Yield Losses In Rice Production Research Articles

Yield components affected by rice black-streaked dwarf virus disease in rice cultivars with different resistance levels.

Rice black-streaked dwarf virus disease (RBSDVD) is one of the most destructive rice viral diseases, leading to severe yield losses in rice production. However, little is known about the yield-related components associated with the disease and no resistance cultivars have been successfully used in rice breeding. Seven rice cultivars were analyzed in this study, including six commercial rice varieties and a new line Zhongjian No. 201 (ZJ201) containing the resistance gene OsAP47. Resistance levels of these cultivars were evaluated by artificial inoculation and yield components were collected, including panicle length (PL), spikelets per panicle (SPP), ripened grains per panicle (RGPP), as well as panicles per square meter (PPSM) and 1000-grain weight (TGW). Seed setting rate (SSR) were calculated with the data of SPP and RGPP. The results showed that ZJ201 displayed the highest resistance level and most of the commercial rice cultivars exhibited susceptible to RBSDVD. Yields of all the rice cultivars were significantly declined except ZJ201 and yield losses produced by RBSDVD were mainly due to the reduction of PL, SPP, RGPP, and TGW, suggesting that developments of these traits are associated with RBSDV infection. Resistant rice cultivar could reduce yield losses by maintaining normal development of these traits. Significant correlations were identified between resistance levels and the yield components except SSR and PPSM. The results provided useful clues for understanding the mechanisms of RBSDV invasion and its effect on rice production. ZJ201 was demonstrated as a resistance material that could be used in rice breeding.

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

Abstract Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.

QTL-seq Identifies Genomic Regions Associated with Resistance to Dirty Panicle Disease in Rice

Dirty panicle disease is one of the most important diseases that can cause yield losses in rice production. Despite the severity of the disease, the molecular basis of resistance to the pathogen is poorly understood. Using QTL-seq with an F2 population, we identified three genomic regions on chromosomes 1, 9, and 10, namely qDP1, qDP9, and qDP10. These regions are significantly associated with resistance to dirty panicle disease caused by two fungal pathogens, Bioplaris oryzae and Cirvularia lunata. qDP1 was significantly associated only with resistance to B. oryzae, whereas qDP9 and qDP10 were significantly associated with both B. oryzae and C. lunata. We also developed KASP markers for each QTL detected and validated them in the F2 population. The markers were able to explain phenotypic variation in a range of 5.87–15.20%. Twelve potential candidate genes with annotated functions as resistance-related genes were proposed. These candidate genes include those encoding RLK, MATE, WAK, NBS-LRR, subtilisin-like protease, and ankyrin repeat proteins. The results of this study provide insights into the genetic mechanism of dirty panicles in rice and will be useful for future breeding programs for dirty panicle resistance. This is the first report of QTLs associated with resistance to dirty panicle disease in rice.

Deep spatial and temporal graph convolutional network for rice planthopper population dynamic forecasting

Rice planthoppers (RPH) are important pests that cause severe yield losses in rice production in China. The widespread and intensive use of insecticides to prevent RPH causes serious issues. Forecasting the population dynamics of RPH is an important part of integrated pest management, which helps to prevent impending RPH outbreaks and reduce the use of insecticide. However, forecasting RPH population dynamics is very challenging as it results from complex spatial and temporal dispersion processes impacted by many factors, such as source populations, meteorological conditions, and host plant characteristics. Therefore, a novel deep learning-based model using graph convolutional network (GCN) and long short-term memory network (LSTM) is proposed in this study to capture RPH population dynamics. This model includes one dynamic GCN (DGCN) for modeling source populations and two attention-based LSTM encoder-decoder network (ALSTM) for modeling meteorological and host plants, respectively. The proposed model can dynamically aggregate the outputs of one DGCN and two ALSTM based on data to produce the final output for each county. The proposed model is evaluated on the dataset collected in South and Southwest China during 2000–2019, which includes populations, meteorological and host plant factors. The results demonstrate that DGCN-ALSTM outperforms other state-of-art deep learning methods and traditional time series forecasting approaches. The improvement brought by DGCN-ALSTM are about 1.95 %, 1.32 %, and 1.60 % for brown planthopper population, and 1.79 %, 0.71 %, and 0.32 % for white back planthopper population according to the R, RMAE, and RRMSE take DGCN as the baseline, respectively. The proposed DGCN-ALSTM provides a new better tool to forecast RPH population dynamics and the accurate forecasting results can guide local plant protection organizations to develop detailed sustainable pest control strategies and methods to control RPH in time.

