Global Rice Research Articles

Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria.

Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51-356 µg ml-1), indole-3 acetic acid (IAA) production (14.3-46.2 µg ml-1), and production of organic acids (72-178 µg ml-1). Inoculation of bacterial consortium (Bacillus subtilis NM-2, Brucella haematophilum NM-4, and Bacillus cereus NM-6) significantly improved seedling growth and vigor index (1009.2-1100) as compared to non-inoculated stressed plants (630-957). Through rhizoscanning, efficiency of the consortium was validated by improved root parameters such as root length (17%), diameter, and surface area (18%) of all tested genotypes as compared with respective non-inoculated stressed treatments. Furthermore, the response of consortium inoculation on three rice genotypes was positively correlated with improved plant growth and drought stress ameliorating traits by the accumulation of osmoprotectant, i.e., proline (85.8%-122%), relative water content (51%), membrane stability index (64%), and production of antioxidant enzymes to reduce oxidative damage by reactive oxygen species. A decrease in temperature and improved chlorophyll content of inoculated plants were found using infrared thermal imaging and soil plant analyzer development (SPAD), respectively. The key supporting role of inoculation toward stress responses was validated using robust techniques like infrared thermal imaging and an infrared gas analyzer. Furthermore, principal component analysis depicts the contribution of inoculation on stress responses and yield of tested rice genotypes under water stress. The integration of drought-tolerant rice genotype (NIBGE-DT02) and potential bacterial strains, i.e., NM-2, NM-4, and NM-6, can serve as an effective bioinoculant to cope with water scarcity under current alarming issues related to food security in fluctuating climate.

First report of rice bacterial leaf blight disease caused by Pantoea ananatis in the United States.

In August 2021, bacterial leaf blight-like symptoms were observed on 14 out of 570 rice genotypes (Oryza sativa) in research field plots of global rice germplasm grown in Arkansas (eXtra Figure S1. A & B). The disease was characterized by spreading lesions on leaves, panicle sterility and reduced yield in highly susceptible, mature rice germplasm. No spread of disease to nearby plants was observed. Isolations were performed at Colorado State University, where soakates from symptomatic leaves were spread onto nutrient agar. After 72 h at 28°C, uniform, distinct, yellow-colored bacterial colonies were observed. To screen for the presence of common rice bacterial pathogens, PCR amplification directly from colonies or from DNA isolated from symptomatic field-collected leaves was performed. Primers specific for Xanthomonas oryzae pvs. oryzae and oryzicola (Lang et al., 2010), Burkholderia glumae (Echeverri-Rico et al., 2021), and Pseudomonas fuscovaginae (Ash et al., 2014) did not amplify indicating these organisms were not present. Sequencing of 16S rRNA gene (Weisburg et al., 1991) amplicons suggested the bacteria belonged to the genera Pantoea and Sphingomonas (NCBI accession no. OP683332 and OP683333, respectively). Amplicons resulting from primers specific to the gyrB gene region of P. ananatis (Kini et al., 2021) were sequenced and the fragment was compared to the P. ananatis PA13 reference genome using a BLAST analysis. One candidate (AR358) showed 100% identity with the P. ananatis gyrB region. Primers specific for Sphingomonas sp. (Bangratz et al., 2020) confirmed the second candidate (AR359) as a Sphingomonas sp. The identity of P. ananatis was confirmed by the Plant Pathogen Confirmatory Diagnostics Laboratory (Beltsville, MD, USA). To determine pathogenicity, leaves from 7-day-old seedlings of rice (Oryza sativa) cultivar Kitaake were scissor-clip inoculated (Kauffman et al., 1973) with four different treatments and compared to control leaves inoculated with sterile water. Treatments for the experiment consisted of bacterial suspensions (108 CFU/ml) of the two candidate organisms, P. ananatis (strain AR358) or Sphingomonas sp. (strain AR359), individually or in a 1:1 ratio of P. ananatis:Sphingomonas sp., or soakate from infected field tissue. Lesions similar to those observed in the field were only detected on leaves inoculated with P. ananatis or infected field tissue soakate at 7-days post-inoculation (eXtra Figure S1. C). Bacteria were recovered from the leaves of the artificially inoculated seedlings from three treatments (P. ananatis, P. ananatis:Sphingomonas sp. and soakate from the infected field tissue) and were determined to be P. ananatis based on colony morphology, amplification of 16s rRNA, and gyrB sequence data. Our results confirm the pathogenicity of P. ananatis to rice and fulfill Koch's postulates. P. ananatis was also recovered from several similarly diseased rice breeding lines at the University of Arkansas System Division of Agriculture Rice Research and Extension Center. We conclude that P. ananatis is the causal pathogen for leaf blight-like symptoms observed in the global rice cultivars grown in Arkansas. P. ananatis was previously reported as a pathogen on rice in several rice growing regions, including China (Yu et al., 2021), India (Reshma et al., 2022), and Africa (Kini et al., 2017), however, this is the first report of P. ananatis as a pathogen of rice in the United States.

