting abscisic acid biosynthesis and accumulation in rice. The superior allele LEA12OR provides a new avenue for improving ST and yield via the application of LEA12OR in current rice through molecular breeding and genome editing. [ABSTRACT FROM AUTHOR]

An extremely hazardous heavy metal called cadmium (Cd) is frequently released into the soil, causing a considerable reduction in plant productivity and safety. In an effort to reduce the toxicity of Cd, silicon dioxide nanoparticles were chosen because of their capability to react with metallic substances and decrease their adsorption. This study examines the processes that underlie the stress caused by Cd and how SiO2NPs may be able to lessen it through modifying antioxidant defense, oxidative stress, and photosynthesis. A 100 μM concentration of Cd stress was applied to the hydroponically grown wild rice line, and 50 μM of silicon dioxide nanoparticles (SiO2NPs) was given. The study depicted that when 50 μM SiO2NPs was applied, there was a significant decrease in Cd uptake in both roots and shoots by 30.2% and 15.8% under 100 μM Cd stress, respectively. The results illustrated that Cd had a detrimental effect on carotenoid and chlorophyll levels and other growth-related traits. Additionally, it increased the levels of ROS in plants, which reduced the antioxidant capability by 18.8% (SOD), 39.2% (POD), 32.6% (CAT), and 25.01% (GR) in wild rice. Nevertheless, the addition of silicon dioxide nanoparticles reduced oxidative damage and the overall amount of Cd uptake, which lessened the toxicity caused by Cd. Reduced formation of reactive oxygen species (ROS), including MDA and H2O2, and an increased defense system of antioxidants in the plants provided evidence for this. Moreover, SiO2NPs enhanced the Cd resistance, upregulated the genes related to antioxidants and silicon, and reduced metal transporters' expression levels. [ABSTRACT FROM AUTHOR]

Photosynthetic induction and stomatal kinetics are acknowledged as pivotal factors in regulating both plant growth and water use efficiency under fluctuating light conditions. However, the considerable variability in methodologies and light regimes used to assess the dynamics of photosynthesis (A) and stomatal conductance (gs) during light induction across studies poses challenges for comparison across species. Moreover, the influence of stomatal morphology on both steady-state and non-steady-state gs remains poorly understood. In this study, we show the strong impact of IRGA Chamber Illumination and Whole Plant Illumination on the photosynthetic induction of two rice species. Our findings reveal that these illuminations significantly enhance photosynthetic induction by modulating both stomatal and biochemical processes. Moreover, we observed that a higher density of smaller stomata plays a critical role in enhancing the stomatal opening and photosynthetic induction to fluctuating light conditions, although it exerts minimal influence on steady-state gs and A under constant light conditions. Therefore, future studies aiming to estimate photosynthetic induction and stomatal kinetics should consider the light environments at both the leaf and whole plant levels. [ABSTRACT FROM AUTHOR]

Summary: Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double‐haplotype genome of O. longistaminata, which displays a 48‐fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding. [ABSTRACT FROM AUTHOR]

Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments. [ABSTRACT FROM AUTHOR]

To better understand the salt tolerance of the wild rice, Oryza coarctata, root tissue‐specific untargeted comparative metabolomic profiling was performed against the salt‐sensitive Oryza sativa. Under control, O. coarctata exhibited abundant levels of most metabolites, while salt caused their downregulation in contrast to metabolites in O. sativa. Under control conditions, itaconate, vanillic acid, threonic acid, eicosanoids, and a group of xanthin compounds were comparatively abundant in O. coarctata. Similarly, eight amino acids showed constitutive abundance in O. coarctata. In contrast, under control, glycerolipid abundances were lower in O. coarctata and salt stress further reduced their abundance. Most phospholipids also showed a distribution similar to the glycerolipids. Fatty acyls were however significantly induced in O. coarctata but organic acids were prominently induced in O. sativa. Changes in metabolite levels suggest that there was upregulation of the arachidonic acid metabolism in O. coarctata. In addition, the phenylpropanoid biosynthesis as well as cutin, suberin, and wax biosynthesis were also more enriched in O. coarctata, likely contributing to its anatomical traits responsible for salt tolerance. The comparative variation in the number of metabolites like gelsemine, allantoin, benzyl alcohol, specific phospholipids, and glycerolipids may play a role in maintaining the superior growth of O. coarctata in salt. Collectively, our results offer a comprehensive analysis of the metabolite profile in the roots of salt‐tolerant O. coarctata and salt‐sensitive O. sativa, which confirm potential targets for metabolic engineering to improve salt tolerance and resilience in commercial rice genotypes. [ABSTRACT FROM AUTHOR]

