International Rice Research Institute
  • Los Baños, Laguna, Philippines
Recent publications
Background Nitrogen is an essential macronutrient for plant growth and development. Crops with a high nitrogen input usually have high yields. However, outbreaks of brown planthoppers ( Nilaparvata lugens ; BPH) frequently occur on rice farms with excessive nitrogen inputs. Rice plants carrying BPH resistance genes are used for integrated pest management. Thus, the impact of nitrogen on the resistance of rice near-isogenic lines (NILs) with BPH resistance genes was investigated. Results We tested these NILs using a standard seedbox screening test and a modified bulk seedling test under different nitrogen treatments. The amount of nitrogen applied had an impact on the resistance of some lines with BPH resistance genes. In addition, three NILs (NIL- BPH9 , NIL- BPH17 , and NIL- BPH32 ) were further examined for antibiosis and antixenosis under varying nitrogen regimes. The N. lugens nymph population growth rate, honeydew excretion, female fecundity, and nymph survival rate on the three NILs were not affected by different nitrogen treatments except the nymph survival rate on NIL- BPH9 and the nymph population growth rate on NIL- BPH17 . Furthermore, in the settlement preference test, the preference of N. lugens nymphs for IR24 over NIL- BPH9 or NIL- BPH17 increased under the high-nitrogen regime, whereas the preference of N. lugens nymphs for IR24 over NIL- BPH32 was not affected by the nitrogen treatments. Conclusions Our results indicated that the resistance of three tested NILs did not respond to different nitrogen regimes and that NIL- BPH17 exerted the most substantial inhibitory effect on N. lugens growth and development.
Forest ecosystems play an indispensable role in addressing various pressing sustainability and social-ecological challenges such as climate change, biodiversity loss, and ecosystem services deterioration, hence the monitoring of the world's forests is crucial. As part of the global forest assessment workflow, a forest is generally classified and mapped based on land use and/or using a tree canopy cover threshold. In this paper, we examine the limitations of this approach and argue that the use of a land use-based forest definition and tree canopy cover thresholds can overlook forest degradation and enhancement, disguise the actual status of forest landscapes, and misinform management planning. These limitations can delay the development and implementation of forest restoration and conservation measures. To help overcome these issues, we propose some enhancements to the global forest assessment workflow, including the sharing of spatial data and inclusion of tree canopy cover estimates in assessment reports. Such enhancements are needed to achieve more meaningful forest monitoring and reporting in the context of global environmental initiatives, such as those related to climate change mitigation and adaptation, forest restoration, biodiversity conservation, and ecosystem services monitoring.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex ( ORSC ), wild progenitor of Asian rice ( Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara , and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 “core” O. rufipogon and 25 “core” O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a “pre-breeding” pool for breeders attempting to incorporate novel variation into elite breeding lines.
Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross‐environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross‐environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water‐use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade‐off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress‐resistant crops.
Shortening the period of rice cropping enables farmers to reduce irrigation water in tropical lowlands. However, grain yield of tropical short-duration rice is often restricted by poor grain filling, whose causes are yet unknown. This study evaluated the source–sink balance, which is closely associated with grain filling, in tropical rice. We compared the percentage of filled grains and stem nonstructural carbohydrates in a popular short-duration cultivar and a high-yielding hybrid cultivar over a wide range of spikelets m⁻² by differentiating the N inputs and planting densities on a lowland farm of the International Rice Research Institute, the Philippines, during four seasons. Grain yield ranged from 2.2 to 8.6 t ha⁻¹, with the hybrid cultivar producing consistently higher yield (by 27% on average). Compared with the hybrid cultivar, the short-duration cultivar had less stem nonstructural carbohydrates at heading per spikelet (by 24% on average) and a lower percentage of filled grains in the wet season (by 13% on average), when the source capacity was lowest. Source capacity per spikelet and stem nonstructural carbohydrates at heading per spikelet were significantly associated with the percentage of filled grains, suggesting that these indicators of the source–sink ratio modulate grain filling in tropical rice. Although the sink capacity of the short-duration cultivar was similar to, or smaller than, that of the hybrid cultivar, its limited source capacity resulted in poorer grain filling. We suggest that the role of stem nonstructural carbohydrates should be emphasized in the breeding of tropical short-duration rice.