Overexpression of OsGF14C enhances salinity tolerance but reduces blast resistance in rice.

High-salinity and blast disease are two major stresses that cause dramatic yield loss in rice production. GF14 (14-3-3) genes have been reported to play important role in biotic and abiotic stresses in plants. However, the roles of OsGF14C remain unknown. To understand the functions and regulatory mechanisms of OsGF14C in regulating salinity tolerance and blast resistance in rice, we have conducted OsGF14C-overexpressing transgenic experiments in the present study. Our results showed that overexpression of OsGF14C enhanced salinity tolerance but reduced blast resistance in rice. The enhanced salinity tolerance is related to the reduction of methylglyoxal and Na+ uptake instead of exclusion or compartmentation and the negative role of OsGF14C in blast resistance is associated with the suppression of OsGF14E, OsGF14F and PR genes. Our results together with the results from the previous studies suggest that the lipoxygenase gene LOX2 which is regulated by OsGF14C may play roles in coordinating salinity tolerance and blast resistance in rice. The current study for the first time revealed the possible roles of OsGF14C in regulating salinity tolerance and blast resistance in rice, and laid down a foundation for further functional study and crosstalk regulation between salinity and blast resistance in rice.

Reduced Toxicities of Insecticides Against Brown Planthopper (Nilaparvata lugens Stål) Collected from Rice Fields in Bangladesh

The brown planthopper, Nilaparvata lugens (Stål), caused severe yield losses in rice production in many Asian countries. Chemical control is the key component of the integrated pest management tool to control rice brown planthopper (BPH). However, reduced toxicity of insecticides against this pest has been reported. We investigated the BPH mortality rate and the evolution of insecticide resistance in BPH collected from Bangladesh to commonly used insecticides by the rice-stem dipping method. Both the BPH laboratory strain and field populations were used in this study. The mortality rate of the Gazipur field population ranges from 15% to 80%, after exposure to imidacloprid in different concentrations. The highest mortality was found in response to dinotefuran followed by chlorpyrifos and etofenprox. The mortality rate increased after the time of exposure in relation to the increased concentrations of the insecticides. Additionally, the selected BPH strain shows a higher level of resistance to imidacloprid (resistance ratio = 179.45-fold), while other field populations show low to moderate levels of resistance. Increased detoxification enzyme activity, cytochrome P450 monooxygenase, was found in imidacloprid-resistant BPH. This study provides important information regarding the reduced toxicities of frequently used insecticides to control BPH.

The effect of integrated pest management on Scirpophaga innotata population and natural enemies on rice field in South Sulawesi, Indonesia

