Rice Cultivar IR24 Research Articles

Characterization of quantitative trait loci from DJ123 (aus) independently affecting panicle structure traits in indica rice cultivar IR64.

The online version contains supplementary material available at 10.1007/s11032-024-01494-5.

Enhancement of genetic transformation efficiency in indica rice cultivar IR64 by vacuum infiltration and exogenous application of polyamines

Enhancement of genetic transformation efficiency in indica rice cultivar IR64 by vacuum infiltration and exogenous application of polyamines

Rice-Magnaporthe transcriptomics reveals host defense activation induced by red seaweed-biostimulant in rice plants.

Red seaweed extracts have been shown to trigger the biotic stress tolerance in several crops. However, reports on transcriptional modifications in plants treated with seaweed biostimulant are limited. To understand the specific response of rice to blast disease in seaweed-biostimulant-primed and non-primed plants, transcriptomics of a susceptible rice cultivar IR-64 was carried out at zero and 48h post inoculation with Magnaporthe oryzae (strain MG-01). A total of 3498 differentially expressed genes (DEGs) were identified; 1116 DEGs were explicitly regulated in pathogen-inoculated treatments. Functional analysis showed that most DEGs were involved in metabolism, transport, signaling, and defense. In a glass house, artificial inoculation of MG-01 on seaweed-primed plants resulted in the restricted spread of the pathogen leading to the confined blast disease lesions, primarily attributed to reactive oxygen species (ROS) accumulation. The DEGs in the primed plants were defense-related transcription factors, kinases, pathogenesis-related genes, peroxidases, and growth-related genes. The beta-D-xylosidase, a putative gene that helps in secondary cell wall reinforcement, was downregulated in non-primed plants, whereas it upregulated in the primed plants indicating its role in the host defense. Additionally, Phenylalanine ammonia-lyase, pathogenesis-related Bet-v-I family protein, chalcone synthase, chitinases, WRKY, AP2/ERF, and MYB families were upregulated in seaweed and challenge inoculated rice plants. Thus, our study shows that priming rice plants with seaweed bio-stimulants resulted in the induction of the defense in rice against blast disease. This phenomenon is contributed to early protection through ROS, protein kinase, accumulation of secondary metabolites, and cell wall strengthening.

Near-isogenic lines for resistance to blast disease, in the genetic background of the Indica Group rice (Oryza sativa L.) cultivar IR64

We developed 21 near-isogenic lines (NILs) in the genetic background of the Indica Group rice ( Oryza sativa L.) cultivar IR64, with each containing one of the 11 blast resistance genes: Pish , Piz , Piz-5 , Pi9 (t), Pii , Pi3 , Pik , Pik-h , Pik-p , Pi1 , and Pi7 (t). The NILs were confirmed to harbor these genes by their reaction patterns to standard differential blast isolates and by analyses for graphical genotypes using DNA markers located on the same chromosome regions as the target resistance genes. The agronomic traits of these NILs, such as days to heading and yield components, were also investigated and found to be very similar to those of IR64, even when grown under the dramatically different environmental conditions of the temperate and subtropical regions of Japan. These NILs and their genetic information will be used as gene sources for Indica Group rice breeding programs, to improve resistance to blast disease, and as a multiline variety that will also be useful as an alternative approach to the development of the durability of rice resistance to blast disease in tropical areas, especially in irrigated lowland ecosystems.

Efficacy of Rhizobacteria to Promote the Growth and Increase the Yield of Several Rice Cultivars

Rice is still play important role as staple food for most of Indonesian population; consequently Indonesia is greatly relying on rice production to maintain food security. This plant is commonly cultivated with intensive use of synthetic agrochemicals such as synthetic chemical fertilizers and pesticides. However, the improper use of agrochemicals may result in adverse effects to the environment including biotic and abiotic components. This study was conducted to evaluate the efficacy of rhizobacteria formulation to promote the growth and increase the yield of four rice cultivars that commonly grown in Indonesia i.e . Ciherang, Cigeulis, Inpari 33, and IR64. Experiment was done in a green house with three concentrations of rhizobacteria formulation i.e. 0%, 1%, and 2% (v/v). Several parameters were observed in this study such as seedling height, leaf chlorophyll content of seedling, plant height at 50 days after transplanting (DAT), leaf chlorophyll content at 50 DAT, number of tillers per plant at 50 DAT, number of productive tillers per plant, and yield per plant. Results showed that significant interactions were observed between rice cultivar and concentration of rhizobacteria formulation in all parameters observed. Rice cultivar IR64 consistently showed superior growth and yield among four rice cultivars tested. Except for cultivar IR64, rhizobacteria concentration at 2% showed superior results compared to 1% and 0% for all parameters observed. This study proved that rhizobacteria formulation containing Stenotrophomonas maltophilia Sg3 and Enterobacter cloacae Al7Kla effectively promoted the growth and increase the yield of four rice cultivars that commonly cultivated in Indonesia, suggested that this rhizobacteria formulation is promising bio-agent to be used for rice production in Indonesia. Keywords: Rhizobacteria, plant growth promotion, rice yield DOI: 10.7176/JBAH/11-16-03 Publication date: August 31 st 2021