Screening of Rice Mutants for Salinity Tolerance and Yield

Soil salinity decreases rice yield by 20%, affecting global rice production including in Bangladesh. Some advanced mutant lines were developed through mutation breeding to observe the performance against salinity at the seedling stage. Mutant lines that are tolerant to salinity at the seedling stage can be used to develop salt tolerant varieties. The first experiment evaluated the salinity tolerance of 20 rice genotypes grown under hydroponic conditions at the seedling stage using a completely randomized design (CRD). Binadhan-10 was used as a salt-tolerant check variety.Salinity level of 15 dS/m, shoot length (SL) and shoot weight (SW) were reduced by 5-44% and 12-22%, respectively, in tolerant genotypes and by 51-73% and 26-75% in susceptible genotypes compared to the control condition. Root length (RL) had a marginal reduction of 10-27% in tolerant genotypes and 18-38% in susceptible genotypes. Susceptible genotypes showed drastic change in SL, SW, shoot dry weight (SDW) and root dry weight (RDW) compared to the tolerant genotypes. According to the heatmap, growth parameters SL, SW, SDW, and RDW formed cluster I while RL formed cluster II. According to the radar plot clustering, tolerant genotypes were in cluster-I, moderately tolerant genotypes in cluster-II, and susceptible genotypes in cluster-III, respectively. Four lines (L-4-P-1-1, LIRG-4Seg 1(1)-3, L-4-P-1(1), and L-4- P-1-P-2) identified as salt tolerant. The second experiment evaluated the yield performance of these lines under normal field conditions. The mutant line LIRG-4Seg-1(1)-3 exhibited higher yield (7.6 t/ha) with higher number of effective tillers per plant (9.0) compared to the tested mutants and a longer panicle length (28.9 cm) compared to Binadhan-10 (23.5 cm). This line along with other selected mutants can be further screened at the reproductive phase or utilized as breeding material to develop a salt tolerant variety.

Effects of Salinity on the Incidence and Severity of Sheath Blight Disease Caused by Rhizoctonia solani (Kuhn) on Some Varieties of Rice (Oryza sativa L.)

As Rice (O. sativa) becomes one of the world's most important cereal crops, its cultivation in arid and semi-arid countries relies heavily on irrigation, and soil salinity remains an environmental or abiotic danger in those regions. Aside from abiotic threats, R. solani-caused sheath blight is one of the most significant fungal diseases restricting global rice output. Because there is a strong link between environmental conditions and plant diseases, determining the effect of salinity on sheath blight disease will be critical. The mycelial block approach was employed to inoculate three rice varieties (Faro44, Faro52, and Jamila) subjected to varying levels of saline treatment. The incidence of sheath blight disease was determined and expressed as a percentage, and plant image analysis (Pliman) was used to measure and determine the severity of sheath blight disease on the affected plant parts. The results revealed that the disease incidence in Faro44 and Faro52 was greater at 8 dSm-1, while Jamila had the highest disease incidence at 6 dSm-1. The disease severity increases with rising salinity level in all varieties, and becomes quite severe when the salinity level exceeds 4 dSm-1. The study concluded that, salt stress is a severe hazard to rice cultivation, and the effect of sheath blight disease can worsen as soil salinity increases.