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.
Rice production has increased significantly with the efforts of international research centers and national governments in the past five decades. Nonetheless, productivity improvement still needs to accelerate in the coming years to feed the growing population that depends on rice for calories and nutrients. This challenge is compounded by the increasing scarcity of natural resources such as water and farmland. This article reviews 17 ex-post impact assessment studies published from 2016 to 2021 on rice varieties, agronomic practices, institutional arrangements, information and communication technologies, and post-harvest technologies used by rice farmers. From the review of these selected studies, we found that stress-tolerant varieties in Asia and Africa significantly increased rice yield and income. Additionally, institutional innovations, training, and natural resource management practices, such as direct-seeded rice, rodent control, and iron-toxicity removal, have had a considerable positive effect on smallholder rice farmers’ economic well-being (income and rice yield). Additional positive impacts are expected from the important uptake of stress-tolerant varieties documented in several Asian, Latin American, and African countries.
Proline is a proteinogenic amino acid synthesized from glutamate and ornithine. Pyrroline-5-carboxylate synthetase and pyrroline-5-carboxylate reductase are the two key enzymes involved in proline synthesis from glutamate. On the other hand, ornithine-δ-aminotransferase converts ornithine to pyrroline 5-carboxylate (P5C), an intermediate in the synthesis of proline as well as glutamate. Both proline dehydrogenase and P5C dehydrogenase convert proline back to glutamate. Proline accumulation is widespread in response to environmental challenges such as high temperatures, and it is known to defend plants against unpropitious situations promoting plant growth and flowering. While proline accumulation is positively correlated with heat stress tolerance in some crops, it has detrimental consequences in others. Although it has been established that proline is a key osmolyte, its exact physiological function during heat stress and plant ontogeny remains unknown. Emerging evidence pointed out its role as an overriding molecule in alleviating high temperature stress (HTS) by quenching singlet oxygen and superoxide radicals. Proline cycle acts as a shuttle and the redox couple (NAD+/NADH, NADP+/NADPH) appears to be highly crucial for energy transfer among different cellular compartments during plant development, exposure to HTS conditions and also during the recovery of stress. In this review, the progress made in recent years regarding its involvement in heat stress tolerance is highlighted.
Trapping is a key method for monitoring small mammals and is also one of a number of methods recommended under an ecologically‐based rodent management program to control rodent pest populations. Live‐traps are widely used globally for studying small mammal populations. In Asia where rodents are major pests of rice, single capture traps typically provide low trap success. We compared the trap success between two types of live‐traps in rice fields in Indonesia and the Philippines. Multiple‐capture traps (MCTs) in conjunction with a linear trap barrier were significantly more effective in catching rodent pest species than single‐capture traps (SCTs) in Indonesia and the Philippines. In Indonesia, MCTs captured more individuals with a mean (±SE) percent trap success rate of (15.54 ± 4.29) compared to SCTs (3.88 ± 1.58). In the Philippines, MCTs captured more species of rodents and had a significantly higher recapture rate (1.96 ± 0.79), than SCTs (0.58 ± 0.32). Multiple‐capture traps with a linear trap‐barrier were more effective for capturing Rattus argentiventer and Rattus tanezumi in rice field ecosystems compared to single‐capture traps. MCTs captured more species of rodent pests in the Philippines and recaptured more individuals of each species. These results indicate that rodent populations can be more effectively monitored and controlled by using a multi‐capture trap with barrier system than the use of single capture traps on their own. This is the first time these two trap types have been compared for use in rice ecosystems in Asia.