Improving growth performance of rice cultivars IR64 and Mentik Wangi in drought stress with applying nano Zn

Increasing temperatures due to climate change caused irregular rainfall in some regions. Changes in rainfall initiate drought to increase every year and negatively impact vital human activities, including agricultural sectors. Drought stress is becoming increasingly important in agriculture because it affects changes in physiological function and leads to a severe decline in crop production. Nano Zn is one of the solutions for drought stress which has a role in enzyme activation, protein synthesis, and carbohydrate metabolism. This study aims to determine the effect of applying nano Zn on rice growth performance in drought stress conditions. The method used was a non-factorial Completely Randomized Design with analysis of variance followed by DMRT at 5% level. The levels of Zn concentration were 0; 0.5; 1; 1.5; 2 ppm Zn. Two varieties were used, ‘IR 64’ as a hybrid cultivar and ‘Mentik Wangi’ as a local cultivar in Indonesia. The variables observed were plant height (cm), number of tillers, number of leaves, biomass weight (g), and root dry weight (g). The result showed that applying nano Zn can increase rice growth due to drought stress on the various variables. The higher the nano Zn dosage, the higher plant height, number of tillers, number of leaves, biomass, and root dry weight by 3-6 %, 2-33 %, 6-23 %, 8-28 %, and 3-34 % respectively compared without Zn. These results can be considered a solution for environmental conditions affected by drought stress by paying attention to Zn concentration level.

Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice (Oryza sativa L.)

Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host–T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.

The Role of Nanochitosan on the Expression of Rice Resistance Genes against Bacterial Leaf Blight

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has been reported to cause ± 20–50% of rice yield loss around the world. Resistant varieties are used to control this disease, however due to rapid evolution of this pathogen, the resistances was broken down in a few years. This study is aimed to determine the role of nanochitosan in the expression of rice Xa21 and Xa1 resistant genes against Xoo. The BLB susceptible rice cultivar IR64, the Xoo isolate MAG2 and a 0.065% concentration of nanochitosan were used in this experiment. Application of nanochitosan was carried out within 1-week intervals starting at rice aged 2–10 weeks after transplanting. The expression of Xa21 and Xa1 genes against Xoo were analyzed using conventional PCR and qPCR methods at 0 and 4 days after Xoo inoculation followed by 4x scoring of disease symptoms in 1-week interval. The treatments used in this study included the mock one/inoculated with sterile distilled water, K (+)/ plants inoculated with Xoo, CNP (-)/ with nanochitosan and sterile distilled water inoculation, and CNP (+)/ with nanochitosan and Xoo inoculation. The results showed that the 0.0065% concentration nanochitosan application was able to increase the expression of Xa21 and Xa1 genes on CNP (-). Disease intensity and AUDPC values did not show any significant difference between K (+) and CNP (+). This study concluded that nanochitosan at 0.065% was able to increase the expression of rice Xa21 and Xa1 resistance genes. However, the gene expression was not able to significantly suppress the infection development of Xoo.

RNAi-mediated down regulation of BADH2 gene for expression of 2-acetyl-1-pyrroline in non-scented indica rice IR-64 (Oryza sativa L.).

