Rice Researchers Research Articles

Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances

Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties.

Toward Food Security in 2050: Gene Pyramiding for Climate-Smart Rice

The decline in crop productivity due to climate change is a major issue that threatens global food security and is the main challenge for breeders today in developing sustainable varieties with a wider tolerance to abiotic and biotic stresses. Breeding climate-smart rice (CSR) cultivars may be the best adaptation to climate change, with the potential to improve future food security and profitability for farmers in many nations. The main objective of this review is to highlight the direction of development of superior rice breeding from time to time, and various studies of new techniques of breeding methods for pyramiding various superior rice characteristics, especially characteristics related to abiotic stress, and to make a climate-suitable genotype that is resilient to climate change. For the design and strategy of the information search, a methodology was followed to compile and summarize the latest existing studies on rice breeding for abiotic stresses. The findings revealed that there is still an empty research gap in the context of supplying CSR products, which should be a priority for rice researchers in order to increase dissemination and ensure food security for future generations, particularly in climatically vulnerable agro-ecologies. And we conclude that, while technological innovation, specifically the integration of DNA markers and the genomic approach into conventional breeding programs, has made major contributions to the development of CSR, there is an urgent need to build strategic plans for the development of varieties with various stress tolerances.

Changes in the Growth and Yield of an Extremely Early-Maturing Rice Variety According to Transplanting Density

This study investigated the impact of transplanting density on the growth and yield characteristics of an extremely early-maturing rice variety that has a short vegetative growth period, as the limited growth period results in reduced tiller development and leads to a lower yield. The experiment was conducted in 2019 and 2020 at Chungcheongnam-do Agricultural Research and Extension Services in Republic of Korea, where various transplanting density treatments were tested using the Bbareumi rice variety with a vegetative growth period of less than 50 days. The results showed that the tiller number seedling−1 and spikelet number m−2 were influenced by the transplanting density and had a significant impact on the milled rice yield. Decreasing the tiller number seedling−1 by increasing the transplanting density led to an increase in the spikelet number m−2, which significantly improve the milled rice yield. Furthermore, the study identified the optimal transplanting density for maximizing yield as a transplanting distance of 30 × 12 cm, with 12 seedlings hill−1, which resulted in the highest milled rice yield of 5.64 ton/ha. These findings provide valuable insights for rice farmers and researchers regarding efforts to improve the cultivation practices of extremely early-maturing rice varieties.

Field rice panicle detection and counting based on deep learning.

Panicle number is directly related to rice yield, so panicle detection and counting has always been one of the most important scientific research topics. Panicle counting is a challenging task due to many factors such as high density, high occlusion, and large variation in size, shape, posture et.al. Deep learning provides state-of-the-art performance in object detection and counting. Generally, the large images need to be resized to fit for the video memory. However, small panicles would be missed if the image size of the original field rice image is extremely large. In this paper, we proposed a rice panicle detection and counting method based on deep learning which was especially designed for detecting rice panicles in rice field images with large image size. Different object detectors were compared and YOLOv5 was selected with MAPE of 3.44% and accuracy of 92.77%. Specifically, we proposed a new method for removing repeated detections and proved that the method outperformed the existing NMS methods. The proposed method was proved to be robust and accurate for counting panicles in field rice images of different illumination, rice accessions, and image input size. Also, the proposed method performed well on UAV images. In addition, an open-access and user-friendly web portal was developed for rice researchers to use the proposed method conveniently.

Predicting single kernel and bulk milled rice alkali spreading value and gelatinization temperature class using NIR spectroscopy