Weeds are one of the key threats in sustaining the productivity of the rice-wheat cropping system in the Indo-Gangetic Plains. The development of sound integrated weed management technologies requires knowledge of mechanisms that influence weed flora composition and weed seedbank dynamics. A long-term study was initiated in 2015 at Patna, Bihar, India to evaluate the effect of seven tillage and crop establishment methods on weed density, weed seedbank composition, and crop productivity in rice-wheat-mungbean rotation. All the treatments included zero-till mungbean after wheat. Tillage and crop establishment methods had differential effects on weed and weed seedbank composition. In rice, zero-till direct-seeded rice recorded 62% lower emergence of Cyperus iria, 82-90% of Echinochloa colona, and 81-83% of total weeds compared to tilled systems, but the system of rice and wheat intensification favoured E. colona. In wheat, the system of wheat intensification favoured the Phalaris minor and Solanum nigrum. Zero-till rice and wheat reduced the seedbank of Trianthema portulacastrum by 95%, and total weed seedbank by 62% compared to the system of rice and wheat intensification. Nearly, 72% of C. iria seeds, 62% of grasses, and 64% of broad-leaved weeds were in 0-15 cm soil layer. Zero-till direct-seeded rice produced a 13% lower rice grain yield than conventional puddled transplanted rice. Compared to the system of wheat intensification, zero-till wheat under triple zero-till systems produced an 11.5% higher grain yield. Managing weed seedbank is a long-term endeavour. The present study revealed that tillage and crop establishment methods influence weed density and diversity. Under zero-till rice-wheat system, rice yield decreases marginally, but the system productivity maintains due to improvement in succeeding wheat yield. This system is also helpful in reducing the weed flora density and soil weed seedbank. Regular monitoring and management of emerging pests such as armyworm (Mythimna separata) are, however, required. The study suggests that the adoption of triple zero-tillage can be a viable option for reducing the weed density and weed seedbank concurrently increasing the system productivity of the rice-wheat-mungbean cropping system in eastern Indo-Gangetic Plains.
CONTEXT: Soil salinity is the main environmental limiting factor for current agricultural farming systems in the Bangladesh coastal zone. Targeting crop selection to ameliorate its impact in food production is a priority to ensure food security, diversifying crop outputs and reducing smallholders' vulnerabilities. In this context, crop growth modelling emerges as a useful tool for exploring different scenarios for crop selection. OBJECTIVE: Studying spatial and -temporal heterogeneity in salinity and crop productivity under different climate scenarios. METHODS: A dataset from the Polder 30 located in the Bangladesh southwest coastal zone, including different farming systems (rice-maize, rice-mungbean, rice-sunflower) comprising two years (2017–2019), was utilized, together with polder-level contiguous layers of factors (i.e., salinity, elevation, precipitation), to create clusters representing different yield-limiting conditions. Two salinity scenarios were defined and included in a long term in-silico assessment to explore dry-season field crop options (maize, sunflower, and mungbean). APSIM models for maize, sunflower and mungbean, were selected to perform all the crop simulations. RESULTS AND CONCLUSIONS: Based on yield, sunflower was the most stable choice under salinity and maize was the best under non-saline conditions. Lastly, yield stability was accounted for different climate conditions, showing a large yield reduction for maize when combining low precipitation and high temperature, whereas mungbean and sunflower presented less sensitivity to different climates. SIGNIFICANCE: Right crop selection for the right environment, considering both salinity restrictions and climate uncertainties, is critical for long-term yield stability. The present study provides a novel framework to better match the most suitable crop under challenging salinity restrictions and climate uncertainties affecting small- holders in the coastal zone of Bangladesh.