2-acetyl-1-pyrroline (2AP) is a principal aroma compound in scented rice and a mutation in betaine aldehyde dehydrogenase 2 (OsBADH2) is responsible aroma in scented rice. The present study was aimed at inducing 2AP production in non-scented indica rice cultivar IR-64 by silencing OsBADH2 via RNAi technique. A vector pBSK was used for the construction of RNAi cassette and pRI101ON as a binary vector. Agrobacterium (GV3101)-mediated transformation was done using embryogenic calli of IR-64. The resultant transgenic lines showed up to 14-fold reduction in expression of OsBADH2 gene and 50% inhibition in enzyme activity. Gas chromatography (GC-MS) analyses showed a significant amount of 2AP production in RNAi callus, leaves, and seeds of IR-64. A total 39 volatile compounds were identified from the control and RNAi seeds of IR-64. Among them, octanal and 2-pentylfuron were found to be increased (30-40%) in RNAi seeds of IR-64. The content of precursors, proline, and methylglyoxal increased substantially, whereas GABA content reduced up to 25% in transgenic IR-64 lines. The study demonstrated that RNAi approach could be successfully used for imparting pleasant aroma character in non-scented indica rice cultivars.

Alteration in plant spacing improves submergence tolerance in Sub1 and non-Sub1 rice (cv. IR64) by better light interception and effective carbohydrate utilisation under stress.

Besides genetic improvement for developing stress-tolerant cultivars, agronomic management may also add considerable tolerance against different abiotic stresses in crop plants. In the present study, we evaluated the effect of six different spacing treatments (S1: 10 × 10 cm; S2: 15 × 10 cm; S3:15 × 15 cm; S4:20 × 10 cm; S5: 20 × 15 cm; S6: 20 × 20 cm (row-row × plant-plant)) for improving submergence tolerance in rice. A high yielding submergence intolerant rice cultivar IR64 was tested against its SUB1 QTL introgressed counterpart (IR64-Sub1) for 12 days of complete submergence for different spacing treatments in field tanks. Relatively wider spaced plants showed higher individual plant biomass and early seedling vigour, which was particularly helpful for IR64 in increasing plant survival (by 150% in S6 over S1) under 12 days of submergence, whereas the improvement was less in IR64-Sub1 (13%). Underwater radiation inside the plant canopy, particularly beyond 40 cm water depth, was significantly greater in wider spacing treatments. Leaf senescence pattern captured by SPAD chlorophyll meter reading and chlorophyll fluorescence imaging data (Fm, Fv/Fm) taken at different time intervals after stress imposition suggested that there was lesser light penetration inside the canopy of closer spaced plants, and that it might hasten leaf senescence and damage to the photosynthetic system. The initial content of total non-structural carbohydrate (NSC) was higher in wider spaced plants of IR64, and also the rate of depletion of NSC was lesser compared with closer spaced plants. In contrast, there was not much difference in NSC depletion rate under different spacing in IR64-Sub1. Further, higher antioxidant enzyme activities in wider spaced plants (both IR64 and IR64-Sub1) after de-submergence indicated better stress recovery and improved tolerance. Taken together we found that wider spacing (row-row: 20 cm and plant-plant: 15 cm and more) can significantly improve submergence tolerance ability in rice, particularly in submergence intolerant non-Sub1 cultivar like IR64, perhaps due to better underwater light penetration, delayed leaf senescence and slower depletion of NSC reserve.

Contrasting root traits and native regulation of aquaporin differentially determine the outcome of overexpressing a single aquaporin (OsPIP2;4) in two rice cultivars.

Overexpressing OsPIP2;4 in the two rice cultivars Giza178 and IR64 resulted in contrasting cultivar-dependent physiological attributes under control and drought conditions in the field. In the T3 plants, PIP2;4 expression was significantly higher in the leaves and roots of Giza178 under control but only in the roots under drought condition and higher in the leaves and roots of IR64 under control but not under drought condition compared with that in the corresponding wild types. The transgene improved the plant growth in Giza178 under both growth conditions but had no significant effect in IR64 under either condition. The transgenic lines of Giza178 recovered their leaf relative water content faster than those of the wild type in the afternoon and showed improved gas exchange parameters, water use efficiency, and grain yield, as a result of improved root hydraulic conductivity (Lpr) and xylem sap flow. No comparable responses were found in IR64 although Lpr and xylem sap flow were enhanced in the transgenic lines under the control condition only, suggesting that the positive effect of PIP2;4 on the well-watered leaves of IR64 was offset by the low root/shoot ratio and the inherent expression of other aquaporins. In the transgenic plants of IR64 under drought, PIP2;4 expression was not induced in the roots presumably due to an overriding post-transcription regulatory mechanisms, leading to the lack of changes in the Lpr and xylem sap flow and consequently, the plant growth, water relations, gas exchange, and grain yield were similar to the wild type. The data suggest that the outcome of overexpressing a single aquaporin gene depends on the plant architecture, internal responses to drought, and native expression of other aquaporins.