Where has all the rice gone in China? A farm-to-fork material flow analysis of rice supply chain with uncertainty analysis

China, with rice as its most important staple food, plays a significant role in the global rice economy. However, China's rice supply and demand throughout the supply chain remains poorly understood due to data inconsistencies and gaps. Here, based on a mass-balance consistent system approach and a meta-analysis of various existing data sources, we identified the plausibility and mutual consistency of different sources for each stage of the rice supply chain and mapped the flows and stocks of rice from farm to fork in China in the past two decades. The results showed that production and trade data of paddy rice on the supply side are relatively consistent, while consumption, stock, and loss and waste data on the utilization side are often uncertain. The reconciled results after error propagation for the entire rice supply chain showed that the production of rice has increased from 134 Mt to 151 Mt, while the direct consumption of rice remained stable during the last two decades. The loss and waste of rice has also increased, accounting for 10%-11% of the total domestic rice production. These cross-checked and mass-balanced results help improve existing estimates and address data gaps and inconsistencies of rice supply and demand for mainland China. We call for more bottom-up and in-depth analysis on the rice utilization (especially feed use and out-of-home direct consumption) and stock, which could eventually better inform food security policy in China.

Genotype-by-environment interaction effects on blast disease severity and genetic diversity of advanced blast-resistant rice lines based on quantitative traits

IntroductionAmong the rice diseases, rice blast caused by the pathogen Magnaporthe oryzae is a major threat to the global rice cultivation. This experiment was aimed at investigating the genotype by environment interaction effects on the severity of blast disease and variability of the advanced blast resistant rice lines using quantitative characters.Materials and methodsThe experiment was laid out in randomized complete block design conducted at three locations. Data were collected on 21 traits which included vegetative, physiological, yield and yield components and were subjected to analysis of variance and variance component analysis. Cluster analysis was authenticated using principal component analysis for genotypes’ classification.Results and discussionAll vegetative and yield traits showed highly significant variation among the advanced lines and the check. Seberang Prai showed the highest average yield (5.62t/ha), followed by Tanjung Karang (5.39t/ha) and UPM (4.97t/ha). All the advanced lines showed high resistance to blast disease. Evaluation across the three environments indicated that genotype G3, from MR219 based population, had the highest yield and resistance to blast infection. Genotype G21, from MR263 based population, performed best across the three environments studied and were selected for further breeding programme. The two selected lines, three and four clusters derived from MR219 and MR263 based populations, respectively, were recommended as new lines for further breeding programmes.

A disease-specific spectral index tracks Magnaporthe oryzae infection in paddy rice from ground to space

Rice blast (RB, caused by the fungus Magnaporthe oryzae) is the most devastating disease in global rice production, and can cause significant yield losses and increasingly threaten global food security. Accurate detection of RB occurrence with a universal metric is crucial to facilitate early disease prevention and curtailing the disease expansion but has not been addressed to date. This study aimed to design a rice blast index (RIBI) for quantifying the disease index (DI) and tracking the smallholder rice blast dispersal over multiple spatial scales. To achieve this goal, a large dataset including leaf- and canopy-scale reflectance spectra and satellite imagery was acquired within the framework of seven independent campaigns over four years (2018–2021). Specifically, an extensive collection of Magnaporthe oryzae infected samples were analyzed to examine the specific spectral response to pathogen infection in paddy rice from leaf to near-ground canopy scales. Two variants of the RIBI were developed, which were RIBInir = (R753-R1102)/(R665 + R1102) and RIBIred = (R753-R1102)/(R665 + R1102) based on the single-band separability and exhaustive search of band combinations. They were subsequently evaluated for quantifying the RB occurrence from ground to space. Spatial cluster analysis was then integrated with the superior RIBI adjusted for Sentinel-2 imagery to explore the spatio-temporal dynamics of pathogen infection, and to reveal the within-field hotspots of potential rice blast dispersal in smallholder farms.The results demonstrated that both RIBInir and RIBIred exhibited high overall accuracies for the classification of infected and healthy samples at the leaf scale under greenhouse in 2018 (RIBInir: 81.41%; RIBIred: 84.62%) and 2019 (RIBInir: 81.30%; RIBIred: 90.37%) and field conditions in 2020 (RIBInir: 86.36%; RIBIred: 89.39%). Compared with traditional VIs (Near-ground: R2 < 0.47, satellite: R2 < 0.54), the RIBInir yielded improved R2 in quantifying the DI from in situ spectra to satellite imagery (Near-ground: R2 = 0.73, satellite: R2 = 0.78). The strongest DI-RIBInir relationship was attributed to the use of two near-infrared (NIR) bands that helped enhance the unique spectral responses in the NIR region induced by pathogen infection, in contrast to the extensively studied visible region. Multi-temporal analysis of Sentinel-2A derived RIBInir successfully captured the temporal dynamics of RB infection and recovery and yielded compelling maps showing the spatial propagation and attenuation of disease over time. This research opens new opportunities towards quantifying field disease occurrence and detecting the within-field hotspots of potential disease dispersal in a timely manner from publicly available satellite imagery.