AbstractBackground and ObjectivesThe alkali spreading value (ASV) of rice is a widely measured quality parameter and accepted indicator of gelatinization temperature (GT) class. However, the alkali test, developed in 1958, is labor intensive and subjective. Better methods to measure ASV and GT, for single kernel and bulk rice would provide an important tool to determine the effects of individual kernels on end‐use quality and rice with desired cooking qualities. An instrument developed by the USDA‐ARS and a commercially available near infrared (NIR) instrument were evaluated for determining ASV and classification of intermediate and low GT levels for single kernel and bulk milled rice, respectively.FindingsQuantitative prediction of ASV scores (2–7) demonstrated the potential of NIR spectroscopy for screening with a standard error of prediction for validation samples ranging from 0.91 to 1.39 for the single kernel NIR instrument, and from 0.97 to 1.19 for the commercial instrument. GT categorization into intermediate and low values, using ASV scores, showed 82.4% and 85.0% correct classification using 1 and 30‐single kernel average calibration models, respectively. GT was correctly classified (93.6%–84.4%) using a commercial NIR instrument.ConclusionNIR spectroscopy has potential for rough screening of ASV and for two‐category GT rice classification.Significance and NoveltyConsidering that NIR spectroscopy has been proven to be applicable for other quality parameters, such as rice starch content and quality, protein content, and milling degree, the addition of calibrations for ASV as a predictor of GT class will be highly beneficial while not requiring additional resources. The rapid and nondestructive classification of individual kernels may also enable physical segregation of individual kernels for use by rice researchers and/or industry for additional studies on kernels with specific quality parameters and for determining the extent of variant kernels in a milled rice lot that could affect end use quality. Future studies on the use of NIR spectroscopy for brown rice should be evaluated so that quality could be assessed, while maintaining seed viability, and then used in field studies.

Deep learning based high-throughput phenotyping of chalkiness in rice exposed to high night temperature

BackgroundRice is a major staple food crop for more than half the world’s population. As the global population is expected to reach 9.7 billion by 2050, increasing the production of high-quality rice is needed to meet the anticipated increased demand. However, global environmental changes, especially increasing temperatures, can affect grain yield and quality. Heat stress is one of the major causes of an increased proportion of chalkiness in rice, which compromises quality and reduces the market value. Researchers have identified 140 quantitative trait loci linked to chalkiness mapped across 12 chromosomes of the rice genome. However, the available genetic information acquired by employing advances in genetics has not been adequately exploited due to a lack of a reliable, rapid and high-throughput phenotyping tool to capture chalkiness. To derive extensive benefit from the genetic progress achieved, tools that facilitate high-throughput phenotyping of rice chalkiness are needed.ResultsWe use a fully automated approach based on convolutional neural networks (CNNs) and Gradient-weighted Class Activation Mapping (Grad-CAM) to detect chalkiness in rice grain images. Specifically, we train a CNN model to distinguish between chalky and non-chalky grains and subsequently use Grad-CAM to identify the area of a grain that is indicative of the chalky class. The area identified by the Grad-CAM approach takes the form of a smooth heatmap that can be used to quantify the degree of chalkiness. Experimental results on both polished and unpolished rice grains using standard instance classification and segmentation metrics have shown that Grad-CAM can accurately identify chalky grains and detect the chalkiness area.ConclusionsWe have successfully demonstrated the application of a Grad-CAM based tool to accurately capture high night temperature induced chalkiness in rice. The models trained will be made publicly available. They are easy-to-use, scalable and can be readily incorporated into ongoing rice breeding programs, without rice researchers requiring computer science or machine learning expertise.

Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers.

Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.

SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice

The information commons for rice (IC4R) database is a collection of 18 million single nucleotide polymorphisms (SNPs) identified by resequencing of 5152 rice accessions. Although IC4R offers ultra-high density rice variation map, these raw SNPs are not readily usable for the public. To satisfy different research utilizations of SNPs for population genetics, evolutionary analysis, association studies, and genomic breeding in rice, raw genotypic data of these 18 million SNPs were processed by unified bioinformatics pipelines. The outcomes were used to develop a daughter database of IC4R – SnpReady for Rice (SR4R). SR4R presents four reference SNP panels, including 2,097,405 hapmapSNPs after data filtration and genotype imputation, 156,502 tagSNPs selected from linkage disequilibrium-based redundancy removal, 1180 fixedSNPs selected from genes exhibiting selective sweep signatures, and 38 barcodeSNPs selected from DNA fingerprinting simulation. SR4R thus offers a highly efficient rice variation map that combines reduced SNP redundancy with extensive data describing the genetic diversity of rice populations. In addition, SR4R provides rice researchers with a web interface that enables them to browse all four SNP panels, use online toolkits, as well as retrieve the original data and scripts for a variety of population genetics analyses on local computers. SR4R is freely available to academic users at http://sr4r.ic4r.org/.