Spermidine application reduces fluoride uptake and ameliorates physiological injuries in a susceptible rice cultivar by activating diverse regulators of the defense machinery.

The manuscript illustrates the ameliorative effects of exogenously applied higher polyamine (PA), spermidine (Spd) in the susceptible indica rice cultivar IR-64 subjected to prolonged fluoride stress. The Spd treatment drastically reduced fluoride bioaccumulation by restricting entry of the anions through chloride channels and enabled better maintenance of the proton gradient via accumulation of P-H+/ATPase, thereby improving the root and shoot lengths, fresh and dry weights, RWC, chlorophyll content and activities of pyruvate dehydrogenase (PyrDH), α-amylase, and nitrate reductase (NR) in the Spd-treated, stressed plants. Expression of RuBisCo, PyrDH, α-amylase, and NR was stimulated. Spd supplementation reduced the molecular damage indices like malondialdehyde, lipoxygenase, protease activity, electrolyte leakage, protein carbonylation, H2O2, and methylglyoxal (detoxified by glyoxalase II). Mitigation of oxidative damage was facilitated by the accumulation and utilization of proline, glycine-betaine, total amino acids, higher PAs, anthocyanin, flavonoids, β-carotene, xanthophyll, and phenolics as verified from the expression of genes like P5CS, BADH1, SAMDC, SPDS, SPMS, DAO, PAO, and PAL. Spd treatment activated the ascorbate-glutathione cycle in the stressed seedlings. Expression and activities of enzymatic antioxidants showed that GPOX, APX, GPX, and GST were the chief ROS scavengers. Exogenous Spd promoted ABA accumulation by upregulating NCED3 and suppressing ABA8ox1 expression. ABA-dependent osmotic stress-responsive genes like Osem, WRKY71, and TRAB1 as well as ABA-independent transcription factor encoding gene DREB2A were induced by Spd. Thus, Spd treatment ameliorated fluoride-mediated injuries in IR-64 by restricting fluoride uptake, refining the defense machinery and activating the ABA-dependent as well as ABA-independent stress-responsive genes.

Characterization of a Novel Gain-of-Function Spotted-Leaf Mutant with Enhanced Disease Resistance in Rice

We here reported the identification and characterization of a novel gain-of-function spotted-leaf 26 (Spl26) mutant from an ethylmethylsulfone (EMS)-induced rice cultivar IR64. Spl26 displayed reddish- brown lesions that firstly appeared on the leaf tips at the early tillering stage and spread gradually downward to cover the whole leaf blades that wilted subsequently. The lesion development was light- dependent under natural conditions. Spl26 exhibited impaired photosynthetic capacity with decreased chlorophyll content and lowered photosynthetic parameters which ultimately led to the poor performance of agronomic traits. Severe cell death occurred in Spl26 in accompany with increased malonaldehyde level and membrane ion leakage rate, elevated reactive oxygen species (ROS) accumulation, altered ROS scavenging activities, increased DNA fragmentation and decreased soluble protein levels. Defense responses were activated in Spl26 with enhanced resistance to rice bacterial blight, up-regulation of defense response genes and altered endogenous hormone levels. The spotted-leaf phenotype is controlled by a single dominant nuclear gene localized to a 305kb region between RM5490 and InDel42 on the short arm of chromosome 7. The data suggested that Spl26 is a novel gain-of-function spotted-leaf mutant with enhanced bacterial disease resistance and immunity-associated premature leaf senescence and would provide the basis for cloning of the target gene.

Biopriming with Piriformospora indica ameliorates cadmium stress in rice by lowering oxidative stress and cell death in root cells

Piriformospora indica is known for plant growth promotion and abiotic stress alleviation potential in several agricultural crops. However, a systemic analysis is warranted to explore potential application of this important fungus to augment heavy metal tolerance in rice. The present study explores potential of P. indica in ameliorating the effect of cadmium (Cd) stress in rice cultivars N22 and IR64. Seedlings inoculated with P. indica recorded significantly higher root-shoot length and biomass as compared to non-inoculated plants under control and Cd stress, respectively. Moreover, P. indica inoculated stressed roots accumulated more Cd as compared to non-inoculated stressed roots in both the varieties. Interestingly, cell death and reactive oxygen species (ROS) accumulation were significantly lower in the inoculated plant roots as compare with non-inoculated roots under Cd stress. The results emphasized significantly higher accumulation of Cd in fungal spores could reduce ROS accumulation in root cells resulting in lower cell death.