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice. Genetic variation present in wild rice is a reservoir of useful genes for rice breeding. Here, the authors report the haplotype-resolved gapless genome assembly of wild rice, the development of two sets of chromosome segment substitution lines, and the cloning of a blast resistance gene originated from wild rice. [ABSTRACT FROM AUTHOR]

This study assessed the mangrove flora of the Kali River estuary, Uttara Kannada district, Karnataka. Fourteen true mangrove species belonging to eight families and 11 genera were documented from four locations: Devbagh, Mavinhole, Kalimatha Island, and Halgejoog. The mangrove species show a discontinuous distribution pattern in the Kali River estuary. The highest IVI in true mangroves was recorded for Avicennia officinalis at Devbagh, Acanthus ilicifolius at Mavinhole, Sonneratia caseolaris (after Oryza coarctata) at Kalimatha Island, and S. caseolaris (after Derris trifoliata) at Halgejoog. Of the four sites, Devbagh has the highest Shannon-Wiener diversity index, and with regard to species composition, Devbagh and Kalimatha Island are the most similar sites. Kalimatha island has the most wellpreserved mangrove community. [ABSTRACT FROM AUTHOR]

Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae, predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR-B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates. [ABSTRACT FROM AUTHOR]

Summary: Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment‐friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss‐of‐function mutants were fully resistant, while loss‐of‐function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in‐frame deletions or replacements in the N‐terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV‐resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits. [ABSTRACT FROM AUTHOR]

Compared to japonica, the lower genetic transformation efficiency of indica is a technical bottleneck for rice molecular breeding. Specifically, callus browning frequently occurs during the culture of the elite indica variety 93-11, leading to poor culturability and lower genetic transformation efficiency. Here, 67 QTLs related to culturability were detected using 97 introgression lines (designated as 9DILs) derived from Dongxiang common wild rice (DXCWR, Oryza rufipogon Griff.) with 93-11 genetic background, explaining 4% ~12% of the phenotypic variations. The QTL qCBT9 on chromosome 9 was a primary QTL for reducing callus browning derived from DXCWR. Five 9DILs with light callus browning and high differentiation were screened. We evaluated the callus browning index (CBI) of 100 F2 population crossed of 93-11 and 9DIL71 and the recombinant plants screened from 3270 individuals. The qCBT9 was delimited to a ~148kb region between the markers X16 and X23. RNA-seq analysis of DEGs between 9DIL71 and 93-11 showed three upregulated DEGs (Os09g0526500, Os09g0527900, Os09g0528200,) and three downregulated DEGs (Os09g0526700, Os09g0526800, Os09g0527700) were located in the candidate region of qCBT9. Furthermore, callus browning may be involved in cell senescence and death caused by oxidative stress. The differentiation of indica and japonica in this region suggested that qCBT9 was possibly a vital QTL contributed to better culturability of japonica. Our results laid a foundation for further cloning of the gene for reduced callus browning in O. rufipogon, and also provided a new genetic resource and material basis for improving the culturability and genetic transformation efficiency of cultivated rice. [ABSTRACT FROM AUTHOR]

Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types. [ABSTRACT FROM AUTHOR]

Introduction: Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource. Methods: A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes. Results and Discussion: More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: The natural variation of plant‐specialized metabolites represents the evolutionary adaptation of plants to their environments. However, the molecular mechanisms that account for the diversification of the metabolic pathways have not been fully clarified. Rice plants resist attacks from pathogens by accumulating diterpenoid phytoalexins. It has been confirmed that the composition of rice phytoalexins exhibits numerous natural variations. Major rice phytoalexins (momilactones and phytocassanes) are accumulated in most cultivars, although oryzalactone is a cultivar‐specific compound. Here, we attempted to reveal the evolutionary trajectory of the diversification of phytoalexins by analyzing the oryzalactone biosynthetic gene in Oryza species. The candidate gene, KSLX‐OL, which accounts for oryzalactone biosynthesis, was found around the single‐nucleotide polymorphisms specific to the oryzalactone‐accumulating cultivars in the long arm of chromosome 11. The metabolite analyses in Nicotiana benthamiana and rice plants overexpressing KSLX‐OL indicated that KSLX‐OL is responsible for the oryzalactone biosynthesis. KSLX‐OL is an allele of KSL8 that is involved in the biosynthesis of another diterpenoid phytoalexin, oryzalexin S and is specifically distributed in the AA genome species. KSLX‐NOL and KSLX‐bar, which encode similar enzymes but are not involved in oryzalactone biosynthesis, were also found in AA genome species. The phylogenetic analyses of KSLXs, KSL8s, and related pseudogenes (KSL9s) indicated that KSLX‐OL was generated from a common ancestor with KSL8 and KSL9 via gene duplication, functional differentiation, and gene fusion. The wide distributions of KSLX‐OL and KSL8 in AA genome species demonstrate their long‐term coexistence beyond species differentiation, suggesting a balancing selection between the genes. [ABSTRACT FROM AUTHOR]