Profitability Analysis of Irradiated Carrageenan as a Biostimulant in Small-Scale Rice Farming in Selected Provinces in the Philippines

iIrradiated carrageenan as a biostimulant was introduced as an alternative to the exclusive use of inorganic fertilizers and chemicals in crop production. This study aimed to contribute to the literature in assessing the farm profitability of using irradiated carrageenan as a biostimulant in small scale rice production in selected provinces in the Philippines. Rice production data with and without the use of irradiated carrageenan were collected from 117 purposely selected farmers during the 2017 dry season. Descriptive statistics, gross margin analysis, and profitability ratios were employed. Results showed that the farmer respondents were, on average, 57 years old, male, reached high school, and were members of farmer groups. Findings included that the average yield of farms increased from 3.5 MT/ha to 4.4 MT/ha, on average, when the farmers used the biostimulant. Consequently, the rice farmers earned an average increase in gross margin of Php 17,000 per ha. The computed benefit-cost ratio was also higher at 3.04 when the carrageenan biostimulant was applied to the rice farm. As rice is the most important staple food in the study area, understanding the farmers’ levels of profitability can assist policy makers in creating enhancing policies that would further enhance rice farmers’ incomes. The results are also encouraging for rice researchers and extensionists to further develop and promote biostimulants such as irradiated carrageenan in augmenting rice farmers’ incomes.

Somaclonal variation does not preclude the use of rice transformants for genetic screening.

Rice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.

Rice & Swansea University Researchers Develop Superhydrophobic Coating for Various Applications

Rice & Swansea University Researchers Develop Superhydrophobic Coating for Various Applications

Improving rice-based rainfed production systems in Southeast Asia for contributing towards food security and rural development through sustainable crop production intensification

Continuing degradation of the environment and the cumulating food, energy, water and financial crises have led to a situation where many people’s access to sufficient, nutritious food is affected as well as their livelihoods, income, and ultimate food and nutrition security. In the wake of these stresses and crises, there is an emerging interest to find efficient, easily accessible and sustainable approaches that can address these crises. One candidate for this is the System of Rice Intensification (SRI) with its “less can produce more” prescription. A regional collaborative project currently underway is being implemented in rainfed areas of the Lower Mekong River Basin (LMB) countries. This involves smallholder rice farmers, researchers, extension personnel, and development professionals, together with staff of relevant government ministries (http://www.sri-lmb.ait.asia/). The project objective is to produce healthier and profitable rice crops under rainfed conditions using SRI methods, evaluated and refined through farmers’ participatory action research (FPAR). As part of the action-research, more than 120 sets of field experiments have been carried out at 60 FPAR sites in Cambodia and Thailand, directly involving 3600 farmers. The experiments have ranged from the integration of many SRI principles with farmers’ current local practices or improved practices which was termed as “SRI-transition” to full demonstrations and assessments of SRI methodology, i.e., SRI demonstration. The initial calculation of yields has showed an average paddy yield of 5.03 t/ha with SRI-transition, whereas with SRI-demonstration the average yield was 6.41 t/ha. These yields were 60 and 100% higher than the average baseline yield in the region, 3.14 t/ha, for the same farmers and same locales. Productivity gains (dollars gained/dollars spent per ha) were calculated for both rainfed and irrigated production areas. In comparative terms, the economic gains for farmers were found to be higher in rainfed areas when using the new methods. This paper addresses the potential of new strategies to promote food security in rainfed areas in the LMB region by managing household and natural resources more productively.