The Role of a Host-Induced Arginase of Xanthomonas oryzae pv. oryzae in Promoting Virulence on Rice.

The plant bacterial pathogen Xanthomonas oryzae pv. oryzae causes bacterial blight of rice, which is one of the most destructive rice diseases prevalent in Asia and parts of Africa. Despite many years of research, how X. oryzae pv. oryzae causes bacterial blight of rice is still not completely understood. Here, we show that the loss of the rocF gene caused a significant decrease in the virulence of X. oryzae pv. oryzae in the susceptible rice cultivar IR24. Bioinformatics analysis demonstrated that rocF encodes arginase. Quantitative real-time PCR and Western blot assays revealed that rocF expression was significantly induced by rice and arginine. The rocF deletion mutant strain showed elevated sensitivity to hydrogen peroxide, reduced extracellular polysaccharide (EPS) production, and reduced biofilm formation, all of which are important determinants for the full virulence of X. oryzae pv. oryzae, compared with the wild-type strain. Taken together, the results of this study revealed a mechanism by which a bacterial arginase is required for the full virulence of X. oryzae pv. oryzae on rice because of its contribution to tolerance to reactive oxygen species, EPS production, and biofilm formation.

Root anatomical traits of wild-rices reveal links between flooded rice and dryland sorghum

The root anatomical and morphological traits and their plasticity under water deficit are essential to improve adaptation of rice cultivars to water-limited conditions. We investigated wild-rice accessions along with a dryland cereal (Sorghum bicolor) for root related traits under non-stress and water deficit during panicle initiation and flowering. Wild-rices from GG genome (Oryza granulata and Oryza meyeriana) recorded high similarity with sorghum in key root anatomical parameters such as larger stele diameter in proportion to root diameter (SD:RD [%]) and more late metaxylem number (LMXN). Comparative analyses between wild-rice accessions and a diverse indica panel revealed narrow genetic variability in LMXN and SD:RD in Oryza sativa panel compared to O. granulata and O. meyeriana. Wild-rices from GG genome had a combination of favorable anatomy (larger SD:RD and more but smaller late metaxylem) and root morphology (thinner roots and higher root surface area) during panicle initiation and flowering compared to popular rice cultivar IR64. The above combination can help facilitate effective water use by regulating axial water flow under water-deficit conditions, while the opposite was noticed in the drought susceptible IR64. Novel sources for root anatomical traits identified from wild-rice accessions can be utilized in rice breeding programs to develop water-deficit stress tolerant rice cultivars.

The Effects of Introgression of the Submergence1 Allele Into Rice Cultivar Ir64 on Post-harvest Seed Dormancy and Longevity

Introgressing the Submergence1 (Sub1) allele into chromosome 9 of high-yielding rice (Oryza sativa L.) cultivars introduced the flood-tolerant trait, but this chromosome also includes quantitative trait loci for seed storage survival. Loss in seed dormancy and viability during post-harvest storage were investigated in cvs IR64 and IR64-Sub1 to test if the introgression of Sub1 affected seed longevity. They were grown in the same controlled environment, mature seeds harvested, and ability to germinate monitored during subsequent hermetic storage at 40°C with 13.5-13.9% moisture content. The overlapping patterns of loss in dormancy and loss in viability during storage were quantified well by a multiplicative model, with similar responses in the two near-isogenic cultivars: both showed almost full dormancy initially with complete, similar, loss in dormancy during the first seven days of storage, loss in viability after 43 days, and 50% viability periods (p50) of 26.4-28.1 days. Hence, introgression of the submergence-tolerant allele Sub1A-1 in rice cv. IR64 did not affect seed dormancy or survival after harvest substantially, but duration to flowering was nine days longer and seed yield also greater in cv. IR64-Sub1.