The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice. [ABSTRACT FROM AUTHOR]

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor‐derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high‐resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v‐test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding. [ABSTRACT FROM AUTHOR]

Rice is cultivated and consumed worldwide. It belongs to genus 'Oryza' with about 21 wild relatives and eight identified genomes which makes it accessible to the huge pool of genetic resources. The rice crop can be distressed by various biotic and abiotic stressors that affect its productivity. Brown planthoppers (BPH) are major pests of different persistent biotypes in different regions. Several major and minor genes and quantitative trait loci (QTLs) regulate BPH resistance, a composite character. These genes/QTLs employ different resistance mechanisms and may be specific to each biotype. 22 of the 44 BPH genes are found in the wild cousins of rice. Several genes have been discovered, cloned, functionally assessed, and introduced into various lines. Most of the identified genes have not been functionally studied rendering their mechanisms to remain unknown. With the discovery that BPH-1 could not provide protection against Biotype 2, there were concerns about a major plant hopper outbreak. To avoid such a scenario, genes from various sources and different resistance mechanisms are being explored. [ABSTRACT FROM AUTHOR]

The protracted domestication of Asian rice is usually defined by the fixation of the domestication syndrome consisting of six main phenotypic traits having all an agronomic importance: seed retention, reduction of seed dispersal aids, increase in seed size, reduction of seed dormancy, a more compact growth habit, and synchronised flowering and ripening. However, during this initial domestication process the mating system of rice has also changed. Indeed, domesticated rice, Oryza sativa L., is predominantly a self-fertilising species while its wild progenitor – Oryza rufipogon Griff. – is partly an outcrossing species. We explain this cross- to self-fertilisation transition and study its consequences. We demonstrate that this transition cannot be explained by mate rarity, and recall it could be a side effect of conscious selection for closed panicles. Then we suggest an alternative explanation based on the 'time limitation hypothesis'. For this purpose, we hypothesise agronomic practices of early cultivators – fostering the rapid maturation of plants and their reproductive isolation – that are likely the selective pressures having led to this transition. Given its consequences and its origins, we contend that the outcrossing-selfing transition should be systematically included in the Asian rice domestication syndrome and even considered as its main trait. [ABSTRACT FROM AUTHOR]

Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement. [ABSTRACT FROM AUTHOR]

Salt stress is the second most devastating abiotic stress after drought and limits rice production globally. Genetic enhancement of salinity tolerance is a promising and cost-effective approach to achieve yield gains in salt-affected areas. Breeding for salinity tolerance is challenging because of the genetic complexity of the response of rice plants to salt stress, as it is governed by minor genes with low heritability and high G x E interactions. The involvement of numerous physiological and biochemical factors further complicates this complexity. The intensive selection and breeding efforts targeted towards the improvement of yield in the green-revolution era inadvertently resulted in the gradual disappearance of the loci governing salinity tolerance and a significant reduction in genetic variability among cultivars. The limited utilization of genetic resources and narrow genetic base of improved cultivars have resulted in a plateau in response to salinity tolerance in modern cultivars. Wild species are an excellent genetic resource for broadening the genetic base of domesticated rice. Exploiting novel genes of underutilized wild rice relatives to restore salinity tolerance loci eliminated during domestication can result in significant genetic gain in rice cultivars. Wild species of rice, Oryza rufipogon and Oryza nivara, have been harnessed in the development of a few improved rice varieties like Jarava and Chinsura Nona 2. Furthermore, increased access to sequence information and enhanced knowledge about the genomics of salinity tolerance in wild relatives has provided an opportunity for the deployment of wild rice accessions in breeding programs, while overcoming the cross-incompatibility and linkage drag barriers witnessed in wild hybridization. Pre-breeding is another avenue for building material that are ready for utilization in breeding programs. Efforts should be directed towards systematic collection, evaluation, characterization, and deciphering salt tolerance mechanisms in wild rice introgression lines and deploying untapped novel loci to improve salinity tolerance in rice cultivars. This review highlights the potential of wild relatives of Oryza to enhance tolerance to salinity, track the progress of work, and provide a perspective for future research. [ABSTRACT FROM AUTHOR]