Combining the microbial agent Rhodopseudomonas palustris strain PSB-06 with fungicides for controlling rice blast

The rice blast disease caused by Magnaporthe oryzae threatens global rice production yields. Tricyclazole and isoprothiolane are widely used fungicides with high activity against rice blast, and our previous study indicated the photosynthetic bacterium Rhodopseudomonas palustris PSB-06 significantly antagonizes rice blast. However the effect of combining these two chemical fungicides with PSB-06 on rice blast control is unclear. Here we test the control effect of photosynthetic bacteria PSB-06 combined with isoprothiolane and tricyclazole on rice blast. The growth of PSB-06 was unaffected by up to 1.25 mg/L of tricyclazole and 0.3 mg/L of isoprothiolane in the photosynthetic medium, indicated the two fungicides have no inhibition on PSB-06. The control efficiency in the field test reached 76.06% when PSB-06 was combined with isoprothiolane. This value was significantly higher than the individual efficiency of PSB-06 (67.99%) and tricyclazole (65.46%) and the combined control efficiency (72.20%) of those two antifungal agents. Our current findings highlighted the potential of combining R. palustris strain PSB-06 with isoprothiolane to control rice blast, providing environmental protection and reducing the use of fungicides.

Differences in grain protein content and regional distribution of 706 rice accessions.

Improving rice quality is one of the main goals of global rice breeding programs, and rice protein content is one of the most important factors affecting rice eating quality. The protein content of rice is mainly determined by genetic factors and also affected by environmental factors. However, the differences and regional distribution of protein content during the evolution of different rice varieties are still unclear. The purpose of this study was to understand the differences in grain protein content of 706 rice accessions in different regions and different rice subtypes. The influencing factors of grain protein content differences were analyzed from the perspectives of genetic characteristics, environment, rice subtypes, and breeding process. The results showed that the grain protein content of indica rice in most countries and regions was higher than that of japonica rice. From the perspective of the rice breeding process, the protein content of modern varieties in japonica was lower than that of landrace varieties. In most countries, modern varieties of indica rice had higher protein content than landrace varieties did. The environment and genetic characteristics caused the change in the protein content of rice. This study has improved our understanding of the differences in protein content of rice from different rice varieties. © 2022 Society of Chemical Industry.

Paddy rice methane emissions across Monsoon Asia

Although rice cultivation is one of the most important agricultural sources of methane (CH4) and contributes ∼8% of total global anthropogenic emissions, large discrepancies remain among estimates of global CH4 emissions from rice cultivation (ranging from 18 to 115 Tg CH4 yr−1) due to a lack of observational constraints. The spatial distribution of paddy-rice emissions has been assessed at regional-to-global scales by bottom-up inventories and land surface models over coarse spatial resolution (e.g., > 0.5°) or spatial units (e.g., agro-ecological zones). However, high-resolution CH4 flux estimates capable of capturing the effects of local climate and management practices on emissions, as well as replicating in situ data, remain challenging to produce because of the scarcity of high-resolution maps of paddy-rice and insufficient understanding of CH4 predictors. Here, we combine paddy-rice methane-flux data from 23 global eddy covariance sites and MODIS remote sensing data with machine learning to 1) evaluate data-driven model performance and variable importance for predicting rice CH4 fluxes; and 2) produce gridded up-scaling estimates of rice CH4 emissions at 5000-m resolution across Monsoon Asia, where ∼87% of global rice area is cultivated and ∼ 90% of global rice production occurs. Our random-forest model achieved Nash-Sutcliffe Efficiency values of 0.59 and 0.69 for 8-day CH4 fluxes and site mean CH4 fluxes respectively, with land surface temperature, biomass and water-availability-related indices as the most important predictors. We estimate the average annual (winter fallow season excluded) paddy rice CH4 emissions throughout Monsoon Asia to be 20.6 ± 1.1 Tg yr−1 for 2001–2015, which is at the lower range of previous inventory-based estimates (20–32 CH4 Tg yr−1). Our estimates also suggest that CH4 emissions from paddy rice in this region have been declining from 2007 through 2015 following declines in both paddy-rice growing area and emission rates per unit area, suggesting that CH4 emissions from paddy rice in Monsoon Asia have likely not contributed to the renewed growth of atmospheric CH4 in recent years.