Abstract. Rahmawasiah, Abadi AL, Mudjiono G, Rizali A. 2022. The effect of integrated pest management on Scirpophaga innotata population and natural enemies on rice field in South Sulawesi, Indonesia. Biodiversitas 23: 4510-4516. White rice stem borer, Scirpophaga innotata, is an important pest on rice plants that needs attention because the population is quite large in Luwu Raya. This pest attacks rice plants at all growth stages and can result in yield losses in rice production. Synthetic insecticides are a common control technique used by farmers to control these pests. The continuous use of pesticides will certainly have a negative impact. Therefore, pursuing effective control strategies and maintaining environmental sustainability is necessary. This study aimed to determine the white rice stem borer population and its natural enemies on rainfed land, and permanent irrigated lands managed conventionally and integrated pest management. The research was carried out using insect sampling techniques and calculating the white rice stem borer population and natural enemies in rice cultivation. In rainfed and irrigated rice fields, rice cultivation was carried out using conventional methods and integrated pest management (in the form of planting refugia and regulating the use of synthetic pesticides). The sampling was carried out on plants from the vegetative phase to the generative phase. The type of insect taken was the white rice stem borer in the form of collecting groups of eggs and larvae. Imago was observed visually and using a farmcop. In addition, the collection of natural enemy insects on the plantation was also carried out. The results showed that the application of the integrated pest management system caused no significant effect on the decline of the white rice stem borer population in both rainfed and permanently irrigated lands in Luwu Raya. The white rice stem borer population was more commonly found in rainfed land than permanently irrigated land. The parasitoids found were Telenomus rowani, Tetrastichus schoenobii and Trichogramma japonicum. The population of Telenomus rowani was more numerous than other types of parasitoids. On average, the parasitoid population was more in the land managed by integrated pest management (IPM) application than the conventionally managed land. The predators found on the land were Oxyopes javanus, Agriocnemis femina, Conocephalus longipennis, Menochilus sexmaculata, Ophionea nigrofasciata, Micraspis lineata, and Paederus fuscipes. Predator populations were more on land managed with the application of IPM than on land managed conventionally.

Searching of Novel Herbicides for Paddy Field Weed Management—A Case Study with Acetyl-CoA Carboxylase

Weed management is the major biological constraint in paddy (Oryza sativa L.) producing areas. Predominantly, barnyard grass (Echinochloa crus-galli) is a rice-mimicking weed that causes 57% of yield loss in rice production. Conventionally, herbicides are the site-specific weed inhibitors often used to suppress E. crus-galli growth. Acetyl-CoA carboxylase (ACCase) is an important target for developing novel herbicides with remarkable selectivity against gramineous weeds. Notably, fenoxaprop-P-ethyl (FPPE) is a selective ACCase herbicide extensively used in paddy fields to inhibit barnyard grass. However, prolonged use of FPPE herbicide elicits phytotoxicity in cultivated rice and herbicide resistance in weeds. Recently, phytotoxins are emerging as an alternative to commercial herbicides with safer environmental profiles. Nevertheless, discovering natural herbicides through in vivo and in vitro techniques is time-consuming and expensive. Therefore, high-end computational screening strategies including Tanimoto similarity, docking, binding free energy, and herbicide-likeness were used to pinpoint the lead molecule. Finally, molecular dynamics and MM/PBSA calculations were employed to validate the binding kinetics of the hit compound. Indeed, sinigrin was identified as a promising phytotoxic inhibitor against the ACCase enzyme. The findings of our study were well correlated with the existing experimental results. Overall, the current work will aid in the development of commercializing phytotoxin herbicides in foreseeable future.

Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies.

AimsRice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses.LocationSub-Saharan Africa.MethodsSince the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). We finally measure the rice production and GPD loss per country through the spatial index named “Pest Aggression Index”, based on the inferred connectivity magnitude.ResultsThe most considerable losses in rice production are observed for Liberia, Sierra Leone and Madagascar in all future scenarios (2030, 2050, 2070). The future economic cost, calculated as USD lost from rice losses/country’s GDP results are high for Central African Republic (−0.6% in SSP_2.45 and −3.0% in SSP_3.70) and Guinea–Bissau (−0.4% in SSP_2.45 and −0.68% in SSP_3.70), with relevant losses also obtained for other countries.Main conclusionsSince our results are spatially explicit and focused on each country, we encourage careful land-use planning. Our findings could support best practices to avoid the future settlement of new cultivations in territories where rice would be attacked by pulla group and the virus, bringing economic and biodiversity losses.

A Histone Deacetylase, Magnaporthe oryzae RPD3, Regulates Reproduction and Pathogenic Development in the Rice Blast Fungus.