The stigma exsertion rate (SER) is one of the important factors affecting the seed production of hybrid rice. In the genus Oryza, wild rice species usually show higher SERs than cultivars. We previously identified one novel SER-QTL, qSERg-1b, from the single-segment substitution line (SSSL) SG22 of O. glumaepatula. In this study, qSERg-1b was fine-mapped by developing the secondary SSSLs (s-SSSLs) of SG22 and substitution mapping among the s-SSSLs. A total of 11 s-SSSLs were developed and used for qSERg-1b fine-mapping. As a result, qSERg-1b was narrowed down to the 122.59 kb physical region between InDel markers M01 and M49. There were 19 genes annotated in both O. glumaepatula and the HJX74 genomes at the qSERg-1b interval. Based on the genome re-sequencing of SG22 and HJX74, and the expression levels of the annotated functional genes, multiple nucleotide variations were found in LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710, including base substitutions and insertions/deletions of the genes, and they also showed significant differences in expression levels between SG22 and HJX74. Therefore, LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710 were selected as the most possible candidate genes of qSERg-1b for further validation. The above results laid an important foundation for qSERg-1b cloning and provided valuable resources for molecular breeding of SER in rice. [ABSTRACT FROM AUTHOR]

Rice production in the Anhui province is threatened by fungal diseases. We obtained twenty-five fungal isolates from rice and wild rice leaves showing leaf spot disease collected along the Yangtze River. A phylogenetic analysis based on internal transcribed spacer (ITS), translation elongation factor 1 alpha (TEF1-α), and beta tubulin (TUB2) sequences revealed one isolate (SS-2-JB-1B) grouped with Nigrospora sphaerica, one (QY) with Nigrospora chinensis, twenty-two with Nigrospora oryzae, and one isolate (QY-2) grouped in its own clade, which are related to but clearly different from N. oryzae. Nineteen tested isolates, including sixteen strains from the N. oryzae clade and the three isolates of the other three clades, caused disease on detached rice leaves. The three isolates that did not belong to N. oryzae were also able to cause disease in rice seedlings, suggesting that they were rice pathogens. Isolate QY-2 differed from the other isolates in terms of colony morphology, cell size, and susceptibility to fungicides, indicating that this isolate represents a new species that we named Nigrospora anhuiensis. Our analysis showed that N. sphaerica, N. chinensis, and the new species, N. anhuiensis, can cause rice leaf spot disease in the field. This research provides new knowledge for understanding rice leaf spot disease. [ABSTRACT FROM AUTHOR]

Seed germination rate is one of the important indicators in measuring seed quality and seed germination ability, and it is also an important basis for evaluating the growth potential and planting effect of seeds. In order to detect seed germination rates more efficiently and achieve automated detection, this study focuses on wild rice as the research subject. A novel method for detecting wild rice germination rates is introduced, leveraging the SGR-YOLO model through deep learning techniques. The SGR-YOLO model incorporates the convolutional block attention module (efficient channel attention (ECA)) in the Backbone, adopts the structure of bi-directional feature pyramid network (BiFPN) in the Neck part, adopts the generalized intersection over union (GIOU) function as the loss function in the Prediction part, and adopts the GIOU function as the loss function by setting the weighting coefficient to accelerate the detection of the seed germination rate. In the Prediction part, the GIOU function is used as the loss function to accelerate the learning of high-confidence targets by setting the weight coefficients to further improve the detection accuracy of seed germination rate. The results showed that the accuracy of the SGR-YOLO model for wild rice seed germination discrimination was 94% for the hydroponic box and 98.2% for the Petri dish. The errors of germination potential, germination index, and average germination days detected by SGR-YOLO using the manual statistics were 0.4%, 2.2, and 0.9 days, respectively, in the hydroponic box and 0.5%, 0.5, and 0.24 days, respectively, in the Petri dish. The above results showed that the SGR-YOLO model can realize the rapid detection of germination rate, germination potential, germination index, and average germination days of wild rice seeds, which can provide a reference for the rapid detection of crop seed germination rate. [ABSTRACT FROM AUTHOR]

Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+/K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status. Moreover, O. rufipogon preserved the overall leaf carbon to nitrogen balance and photosynthetic apparatus integrity. Conversely, Vialone Nano showed the lowest percentage of plants surviving after treatment, and displayed a higher reduction in the growth of shoots rather than roots, with leaves compromised in water and ionic balance, negatively affecting the photosynthetic performance (lowest performance index by JIP-test) and apparatus integrity. Baldo showed intermediate salt tolerance. Being O. rufipogon interfertile with O. sativa, it resulted a good candidate for pre-breeding towards salt-tolerant lines. [ABSTRACT FROM AUTHOR]

Tandemly organized rRNA genes are a typical example of a multigene family, where individual members evolve co-ordinately within—but independently between—species due to gene conversion and unequal crossing over. More frequently, in eukaryotic species with an interspecies hybrid origin, expression of unhomogenized rRNA genes from one progenitor is epigenetically silenced because of nucleolus dominance, and distinct rRNA genes may lose functionality and evolve faster. Interestingly, we obtained unusual ribosomal gene sequences from Oryza species that showed great diversity and did not appear in the present rice genomic sequence. The diversity of rDNA sequences indicated that the homogenization in rice is incomplete and explains the introgression of distinct rRNA gene families into ancestral rice genomes before speciation and continent separation. The divergent large subunit (LSU) ribosomal genes are expressed, some of them differentially, depending on the N fertilization of plants. Detection of differential transcripts of the rRNA genes suggested that rRNA gene families are not functionally equivalent. Phylogenetic analysis assigned Oryza species branching order to monocots, and monocot lineages probably have the same ecological origin by molecular clock calculation. Therefore, our results suggested that the geographical distances of continent-separation cause barriers to the gene flow and homogenization among Oryza species which requires further explanation. [ABSTRACT FROM AUTHOR]

Wetland plants, including rice (Oryza spp.), have developed multiple functional adaptive traits to survive soil flooding, partial submergence or even complete submergence. In waterlogged soils and under water, diffusion of O2 and CO2 is extremely slow with severe impacts on photosynthesis and respiration. As a response to shallow floods or rising floodwater, several rice varieties, including deepwater rice, elongate their stems to keep their leaves above the water surface so that photosynthesis can occur unhindered during partial submergence. In stark contrast, some other varieties hardly elongate even if they become completely submerged. Instead, their metabolism is reduced to an absolute minimum so that carbohydrates are conserved enabling fast regrowth once the floodwater recedes. This review focuses on the fascinating functional adaptive traits conferring tolerance to soil flooding, partial or complete submergence. We provide a general analysis of these traits focusing on molecular, anatomical and morphological, physiological and ecological levels. Some of these key traits have already been introgressed into modern highyielding genotypes improving flood tolerance of several cultivars used by millions of farmers in Asia. However, with the ongoing changes in climate, we propose that even more emphasis should be placed on improving flood tolerance of rice by breeding for rice that can tolerate longer periods of complete submergence or stagnant flooding. Such tolerance could be achieved via additional tissues; i.e. aquatic adventitious roots relevant during partial submergence, and leaves with higher underwater photosynthesis caused by a longer gas film retention time. [ABSTRACT FROM AUTHOR]

Copyright of BIOAGRO is the property of Revista BIOAGRO and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The present study aimed to evaluate the impact of planting date on the growth and yield of rice genotypes. The study was conducted during Khaif season of 2022; the field experiment was conducted at the Rice Research Center (RRC) Dokri. The experiment was laid out in split plot design containing three sowing dates' viz. 30thJune, 15th July and 30thJuly in main plots and four rice genotypes viz. NUYT-M-11, N U Y T -M-8, NUYTM-10 and Latify (check) as sub plot treatments. Nevertheless, rice crops sown on June 30th demonstrated markedly superior performance compared to other sowing dates. These crops exhibited a plant height of 97.27 cm, 19.18 tillers per plant, a panicle length of 24.77 cm, a seed index of 29.82 g, a biological yield of 8964 kg/ha, a grain yield of 6000 kg/ha, and a harvest index of 84.11%. The interaction between genotypes and sowing dates significantly influenced the observed plant height, tillers per plant, panicle length, seed index, biological yield, grain yield, and harvest index. Among the genotypes, NUYT-M-11 sown on June 30th displayed the highest values for these parameters. [ABSTRACT FROM AUTHOR]