Relationship between rice grain quality traits and starch pasting properties using early maturing rice cultivars in Chungnam plain area

This study was conducted to know the variation and relationship of rice grain quality and starch pasting properties by transplanting times. Two early maturing rice cultivars which accounted for the most area of early maturing rice cultivar in Chungnam province were used. The experiment was laid out in a split-plot design with 3 replications. The main plot consisted of three transplanting times viz. early (April 25), ordinary (May 25) and late (June 25) with sub-plots containing two cultivars. According to the transplanting times, most of rice grain quality and starch pasting properties showed significant difference and Joami showed higher grain quality than Unkwang in all transplanting times. Especially, rice grain quality was improved when transplanted late, showing high head rice and glossiness of cooked rice due to the lower mean temperature during grain filling stage. Glossiness of cooked rice was positively correlated with head rice ratio, amylose content and setback value, and negatively correlated with chalky rice ratio and protein content. The highest positive and negative correlation were observed between breakdown value and peak viscosity (r = 0.98**), and breakdown and setback (r = -0.94**), respectively. These results provide some information for rice researchers and producers producing cultivars with an improved quality, suggesting that rice quality is highly influenced by temperature at grain filling stage, and transplanting times is crucial in improving rice quality. In addition, starch pasting properties are useful for determining rice quality because rice grain quality and starch pasting properties are dependent on each other.

Rice researchers redress retraction

Rice researchers redress retraction

BIOBOARD

AUSTRALIA – Cynata achieves major stem cell manufacturing milestone. INDONESIA – Rice crucial to Indonesia's food security. JAPAN – Japan joins Gates's Grand Challenge on tropical diseases. JAPAN – On-farm system turns rice plants into biofuel and fodder. SINGAPORE – Infant gut microbiota linked with gestation duration, delivery method and healthy weight gain. SINGAPORE – Mundipharma demonstrates efficacy of BETADINE(R) formulations against Ebola virus. SINGAPORE – Scientists determine mechanical forces that drive epithelial wound healing. SINGAPORE – A*STAR researchers develop expert systems for identifying treatment targets for cancer and rare diseases. SINGAPORE – NUS researchers pioneer novel strategy to prevent progression of inflammation-associated cancers. THE PHILIPPINES – New biotech hub aims to nurture more rice researchers. AFRICA – NAU researcher works to understand forces of abrupt climate change. AFRICA – Researchers create new model to aid tech selection. AFRICA – Combining bednets, vaccines ‘good or bad for malaria’. AFRICA – Experts call for innovations to aid Africa's healthcare. EUROPE – Europe's first fully remote diabetes trial approved. UNITED STATES – Scientists identify genetic variations leading to hearing loss in young cancer patients. UNITED STATES – 3D vaccine spontaneously assembles to pack a powerful punch against cancer, infectious diseases. UNITED STATES – Researchers design “evolutionary trap” to thwart drug resistance. UNITED STATES – Common allergy medication may be effective in starving and killing the bacteria that causes Lyme disease. UNITED STATES – Scripps Research Institute scientists develop anti-HIV agent so powerful it can work in a vaccine. UNITED STATES – Possible strategy identified to combat major parasitic tropical disease.

Augmentation of Mineral and Protein Content in Rice (<i>Oryza sativa</i> L.)

Rice ( Oryza sativa L.) is the major source of food for more than half of the world’s population. As a model cereal crop, the complete genome sequences of rice has become fundamental tool for study gene functions and correlate it with the practical applications in plants. At present, rice researchers devote much effort to generating mineral rich rice genotypes to combact the micronutrient malnutrition. Such processes combine different techniques such as mineral content analysis for the available rice gemplasm, genetic transformation, molecular analysis, molecular breeding etc. Here, we briefly review the progress in biofortification of rice with micronutrient elements (Fe, Zn, and Vitamin A) and discuss the various aspects such as:- Rice and genetic diversity for mineral content, micronutrient malnutrition the hidden-hunger, biofortification, molecular and transgenic strategies for improving iron, zinc content, protein quality in rice.