ABSTRACTAcetylation and deacetylation of histones are key epigenetic mechanisms for gene regulation in response to environmental stimuli. RPD3 is a well-conserved class I histone deacetylase (HDAC) that is involved in diverse biological processes. Here, we investigated the roles of the Magnaporthe oryzae RPD3 (MoRPD3) gene, an ortholog of Saccharomyces cerevisiae Rpd3, during development and pathogenesis in the model plant-pathogenic fungus Magnaporthe oryzae. We demonstrated that the MoRPD3 gene is able to functionally complement the yeast Rpd3 deletion mutant despite the C-terminal extension of the MoRPD3 protein. MoRPD3 localizes primarily to the nuclei of vegetative hyphae, asexual spores, and invasive hyphae. Deletion of MoRPD3 appears to be lethal. Depletion of MoRPD3 transcripts via gene silencing (MoRPD3kd, where “kd” stands for “knockdown”) has opposing effects on asexual and sexual reproduction. Although conidial germination and appressorium formation rates of the mutants were almost comparable to those of the wild type, in-depth analysis revealed that the appressoria of mutants are smaller than those of the wild type. Furthermore, the MoRPD3kd strain shows a significant reduction in pathogenicity, which can be attributed to the delay in appressorium-mediated penetration and impaired invasive growth. Interestingly, MoRPD3 does not regulate potassium transporters, as shown for Rpd3 of S. cerevisiae. However, it functioned in association with the target of rapamycin (TOR) kinase pathway, resulting in the dependency of appressorium formation on hydrophilic surfaces and on TOR’s inhibition by MoRPD3. Taken together, our results uncovered distinct and evolutionarily conserved roles of MoRPD3 in regulating fungal reproduction, infection-specific development, and virulence.

Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice.

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn’t any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.

Floating chitosan-alginate microspheres loaded with chlorantraniliprole effectively control Chilo suppressalis (Walker) and Sesamia inferens (Walker) in rice fields

Striped rice stem borer, Chilo suppressalis (Walker) and pink stem borer, Sesamia inferens (Walker) are two important pests, causing substantial yield loss in rice production. Application of conventional synthetic pesticides, such as suspension concentrates and water-dispersible granules, is a primary method for control of the two pests. Due to the flow of water in rice field, spray drift, and soil adsorption, applied such pesticides are often out of the target, resulting in low control efficacy, potential contamination of soil or surface water, and also threat to human health. Thus, there is an urgent need for developing environmentally friendly and highly targeted pesticide formulations to meet the challenges. The present study synthesized chlorantraniliprole loaded chitosan-alginate floating hydrogel microspheres (CCAM) through physical embedding, ionic crosslinking, and incorporation of citronellol as an oil phase. The morphology, particle size, entrapment efficiency, loading capacity, in vitro slow-release kinetics, and floating ability of the CCAM were tested in laboratory conditions. The CCAM and two commercial formulations (suspended and granulated) of chlorantraniliprole were respectively evaluated in two rice fields located in two provinces of China. The CCAM was able to float on the surface of rice field, gather around rice stems, and slowly release chlorantraniliprole, which resulted in significantly higher concentrations of chlorantraniliprole in rice stems and leaves for a prolonged time than suspended and granulated controls. The application of CCAM provided an on-target control of both striped stem borer and pink stem borer. Furthermore, CCAM application had very low residue of chlorantraniliprole in soils. As far as is known, this is the first report of chlorantraniliprole loaded on chitosan-alginate floating hydrogel microspheres for rice stem borer control. Our results indicate that the synthesized CCAM could potentially be used as a controlled-release product for effective control of the two rice pests, while reducing the residual chlorantraniliprole in the soil and avoiding pesticide drift.

Control of bacterial leaf blight and rice blast with antagonist microbial in the agroecosystem of irrigated rice

Bacterial leaf blight (Xanthomonas oryzae) and rice blast (Pyricularia oryzae) cause yield losses in rice production. Antagonist microbial application through seed treatment and foliar spray during rice growing stage is suggested to prevent the disease which is more reliable to reduce the disease incidence than curing it. This research aimed to determine the severity of bacterial leaf blight and rice blast among varieties that treated with antagonist microbial complex in the agro ecosystem of irrigated rice. Research was conducted in Kalibawang sub district, Kulon Progo, Yogyakarta, October 2018 to January 2019. The experimental design was randomized block design with 7 treatments and 4 replications. The treatments were the application of antagonist microbial complex formula A (Azotobacter vinelandii, Azospirillum sp., Bacillus cereus, Bradyzhizobium sp., and Methylobacterium sp. >107 CFU/g) and formula B (Azotobacter chroococum, Azotobacter vinelandii, Azospirillum sp., Pseudomonas cepacia, Penicillium sp., and Acinetobacter sp. >107 CFU/g) to several rice varieties (Inpari 9, Inpari 33, and Ciherang). Results shows that formula B had the lowest severity of bacterial leaf blight (14.44%) and leaf blast (6.94%) at Ciherang while formula A had the lowest panicle blast (6.55%). The highest yield (10.62 t/ha) was obtained from Ciherang treated with formula B.