Rice (Oryza sativa L.) is the staple food of more than 50% of the world’s population. Manual puddled transplanted rice (PTR) system is still the predominant method of rice establishment. However, due to declining water tables, increasing water scarcity, water, labor- and energy-intensive nature of PTR, high labor wages, adverse effects of puddling on soil health and succeeding crops, and high methane emissions, this production system is becoming less profitable. These factors trigger the need for an alternative crop establishment method. The direct-seeded rice (DSR) technique is gaining popularity because of its low input demand compared to PTR. It is done by sowing pre-germinated seeds in puddled soil (wet-DSR), standing water (water seeding), or dry seeding on a prepared seedbed (dry-DSR). DSR requires less water and labor (12–35%), reduces methane emissions (10–90%), improves soil physical properties, involves less drudgery and production cost (US$9–125 per hectare), and gives comparable yields. Upgraded short-duration and high-yielding varieties and efficient nutrient, weed, and resource management techniques encouraged the farmers to switch to DSR culture. However, several constraints are associated with this shift: more weeds, the emergence of weedy rice, herbicide resistance, nitrous oxide emissions, nutrient disorders, primarily N and micro-nutrients, and an increase in soil-borne pathogens lodging etc. These issues can be overcome if proper weed, water, and fertilizer management strategies are adopted. Techniques like stale bed technique, mulching, crop rotation, Sesbania co-culture, seed priming, pre-emergence and post-emergence spray, and a systematic weed monitoring program will help reduce weeds. Chemical to biotechnological methods like herbicide-resistant rice varieties and more competitive allelopathic varieties will be required for sustainable rice production. In addition, strategies like nitrification inhibitors and deep urea placement can be used to reduce N2O emissions. Developing site and soil-specific integrated packages will help in the broader adoption of DSR and reduce the environmental footprint of PTR. The present paper aims to identify the gaps and develop the best-bet agronomic practices and develop an integrated package of technologies for DSR, keeping in mind the advantages and constraints associated with DSR, and suggest some prospects. Eco-friendly, cost-effective DSR package offers sustainable rice production systems with fewer resources and low emissions. Graphical abstract
MicroRNAs (miRNAs) are tiny (20–24 nucleotides long), non-coding, highly conserved RNA molecules that play a crucial role within the post-transcriptional regulation of gene expression via sequence-specific mechanisms. Since the miRNA transcriptome is involved in multiple molecular processes needed for cellular homeostasis, its altered expression can trigger the development and progression of several human pathologies. In this context, over the last few years, several relevant studies have demonstrated that dysregulated miRNAs affect a wide range of molecular mechanisms associated with irritable bowel syndrome (IBS), a common gastrointestinal disorder. For instance, abnormal miRNA expression in IBS patients is related to the alteration of intestinal permeability, visceral hyperalgesia, inflammatory pathways, and pain sensitivity. Besides, specific miRNAs are differentially expressed in the different subtypes of IBS, and therefore, they might be used as biomarkers for precise diagnosis of these pathological conditions. Accordingly, miRNAs have noteworthy potential as theragnostic targets for IBS. Hence, in this current review, we present an overview of the recent discoveries regarding the clinical relevance of miRNAs in IBS, which might be useful in the future for the development of miRNA-based drugs against this disorder.
Introduction Root development is a fundamental process that supports plant survival and crop productivity. One of the essential factors to consider when developing biotechnology crops is the selection of a promoter that can optimize the spatial-temporal expression of introduced genes. However, there are insufficient cases of suitable promoters in crop plants, including rice. Objectives This study aimed to verify the usefulness of a new rice root-preferred promoter to optimize the function of a target gene with root-preferred expression in rice. Methods osrns1 mutant had defects in root development based on T-DNA insertional mutant screening and CRISPR technology. To optimize the function of OsRNS1, we generated OsRNS1-overexpression plants under two different promoters: a whole-plant expression promoter and a novel root-preferred expression promoter. Root growth, yield-related agronomic traits, RNA-seq, and reactive oxygen species (ROS) accumulation were analyzed for comparison. Results OsRNS1 was found to be involved in root development through T-DNA insertional mutant analysis and gene editing mutant analysis. To understand the gain of function of OsRNS1, pUbi1::OsRNS1 was generated for the whole-plant expression, and both root growth defects and overall growth defects were found. To overcome this problem, a root-preferential overexpression line using Os1-CysPrxB promoter (Per) was generated and showed an increase in root length, plant height, and grain yield compared to wild-type (WT). RNA-seq analysis revealed that the response to oxidative stress-related genes was significantly up-regulated in both overexpression lines but was more obvious in pPer::OsRNS1. Furthermore, ROS levels in the roots were drastically decreased in pPer::OsRNS1 but were increased in the osrns1 mutants compared to WT. Conclusion The results demonstrated that the use of a root-preferred promoter effectively optimizes the function of OsRNS1 and is a useful strategy for improving root-related agronomic traits as well as ROS regulation.