Downscaling Global Gridded Crop Yield Data Products and Crop Water Productivity Mapping Using Remote Sensing Derived Variables in the South Asia.

The online version contains supplementary material available at 10.1007/s42106-022-00223-2.

Cytological observation and transcriptome analysis reveal dynamic changes of Rhizoctonia solani colonization on leaf sheath and different genes recruited between the resistant and susceptible genotypes in rice.

Sheath blight, caused by Rhizoctonia solani, is a big threat to the global rice production. To characterize the early development of R. solani on rice leaf and leaf sheath, two genotypes, GD66 (a resistant genotype) and Lemont (a susceptible genotype), were observed using four cytological techniques: the whole-mount eosin B-staining confocal laser scanning microscopy (WE-CLSM), stereoscopy, fluorescence microscopy, and plastic semi-thin sectioning after in vitro inoculation. WE-CLSM observation showed that, at 12h post-inoculation (hpi), the amount of hyphae increased dramatically on leaf and sheath surface, the infection cushions occurred and maintained at a huge number from about 18 to 36 hpi, and then the infection cushions disappeared gradually from about 42 to 72 hpi. Interestingly, R. solani could not only colonize on the abaxial surfaces of leaf sheath but also invade the paraxial side of the leaf sheath, which shows a different behavior from that of leaf. RNA sequencing detected 6,234 differentially expressed genes (DEGs) for Lemont and 7,784 DEGs for GD66 at 24 hpi, and 2,523 DEGs for Lemont and 2,719 DEGs for GD66 at 48 hpi, suggesting that GD66 is recruiting more genes in fighting against the pathogen. Among DEGs, resistant genes, such as OsRLCK5, Xa21, and Pid2, displayed higher expression in the resistant genotype than the susceptible genotype at both 24 and 48 hpi, which were validated by quantitative reverse transcription-PCR. Our results indicated that the resistance phenotype of GD66 was the consequence of recruiting a series of resistance genes involved in different regulatory pathways. WE-CLSM is a powerful technique for uncovering the mechanism of R. solani invading rice and for detecting rice sheath blight-resistant germplasm.

Inquiring the inter-relationships amongst grain-filling, grain-yield, and grain-quality of Japonica rice at high latitudes of China.

The widespread impacts of projected global and regional climate change on rice yield have been investigated by different indirect approaches utilizing various simulation models. However, direct approaches to assess the impacts of climatic variabilities on rice growth and development may provide more reliable evidence to evaluate the effects of climate change on rice productivity. Climate change has substantially impacted rice production in the mid-high latitudes of China, especially in Northeast China (NEC). Climatic variabilities occurring in NEC since the 1970s have resulted in an obvious warming trend, which made this region one of the three major rice-growing regions in China. However, the projections of future climate change have indicated the likelihood of more abrupt and irregular climatic changes, posing threats to rice sustainability in this region. Hence, understanding the self-adaptability and identifying adjustive measures to climate variability in high latitudes has practical significance for establishing a sustainable rice system to sustain future food security in China. A well-managed field study under randomized complete block design (RCBD) was conducted in 2017 and 2018 at two study sites in Harbin and Qiqihar, located in Heilongjiang province in NEC. Four different cultivars were evaluated: Longdao-18, Longdao-21 (longer growth duration), Longjing-21, and Suijing-18 (shorter growth duration) to assess the inter-relationships among grain-filling parameters, grain yield and yield components, and grain quality attributes. To better compare the adaptability mechanisms between grain-filling and yield components, the filling phase was divided into three sub-phases (start, middle, and late). The current study evaluated the formation and accumulation of the assimilates in superior and inferior grains during grain-filling, mainly in the middle sub-phase, which accounted for 59.60% of the yield. The grain yields for Suijing-18, Longjing-21, Longdao-21, and Longdao-18 were 8.02%, 12.78%, 17.19%, and 20.53% higher in Harbin than those in Qiqihar, respectively in 2017, with a similar trend observed in 2018. At Harbin, a higher number of productive tillers was noticed in Suijing-18, with averages of 17 and 15 in 2017 and 2018, respectively. The grain-filling parameters of yield analysis showed that the filling duration in Harbin was conducive to increased yield but the low dry weight of inferior grains was a main factor limiting the yield in Qiqihar. The average protein content values in Harbin were significantly higher (8.54% and 9.13%) than those in Qiqihar (8.34% and 9.14%) in 2017 and 2018, respectively. The amylose content was significantly higher in Harbin (20.03% and 22.27%) than those in Qiqihar (14.44% and 14.67%) in 2017 and 2018, respectively. The chalkiness percentage was higher in Qiqihar, indicating that Harbin produced good quality rice. This study provides more direct evidence of the relative changes in rice grain yield due to changes in grain-filling associated with relative changes in environmental components. These self-adaptability mechanisms to climatic variability and the inter-relationships between grain-filling and grain yield underscore the urgent to investigate and explore measures to improve Japonica rice sustainability, with better adaptation to increasing climatic variabilities. These findings may also be a reference for other global rice regions at high latitudes in addressing the impacts of climate change on future rice sustainability.