Marker-Assisted Introgression of Multiple Resistance Genes Confers Broad Spectrum Resistance against Bacterial Leaf Blight and Blast Diseases in PUTRA-1 Rice Variety

Bacterial leaf blight caused by Xanthomonas oryzae pv oryzae (Xoo) and blast caused by Magnaporthe oryzae are major diseases responsible for significant yield loss in rice production across all rice growing regions. Host plant resistance has been advocated as a sustainable means of guarding against the diseases. This experiment was conducted with the aim to introgress multiple resistance genes against bacterial leaf blight and blast diseases through marker-assisted backcross breeding. Two dominant (Xa4 and Xa21) and two recessive (xa5 and xa13) Xoo resistance genes were introgressed into a high yielding Malaysian rice variety Putra-1 with genetic background of three blast resistance (Piz, Pi2 and Pi9) genes. Eight polymorphic tightly linked functional and SSR markers were used for foreground selection of target genes. Seventy nine polymorphic SSR markers were used in background selection. The plants were challenged at initial stage of breeding and challenged again at BC2F2 with the most virulent Malaysian pathotypes of Xoo (P7.7) and Magnaporthe oryzae (P7.2) to test their resistance. Results obtained from foreground marker segregation analysis at BC1F1 and BC2F1 showed that the marker polymorphism both fitted into the Mendel’s single gene segregation ratio of 1:1 for both Xoo and blast resistance. At BC2F2, results indicated that foreground marker polymorphism fitted into the expected Mendelian ratio of 1:2:1 for blast resistance only. Marker-assisted background selection revealed high percentage of recurrent parent genome recovery (95.9%). It was concluded that the inheritance of blast resistance in the introgressed lines was mainly due to single gene action while the inheritance of Xoo resistance was substantially due to single nuclear gene action. The incorporation of four bacterial leaf blight and three blast resistance genes (Xa4 + xa5 + xa13 + Xa21; Pi9 + Pi2 + Piz) in the newly developed lines would provide for broad spectrum and durable resistance against the two major diseases studied.

Antagonistic activity against rice blast disease and elicitation of host‐defence response capability of an endophytic Streptomyces albidoflavus OsiLf‐2

Rice blast, caused by the fungus Magnaporthe oryzae, can result in notable yield losses in rice production. The objective of this study was to investigate the potential of a rice endophytic isolate, Streptomyces albidoflavus OsiLf‐2, on the control of rice blast and the possible mechanisms involved. In vitro assays displayed a variety of antagonistic effects of OsiLf‐2 against different physiological races of M. oryzae, with peak mycelial growth inhibition ranging from 74.1% to 83.0%. In vivo tests of OsiLf‐2 showed 18.0% and 19.6% reduction in disease index in greenhouse and field conditions, respectively. The stable active metabolites in its cell‐free culture filtrate inhibited the mycelial growth, spore germination and appressorial formation of M. oryzae in a dose‐dependent manner. They also possessed strong antifungal capacities toward various phytopathogens in vitro. OsiLf‐2 secreted multiple antimicrobial compounds, cell wall degradation enzymes, siderophore, plant hormones, and 1‐aminocyclopropane‐1‐carboxylate deaminase, which might function in direct or indirect resistance to M. oryzae. In addition, a variety of defence responses were induced in OsiLf‐2‐treated rice, including hydrogen peroxide (H2O2) accumulation, callose deposition, defence‐related enzymes activation, and elevated expression of salicylic acid (SA) and jasmonic acid (JA) pathways genes, which might contribute in resisting pathogen attack. The significant biological control activity and host defence‐stimulation ability of OsiLf‐2 suggest that this endophytic actinobacterial strain could be a promising candidate in the management of rice blast disease.