Aromatic rice cultivars fetch premium price globally. Jeerakasala and Gandhakasala are the two most important and popular tropical scented rice cultivars of Kerala with GI (geographical indication) tags. Reliable procedures are essential and need of the hour for preventing adulteration in aromatic rice cultivars. Molecular technologies using polymerase chain reaction based microsatellite markers are the most reliable and efficient, compared to morphological and biochemical strategies. In this study, we aimed to identify simple sequence repeats (SSR) markers to distinguish between aromatic and non-aromatic rice cultivars at the Regional Agricultural Research Station, Pattambi, Kerala, India. Two aromatic (Gandhakasala and Jeerakasala) and two non-aromatic popular rice cultivars (Jyothi and Aathira) of Kerala, were used for the study. In the bulked line analysis using five SSR markers, RM163, RM202, and RM342 exhibited polymorphism between the aromatic and non-aromatic bulks. In addition, these three SSR markers exhibited polymorphism in individual genotyping. Hence these SSR markers are promising for discriminating between aromatic and non-aromatic tropical rice genotypes and for preventing adulteration. [ABSTRACT FROM AUTHOR]

Spot spraying applications offer the opportunity to target specific weeds in a field, while simultaneously reducing herbicide usage and increasing the long‐term efficacy of chemical control options. The study is focused on controlling California weedy rice accessions (Oryza spp.) and problematic grass weeds with a spot spray application of clethodim in a flooded rice system. The efficacy of incorporating nonionic surfactant to clethodim applications was also assessed. Dose‐response experiments were carried out in a greenhouse on five weedy rice accessions, common grass rice weeds, and cultivated rice varieties L207, M105, M206, M209, M211, and S102 to determine the dose needed to affect these populations. Clethodim was applied in a field setting to assess spot spraying efficacy, the possibility of herbicide dispersion in the water, and crop injury. Clethodim successfully controlled weedy rice and grasses in the greenhouse. The effective rates to control 90% of the five test populations (ED90) were between 51 and 74 g ai ha−1 clethodim for weedy rice accessions. Adding nonionic surfactant to clethodim increased its efficacy by 1.6‐ to 1.9‐fold. Cultivated rice varieties did not exhibit any tolerance to clethodim, however, spot spraying applications at 150 g ai ha−1 clethodim did not cause any dispersion in the field. Clethodim spot spray application was effective both at the three‐ to four‐leaf growth stage and tillering growth stage for weedy rice. Core Ideas: Spot spray herbicide application successfully controlled weedy rice.Adding nonionic surfactant (NIS) increased the efficacy of clethodim.Clethodim at labeled rate did not cause rice injury outside the spot spray area in rice field.Clethodim spot spray was effective both at the three to four‐leaf growth stage and tillering growth stage for weedy rice. [ABSTRACT FROM AUTHOR]

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes’ expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.

Intercropping stands as a crucial strategy in promoting sustainable crop intensification while optimizing the use of natural resources. Rice intercropping, predominantly prevalent in upland and deepwater ecosystems characterized by less favorable conditions, represents a crucial area of research within this context. To the best of our knowledge, no prior research has explored the landscape of rice intercropping through bibliometric methods. Using the comprehensive Web of Science database, we conducted a meticulous analysis of 187 articles spanning the years 1980–2022, employing specialized software tools such as VOSviewer, Biblioshiny, and OriginPro. These articles were authored by a diverse group of 561 researchers hailing from 68 different organizations across 36 countries and disseminated through 67 distinct journals. Notably, the average annual growth rate of publications in this field was found to be 5.37 %. Our findings reveal that India, China, Brazil, and Indonesia emerged as the leading countries in publishing rice intercropping research. Among the numerous organizations, South China Agricultural University secured the highest rank, closely followed by the Indian Council of Agricultural Research and the Consortium of International Agricultural Research Centers. The research landscape was further illuminated by identifying the three most prominent journals in which these articles were published: Indian Journal of Agronomy, Indian Journal of Agricultural Sciences, and Field Crops Research. Classification of these research publications into categories exposed the primary domains of interest, including agronomy, multidisciplinary subject, soil science, and environmental science. A keyword analysis unequivocally pointed to ‘intercropping’ as the focal point of interest within this research area. As we look to the future, it is imperative that forthcoming studies delve into the realms of mechanization in rice intercropping, soil microbiology, and harnessing solar energy for more efficient agricultural practices. This comprehensive review serves as a valuable reference for pinpointing research priorities in tackling global food security challenges.

The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes. • Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. • The study of these halophytes will help us improve the salt tolerance of our existing crops and diversify the human diets. • We conclude the available strategies and technologies that enable the researchers to improve the salt tolerance performance of the major crops and the genetics of halophytes. [ABSTRACT FROM AUTHOR]