A Review of Vector-Borne Rice Viruses.

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

Can rice yield more with less water?

Can rice yield more with less water? Examining global warming and rice yield productivity with Professor Dr Apichart Vanavichit, Director of the Rice Science Center. Rice (Oryza sativa L.) is a major crop, providing food for billions of people globally. However, rice yield and cultivation is less water productive, requiring approximately 2,500 litres of water per kilogram of polished grain produced (Bouman, 2009). Here, Professor Dr Apichart Vanavichit explores how if Thailand’s maximum temperature is increased by 1%, half of the rice yield may risk crop loss and what can be done to future-proof rice production.

The Impact of COVID-19 on Global Indica and Japonica Rice Markets: Examining by an Endogenous Agricultural Investment Model

Indica and japonica rice are commonly subjected to different market structures, and the international prices for both subspecies display different trends. The global indica and japonica rice markets in the mid and long term under climate change conditions were projected by the Rice Economy Climate Change (RECC) model. Additionally, endogenous agricultural investments were incorporated into the projections. A COVID-19 pandemic scenario was stimulated to observe its impact on the global indica and japonica rice markets. The results indicated that agricultural investments are expected to decrease in many indica rice-producing countries, whereas the investments will increase in many japonica rice-producing countries in the long term. Therefore, the global indica rice production will decrease due to its investment reduction; however, global japonica rice production will increase in the mid and long term. Due to the COVID-19 scenario, the international indica and japonica rice prices would decrease in 2020 due to the unprecedented shrinking economies worldwide, but the prices would increase from 2021 to 2040 compared with the baseline average of the price projections with the RECC model. The scenario simulation results reveal that the japonica rice markets are projected to have less impact than the indica rice markets from the COVID-19 pandemic.

Genome-wide association mapping for identification of sheath blight resistance loci from wild rice Oryza rufipogon

Sheath blight (ShB) caused by Rhizoctonia solani is one of the serious constraints that hamper global rice production. It causes severe yield loss of up to 69% under favorable environmental conditions. The application of chemical fungicides remains the primary approach for the management of this disease. But, overuse of chemical fungicides causes potential health and environmental risk. The use of host plant resistance is a very effective, economic, and sustainable strategy to control sheath blight disease in rice. In this report, we have evaluated 405 accessions of Oryza rufipogon for four ShB-related traits i.e. lesion height (LH), plant height (PH), relative lesion length (RLH), and disease score (DS) during the years 2015, 2016, and 2017. A total of 44,109 high-quality SNP markers on 301 accessions were employed to identify significant marker-trait associations using a genome-wide association study (GWAS). The GWAS analysis revealed a total of 22 significant SNPs associated with the ShB-related traits distributed on all the rice chromosomes except 10 and 12. Among them, eleven were associated with RLH, seven with PH, and one each with LH and DS. The SNPs on chromosomes 3 and 9 were associated with multiple traits. Furthermore, seven ShB resistance loci were also found to be co-localized with previously reported ShB resistance genes/QTLs. These findings provide valuable information to identify key SNPs associated with ShB resistance. Significantly associated SNPs could be used for introgression of ShB resistance traits into rice cultivars using marker-assisted selection.