Automated spectral feature extraction from hyperspectral images to differentiate weedy rice and barnyard grass from a rice crop

Barnyard grass (Echinochloa crusgalli) and weedy rice (Oryza sativa f. spontanea) are two common and troublesome weed species in rice (Oryza sativa L.) crop. They cause significant yield loss in rice production while it is difficult to differentiate them for site-specific weed management. In this paper, we aimed to develop a classification model with important spectral features to recognize these two weeds and rice based on hyperspectral imaging techniques. There were 287 plant leaf samples in total which were scanned by the hyperspectral imaging systems within the spectral range from 380 nm to 1080 nm. After obtaining hyperspectral images, we first developed an algorithmic pipeline to automatically extract spectral features from line scan hyperspectral images. Then the raw spectral features were subjected to wavelet transformation for noise reduction. Random forests and support vector machine models were developed with the optimal hyperparameters to compare their performances in the test set. Moreover, feature selection was explored through successive projection algorithm (SPA). It is shown that the weighted support vector machine with 6 spectral features selected by SPA can achieve 100%, 100%, and 92% recognition rates for barnyard grass, weedy rice and rice, respectively. Furthermore, the selected 6 wavelengths (415 nm, 561 nm, 687 nm, 705 nm, 735 nm, 1007 nm) have the potential to design a customized optical sensor for these two weeds and rice discrimination in practice.

Rice Calcineurin B-Like Protein-Interacting Protein Kinase 31 (OsCIPK31) Is Involved in the Development of Panicle Apical Spikelets.

Panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Herein, a PAA mutant, paa1019, was identified among the progeny of an elite indica maintainer rice line Yixiang 1B (YXB) mutagenized population obtained using ethyl methyl sulfonate. The abortion rate of spikelets in paa1019 was observed up to 60%. Genetic mapping combined with Mutmap analysis revealed that LOC_Os03g20380 harbored a single-bp substitution (C to T) that altered its transcript length. This gene encodes calcineurin B-like protein-interacting protein kinase 31 (OsCIPK31) localized into the cytoplasm, and is preferentially expressed in transport tissues of rice. Complementation of paa1019 by transferring the open reading frame of LOC_Os03g20380 from YXB reversed the mutant phenotype, and conversely, gene editing by knocking out of OsCIPK31 in YXB results in PAA phenotype. Our results support that OsCIPK31 plays an important role in panicle development. We found that dysregulation is caused by the disruption of OsCIPK31 function due to excessive accumulation of ROS, which ultimately leads to cell death in rice panicle. OsCIPK31 and MAPK pathway might have a synergistic effect to lead ROS accumulation in response to stresses. Meanwhile the PAA distribution is related to IAA hormone accumulation in the panicle. Our study provides an understanding of the role of OsCIPK31 in panicle development by responding to various stresses and phytohormones.

Genome-wide analysis of chitinase genes and their varied functions in larval moult, pupation and eclosion in the rice striped stem borer, Chilo suppressalis.

Some insect chitinases are required to degrade chitin and ensure successful metamorphosis. Although chitinase genes have been well characterized in several model insects, no reports exist for the rice striped stem borer, Chilo suppressalis, a highly destructive pest that causes huge yield losses in rice production. Here, we conducted a genome-level analysis of chitinase genes in C.suppressalis. After amplification of full-length transcripts with rapid amplification of cDNA ends, we identified 12 chitinase genes in C. suppressalis. All these genes had the conserved domains and motifs of glycoside hydrolase family 18 and grouped phylogenetically into five subgroups. C.suppressalis chitinase 1 (CsCht1) was highly expressed in late pupae, whereas CsCht3 was abundant in early pupae. Both CsCht2 and CsCht4 were highly expressed in larvae. CsCht2 was abundant specifically in the third-instar larvae and CsCht4 showed periodic high expression in 2- to 5-day-old larvae in each instar. Tissue specific expression analysis indicated that CsCht1 and CsCht3 were highly expressed in epidermis whereas CsCht2 and CsCht4 were specifically abundant in the midgut. Knockdown of CsCht1 resulted in adults with curled wings, indicating that CsCht1 might have an important role in wing expansion. Silencing of CsCht2 or CsCht4 arrested moulting, suggesting essential roles in larval development. When the expression of CsCht3 was interfered, defects in pupation occurred. Overall, we provide here the first catalogue of chitinase genes in the rice striped stem borer and have elucidated the functions of four chitinases in metamorphosis.