Rice bacterial blight is caused by Xanthomonas oryzae pv. oryzae (Xoo), which is one of the most common diseases in most rice-growing countries. The study aims to determine the diversity of Xoo races on resistant and susceptible rice lines during the peak of the epidemic in two hot spot areas in the province of Laguna, Philippines. Knowledge of pathogen diversity is important to deploy suitable rice varieties that would prolong their resistance and prevent disease outbreaks. Rice leaf samples with typical bacterial blight lesions were collected from the susceptible IR24 and the resistant IRBB57 lines within an experimental plot. Leaf samples were taken at five growth stages of rice, i.e., booting (62–66 days), heading (69–73 days), milky (76–80 days), dough (83–87 days), and maturity (90–95 days). Identification of Xoo race was conducted by molecular analysis using race-specific SNP markers. Three Xoo races (Race-2 complex, Race 8, and Race-9 complex) were identified on susceptible rice IR24. Only one race of Xoo (Race-9 complex) was identified on resistant rice IRBB57. Race 8 was the most abundant in IR24 rice population (51%), followed by Race-9 complex and Race-2 complex with 33% and 16%, respectively. On rice IR24, the presence of Xoo races varied in every rice stage. Race-9 complex was predominantly detected in all growth stages of IRBB57, but the infection in this resistant line did not progress during rice growth. The Xoo pathogen was still present on the resistant rice but could not develop into a disease. Race 8 was first detected in the irrigated lowland rice-growing areas in Laguna province and deserves further study.
Rice is a major crop in Bangladesh that supports both food security and livelihoods. However, a need remains for improved productivity and adaptation to the risks associated with climate change. To accomplish this, the increased adoption of climate-resilient and high-yielding rice varieties can be beneficial. Therefore, we conducted a study in Bangladesh over three consecutive years: 2016, 2017, and 2018. The scope of the study included the major cropping season (wet), Aman. The yield advantages of climate-resilient rice varieties were evaluated and compared with those of the varieties popular with farmers. We included new stress-tolerant varieties, such as submergence-tolerant rice (BRRI dhan51 and BRRI dhan52) and drought-tolerant rice (BRRI dhan56 and BRRI dhan71), along with farmer-chosen controls, in the study. We conducted the evaluation through on-farm trials to compare the varieties in both submergence- and drought-affected environments. The seasonal trials provided measured results of yield advantages. The participating farmers were also studied over the three-year-period to capture their varietal adoption rates. We calculated both the location estimated yield advantages (LEYA) and the location observed yield advantages (LOYA). The results revealed that, under non-stress conditions, the grain yields of climate-resilient varieties were either statistically similar to or higher than those of the farmer-chosen controls. Our study also revealed a year-to-year progressive adoption rate for the introduced varieties. The study suggests that the wide-scale introduction and popularization of climate-resilient varieties can ensure higher productivity and climate risk adaptation. The close similarity between LOYA and LEYA indicated that the observational and experiential conclusions of the host farmers were similar to the scientific performance of the varieties. We also found that comparison performed through on-farm trials was a critical method for enhancing experiential learning and obtaining an accurate estimation of yield advantages.
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535 members
Jauhar Ali
  • Rice Breeding Platform
Sabiha Parween
  • Grain Quality and Nutrition Center
Mahender Anumalla
  • Rice Breeding Platform
Vikas Kumar Singh
  • South Asia Hub
4031, Los Baños, Laguna, Philippines
Head of institution
Matthew Morell