MyRice: Pangkalan Data Pengetahuan Padi Malaysia

Currently, all information regarding rice research in Malaysia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although several international databases of rice research are available, they are not linked to geolocation and other basic archival information. We present MyRice; a systematic Malaysian online rice knowledge database for researchers and citizen scientists to curate their data. The creation of this database will enable scientific researchers to trace back rice research information and their locality effectively. It is constructed using a digitization pipeline that allow high throughput digitization of archival data and connected with publication search engine such as Google Scholar. The main functions include bibliography, map locational visualization and media uploader to share videos and images. We believe that MyRice will contribute to the digital knowledge ecosystem among rice researchers to elevate access and become a focal point for driving Malaysian rice research towards a sulf-sufficient country on food security. The database is available http://biodiversity.fbb.utm.my/myrice/.

On Labor and Creative Transformations in the Experimental Fields of the Philippines

Through an ethnography of the C4 Rice Project's sorghum experiment in the Philippines, this article analyzes particular practices in experimental rice fields and how rice researchers understand their work through specific material practices and engagements with the plants. Returning to the critiques of disembodied science, the author looks at the particular, situated, and subjective labor that researchers do in the fields to argue that these relationships offer different and richer ways to understand scientific knowledge production and practices. Drawing out a distinction between working on plants (the human as producer and plant as passive raw material) and working with plants (a process of humans and plants working together in a situated and particular relationship), the article offers an different approach to Marx's concept of labor by incorporating nonhumans as active and relational actors in the labor process. Labor, then, can be seen as a creative relationship between humans and nonhumans situated in particular times and places.

Assessing the potential of SRI management principles and the FFS approach in Northeast Thailand for sustainable rice intensification in the context of climate change

The paper describes the facilitated learning process of farmers, its results and implications in addressing the low productivity of Jasmine rice in northeast Thailand using the SRI-FFS approach in a collaborative action research. Other involved included rice traders, millers, researchers, government and non-governmental organizations. Working through an inclusive process of dialogue, observation, diagnosis, experimentation and exposure to different types of innovative agronomic crop management (IACM) practices resulting from the SRI–FFS approach, participants made a thorough analysis of the current management practices and evaluated various IACM practices for their productivity and profitability. The results confirmed the potential of IACM in enhancing crop and water productivity along with soil fertility with relatively low input-use (seed, water and fertilizers) and higher net farm-income compared to existing crop management practices. However, factors such as (i) the age of the farmers and (ii) off-farm employment opportunity are key drivers that affect the crop management decision-making process. Therefore, exploration of value-added production alternatives and favourable policies is required to sustain IACM that can benefit farmers, consumers and the environment. The participation of policy-makers at the action research continuum is essential for effective follow up, scaling up and sustainability of such environmentally sound practices.

Comprehensive Network Analysis of Anther-Expressed Genes in Rice by the Combination of 33 Laser Microdissection and 143 Spatiotemporal Microarrays

Co-expression networks systematically constructed from large-scale transcriptome data reflect the interactions and functions of genes with similar expression patterns and are a powerful tool for the comprehensive understanding of biological events and mining of novel genes. In Arabidopsis (a model dicot plant), high-resolution co-expression networks have been constructed from very large microarray datasets and these are publicly available as online information resources. However, the available transcriptome data of rice (a model monocot plant) have been limited so far, making it difficult for rice researchers to achieve reliable co-expression analysis. In this study, we performed co-expression network analysis by using combined 44 K agilent microarray datasets of rice, which consisted of 33 laser microdissection (LM)-microarray datasets of anthers, and 143 spatiotemporal transcriptome datasets deposited in RicexPro. The entire data of the rice co-expression network, which was generated from the 176 microarray datasets by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off, contained 24,258 genes and 60,441 genes pairs. Using these datasets, we constructed high-resolution co-expression subnetworks of two specific biological events in the anther, “meiosis” and “pollen wall synthesis”. The meiosis network contained many known or putative meiotic genes, including genes related to meiosis initiation and recombination. In the pollen wall synthesis network, several candidate genes involved in the sporopollenin biosynthesis pathway were efficiently identified. Hence, these two subnetworks are important demonstrations of the efficiency of co-expression network analysis in rice. Our co-expression analysis included the separated transcriptomes of pollen and tapetum cells in the anther, which are able to provide precise information on transcriptional regulation during male gametophyte development in rice. The co-expression network data presented here is a useful resource for rice researchers to elucidate important and complex biological events.