Effect of Different Kinds of Environmental Freindly Materials on the Growth of Rice

Over last three decades, farming system has been directed to maximize agricultural production and to increase farmer’s income through adoption of high–yielding crop varieties with high input of agro–chemicals (Yoo, 1999). These farming practices have resulted in many problems like food safety, soil fertility, and deterioration of fresh and underground water–quality (Bouwnan, 1990; Duxbury and Moiser, 1993; Jones and Schwab, 1993). Loess soil being one of the important economic consequences of quaternary environmental change, in that it resulted in large areas of soil that have an agriculturally more favorable particle size distribution and mineralogical composition than other common sediment types and also plays an important role in maintaining yields of arable crops (Catt, 2001). Although the environment is very important, no use of fertilizers and agricultural chemicals causes significant yield loss in rice production (Ku et al., 1999). Thus, environmental–friendly agricultural practice has been drawing a global attention as a promising alternative for sustainable food production. Lately circulated environmental–friendly agricultural materials include microbial products, amino acids, pyroligneous acid, charcoal, mixture of charcoal with pyroligneous acid (MCPA), chitosan and brown rice vinegar etc (Choi, 1998). Loess soils are among the most fertile soils in the world, principally because the abundance of silt particles ensures good water supply, aeration, root penetration, and seedbed production (Catt, 2001). Research reports indicate favorable effects of MCPA and charcoal in improving soil productivity and yield in crops such as sweet potato, sorghum, melon, sugarcane (Tsuzuki et al., 1993; Uddin et al., 1994; Shibayama et al., 1998). However, there have been no attempts for the application of these materials on paddy soil and loess “Hwangto” for rice, which is one of the most important crops in Asia. Therefore, this study was carried out to investigate the effect of environmentally–friendly materials treated in paddy soils and loess soil “Hwangto” on the growth and yield of rice.

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods

BackgroundRice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using massively parallel signature sequencing (MPSS), robust-long serial analysis of gene expression (RL-SAGE) and oligoarray methods.ResultsThe MPSS analyses identified 12,531 and 12,927 distinct significant tags from mycelia and appressoria, respectively, while the RL-SAGE analysis identified 16,580 distinct significant tags from the mycelial library. When matching these 12,531 mycelial and 12,927 appressorial significant tags to the annotated CDS, 500 bp upstream and 500 bp downstream of CDS, 6,735 unique genes in mycelia and 7,686 unique genes in appressoria were identified. A total of 7,135 mycelium-specific and 7,531 appressorium-specific significant MPSS tags were identified, which correspond to 2,088 and 1,784 annotated genes, respectively, when matching to the same set of reference sequences. Nearly 85% of the significant MPSS tags from mycelia and appressoria and 65% of the significant tags from the RL-SAGE mycelium library matched to the M. grisea genome. MPSS and RL-SAGE methods supported the expression of more than 9,000 genes, representing over 80% of the predicted genes in M. grisea. About 40% of the MPSS tags and 55% of the RL-SAGE tags represent novel transcripts since they had no matches in the existing M. grisea EST collections. Over 19% of the annotated genes were found to produce both sense and antisense tags in the protein-coding region. The oligoarray analysis identified the expression of 3,793 mycelium-specific and 4,652 appressorium-specific genes. A total of 2,430 mycelial genes and 1,886 appressorial genes were identified by both MPSS and oligoarray.ConclusionThe comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages. The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity. Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.