Integrated analysis of transcriptome and metabolome reveals molecular mechanisms of salt tolerance in seedlings of upland rice landrace 17SM-19.

Salt stress is a major abiotic stress that threatens global rice production. It is particularly important to improve salt tolerance in upland rice because of its growth environment. Upland rice landrace 17SM-19 with high salt tolerance was obtained from a previous study. In this study, an integrated analysis of transcriptome and metabolome was performed to determine the responses of the rice seedling to salt stress. When treated with 100 mm NaCl, the rice seedling growth was significantly inhibited at 5 d, with inhibition first observed in shoot dry weight (SDW). Changes in potassium (K+) content were associated with changes in SDW. In omics analyses, 1,900 differentially expressed genes (DEGs) and 659 differentially abundant metabolites (DAMs) were identified at 3 d after salt stress (DAS), and 1,738 DEGs and 657 DAMs were identified at 5 DAS. Correlation analyses between DEGs and DAMs were also conducted. The results collectively indicate that salt tolerance of upland rice landrace 17SM-19 seedlings involves many molecular mechanisms, such as those involved with osmotic regulation, ion balance, and scavenging of reactive oxygen species.

The dynamic of pests and plant diseases during three consecutive rice growing seasons

Pests and diseases are significant factors that affecting global rice production. There is a need that pests and diseases have continuously been controlled, in order to solve the pest and disease problem. The aim of this study was to observe the population dynamics of pests and diseases infestation in lowland rice field during different cropping seasons. The data of pest and disease infestation in Pati District, Central Java Province, Indonesia during the Rainy Season (RS) 2018/2019, the Dry Season (DS) 2019, and the RS 2019/2020 were observed and analyzed. The results showed that the rice fields in Pati were susceptible to stem borer, brown plant hopper, rats, fake white pests, blast and bacterial blight during three consecutive seasons. Tungro was not found. During both the RS and DS, the areas of rice paddy in Pati approximately 470 ha season−1 were affected by stem borer. The second largest damage rice area approximately 221 ha season−1 was affected by blast. Grain loses due to pests and diseases infestation during the RS was higher than during the DS. Micro-climate significantly affected pests and plant diseases. The dynamic of pests and plant disease infestation provide information early warning for high-risk areas of rice production and for pests-diseases management.

Morpho-physiological, biochemical and molecular characterization of coastal rice landraces to identify novel genetic sources of salinity tolerance

Soil salinity is a leading cause for yield losses in rice, affecting nearly 6% of global rice cultivable area. India is host to a rich diversity of coastal rice landraces that are naturally tolerant to salinity and an untapped source to identify novel determinants of salinity tolerance. In the present study, we have assessed the relative salinity tolerance of 43 previously genotyped rice landraces at seedling stage, using thirteen morpho-physiological and biochemical parameters using a hydroponics system. Among 43 rice varieties, 25 were tolerant, 15 were moderately tolerant, 1 was moderately susceptible and 2 sensitive checks were found to be highly susceptible based on standard salinity scoring methods. In addition to previously known saline tolerant genotypes (Pokkali, FL478 and Nona Bokra), the present study has novel genotypes such as Katrangi, Orkyma, Aduisen 1, Orumundakan 1, Hoogla, and Talmugur 2 as potential sources of salinity tolerance through measurement of morpho-physiological and biochemical parameters including Na+, K+ estimations and Na+/K+ ratios. Further, Pallipuram Pokkali may be an important source of the tissue tolerance trait under salinity. Four marker trait associations (RM455-root Na+; RM161-shoot and root Na+/K+ ratios; RM237-salinity tolerance index) accounted for phenotypic variations in the range of 20.97–39.82%. A significant increase in root endodermal and exodermal suberization was observed in selected rice landraces under salinity. For the first time, variation in the number of suberized sclerenchymatous layers as well as passage cells is reported, in addition to expression level changes in suberin biosynthetic genes (CYP86A2, CYP81B1, CYP86A8 and PERL).