Herbal Extracts in Combination with Nanosilver Inhibit Blight Disease Caused by Xanthomonas oryzae pv. oryzae in Rice

Bacterial rice leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), has a massive impact on the quality and productivity of rice. Besides BLB resistant rice cultivars, herbal extracts and nanosilver have increasingly demonstrated their important roles in controlling the disease as alternatives to synthetic chemical pesticides. Therefore, this research aimed to examine the Xoo antibacterial effects of several herbal extracts and nanosilver in vitro and in vivo. In the study, Wedelia chinensis Osbeck Merr., Clerodendrum fragrans Vent., Excoecaria cochinchinensis Lour., Polyathia longifolia var. Pendula, and Caesalpinia sappan L. were extracted by maceration with six types of solvents (distilled water, 70% ethanol, chloroform, n-hexane, and 100% acetonitrile), then used in an agar diffusion test to evaluate their Xoo antibacterial effects. The results showed that 70% ethanol was the best extracting solvent for the targeted plants. C. fragrans, E. Cochinchinensis, and C. sappan showed significant antibacterial effects with inhibition zone diameters of 28.50 cm, 21.00 cm, and 25.70 cm, respectively. Finally, the individual extract from C. fragrans, E. Cochinchinensis, and C. sappan were combined with nanosilver particles and used to access BLB inhibition capacity in vivo, using the rice cultivar IR24 as the target for Xoo infection. Application of the C. fragrans extract resulted in resistance of IR24 rice to BLB. Similar results were also observed in the infected rice when products combining nanosilver and E. cochinchinensis or C. sappan were applied to infected rice leaves.

Contribution of the cold shock protein CspA to virulence in Xanthomonas oryzae pv. oryzae.

Summary Xanthomonas oryzae pv. oryzae (Xoo) causes a damaging bacterial leaf blight disease in rice. Cold shock proteins (Csps) are highly conserved nucleic acid‐binding proteins present in various bacterial genera, but relatively little is known about their functions in Xanthomonas. Herein, we identified four Csps (CspA–CspD) in the Xoo PXO99A strain. Deletion of cspA decreased cold adaptation and a few known pathogenic factors, including bacterial pathogenicity, biofilm formation and polysaccharide production. Furthermore, we performed transcriptomic and chromosome immunoprecipitation (ChIP) experiments to identify direct targets of CspA and to determine its DNA‐binding sequence. Integrative data analysis revealed that CspA directly regulates two genes, PXO_RS11830 and PXO_RS01060, by binding to a conserved CCAAT sequence in the promoter region. We generated single‐deletion mutants of each gene and the results indicate that both are responsible for Xanthomonas pathogenicity. In addition, quantitative real‐time polymerase chain reaction and western blotting showed that CspA suppressed the expression of its direct targets. In summary, our study clarifies the characteristics of Csps in Xanthomonas and greatly advances our understanding of the mechanisms underlying the contribution of CspA to bacterial virulence.

Effect of short-term heat exposure on physiological traits of indica rice at grain-filling stage

Heat stress impacts the quantity and quality of rice grains, particularly during grain-filling stage needed for grain development. In this study, the effect of short heat stress (42 °C, 30 min) on indica rice plants at the grain-filling stage (dough grain stage) was found by determining their physiological and growth traits Fv/Fm, ∆F/Fm′, chlorophyll content, leaf water potential (LWP), membrane stability, relative leaf area (RLA), relative plant height (RPH), total grain weight per panicle (TGW) and 1000 GW. Thai economic rice cvs. KDML105 and Pathumthani 1 (PTT1) were compared to the heat-tolerant rice cultivars N22 and Dular and to the heat-sensitive rice cultivar IR64. The results showed that short heat stress exhibited effects on physiology and growth greater than the control (35 °C, 30 min) by reducing of Fv/Fm, ∆F/Fm′, chlorophyll content, LWP, membrane stability and RLA. This result impacted the TGW and 1000 GW. A higher reduction of physiological traits was shown in IR64, followed by KDML105. In contrast, N22 and Dular were minimally affected by heat stress and were able to adapt and recover based on their grain weight that exhibited less of an effect. PTT1 was also impacted by heat stress similarly to Dular. Thus, short heat stress affected the physiological parameters of five rice cultivars at the dough grain stage. In addition, the five indica rice cultivars were classified into three groups: (1) the heat-tolerant group (N22, Dular and PTT1), (2) the moderately heat-tolerant group (KDML105), and (3) the heat-sensitive group (IR64) by PC-ORD program at 50% of similarity of the 13 physiological traits.