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Mazid M.S.,University Putra Malaysia | Rafii M.Y.,University Putra Malaysia | Hanafi M.M.,University Putra Malaysia | Rahim H.A.,Malaysian Nuclear Agency | And 2 more authors.
Physiologia Plantarum | Year: 2013

A field experiment was carried out in order to evaluate genetic diversity of 41 rice genotypes using physiological traits and molecular markers. All the genotypes unveiled variations for crop growth rate (CGR), relative growth rate (RGR), net assimilation rate (NAR), yield per hill (Yhill-1), total dry matter (TDM), harvest index (HI), photosynthetic rate (PR), leaf area index (LAI), chlorophyll-a and chlorophyll-b at maximum tillering stage. The CGR values varied from 0.23 to 0.76 gm cm-2day-1. The Yhill-1 ranged from 15.91 to 92.26g, while TDM value was in the range of 7.49 to 20.45g hill-1. PR was found to vary from 9.40 to 22.34 μmol m-2 s-1. PR expressed positive relation with Yhill-1. Significant positive relation was found between CGR and TDM (r=0.61**), NAR and CGR (r=0.62**) and between TDM and NAR (r=0.31**). High heritability was found in RGR and Yhill-1. Cluster analysis based on the traits grouped 41 rice genotypes into seven clusters. A total of 310 polymorphic loci were detected across the 20 inter-simple sequence repeats (ISSR) markers. The UPGMA dendrogram grouped 41 rice genotypes into 11 clusters including several sub-clusters. The Mantel test revealed positive correlation between quantitative traits and molecular markers (r=0.41). On the basis of quantitative traits and molecular marker analyses parental genotypes, IRBB54 with MR84, IRBB60 with MR84, Purbachi with MR263, IRBB65 with BR29, IRBB65 with Pulut Siding and MRQ74 with Purbachi could be hybridized for future breeding program. © 2013 Scandinavian Plant Physiology Society.

Rashid M.M.,Kyoto Prefectural University | Rashid M.M.,Bangladesh Rice Research Institute | Ikawa Y.,Kyoto Prefectural University | Tsuge S.,Kyoto Prefectural University
Applied and Environmental Microbiology | Year: 2016

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight of rice. For the virulence of the bacterium, the hrp genes, encoding components of the type III secretion system, are indispensable. The expression of hrp genes is regulated by two key hrp regulators, HrpG and HrpX: HrpG regulates hrpX, and HrpX regulates other hrp genes. Several other regulators have been shown to be involved in the regulation of hrp genes. Here, we found that a LysR-type transcriptional regulator that we named GamR, encoded by XOO_2767 of X. oryzae pv. oryzae strain MAFF311018, positively regulated the transcription of both hrpG and hrpX, which are adjacent to each other but have opposite orientations, with an intergenic upstream region in common. In a gel electrophoresis mobility shift assay, GamR bound directly to the middle of the upstream region common to hrpG and hrpX. The loss of either GamR or its binding sites decreased hrpG and hrpX expression. Also, GamR bound to the upstream region of either a galactose metabolism-related gene (XOO_2768) or a galactose metabolism-related operon (XOO_2768 to XOO_2771) located next to gamR itself and positively regulated the genes. The deletion of the regulator gene resulted in less bacterial growth in a synthetic medium with galactose as a sole sugar source. Interestingly, induction of the galactose metabolismrelated gene was dependent on galactose, while that of the hrp regulator genes was galactose independent. Our results indicate that the LysR-type transcriptional regulator that regulates the galactose metabolism-related gene(s) also acts in positive regulation of two key hrp regulators and the following hrp genes in X. oryzae pv. oryzae. © 2016, American Society for Microbiology. All Rights Reserved.

Islam A.,Bangladesh Rice Research Institute | Muttaleb A.,Bangladesh Rice Research Institute
Archives of Agronomy and Soil Science | Year: 2016

Effect of potassium (K) fertilization (0, 20, 40, 60, 80 and 100 kg K ha−1) on yield, nitrogen (N) and K nutrition of Boro (dry season) rice and apparent soil K balance was studied. Experiment was conducted at Bangladesh Rice Research Institute (BRRI) regional station farm, Habiganj, Bangladesh during 2007–2008 to 2009–2010 in a wetland rice ecosystem under haor area. Cropping pattern was Boro–Fallow–Fallow. A popular rice variety BRRI dhan29 was tested in a randomized complete block design with three replications. Results indicated that BRRI dhan29 maintained an average grain yield of 5.19 t ha−1 year−1 without K fertilization. Potassium fertilization significantly increased the grain yield to 6.86 t ha−1 year−1. Quadratic equations best explained the progressive increase of rice yield with increasing K rates. Optimum dose of K in 3 years ranged from 78 to 93 kg ha−1. Internal N use efficiency of rice decreased with increasing K rates. However, K use efficiency was inconsistent. Apparent K balance study revealed that application of 100 kg K ha−1 was not able to maintain a positive K balance in soil under wetland ecosystem with Boro–Fallow–Fallow cropping system. However, K fertilization decreased the negativity of K balance in soil. © 2016 Taylor & Francis

Miah G.,University Putra Malaysia | Rafii M.Y.,University Putra Malaysia | Ismail M.R.,University Putra Malaysia | Puteh A.B.,University Putra Malaysia | And 4 more authors.
Molecular Biology Reports | Year: 2013

Blast disease caused by the fungal pathogen Magnaporthe oryzae is the most severe diseases of rice. Using classical plant breeding techniques, breeders have developed a number of blast resistant cultivars adapted to different rice growing regions worldwide. However, the rice industry remains threatened by blast disease due to the instability of blast fungus. Recent advances in rice genomics provide additional tools for plant breeders to improve rice production systems that would be environmentally friendly. This article outlines the application of conventional breeding, tissue culture and DNA-based markers that are used for accelerating the development of blast resistant rice cultivars. The best way for controlling the disease is to incorporate both qualitative and quantitative genes in resistant variety. Through conventional and molecular breeding many blast-resistant varieties have been developed. Conventional breeding for disease resistance is tedious, time consuming and mostly dependent on environment as compare to molecular breeding particularly marker assisted selection, which is easier, highly efficient and precise. For effective management of blast disease, breeding work should be focused on utilizing the broad spectrum of resistance genes and pyramiding genes and quantitative trait loci. Marker assisted selection provides potential solution to some of the problems that conventional breeding cannot resolve. In recent years, blast resistant genes have introgressed into Luhui 17, G46B, Zhenshan 97B, Jin 23B, CO39, IR50, Pusa1602 and Pusa1603 lines through marker assisted selection. Introduction of exotic genes for resistance induced the occurrence of new races of blast fungus, therefore breeding work should be concentrated in local resistance genes. This review focuses on the conventional breeding to the latest molecular progress in blast disease resistance in rice. This update information will be helpful guidance for rice breeders to develop durable blast resistant rice variety through marker assisted selection. © 2012 Springer Science+Business Media Dordrecht.

Ali M.P.,Bangladesh Rice Research Institute | Chowdhury T.R.,Bangladesh Atomic Energy Commission
Euphytica | Year: 2014

The brown plant hopper, Nilaparvata lugens Stål (Hemiptera: Delphacidae) is an important pest of rice, Oryza sativa L. (Poales: Poaceae). The need for N. lugens-resistant rice varieties able to cope with stressful conditions obviously requires that breeders better comprehend the physiology and genetic control of N. lugens resistance. In spite of several good reviews recently published, an integrated vision of current information on rice resistance to N. lugens stress has been lacking. Here the most recent data on the N. lugens resistance rice varieties is presented. An inventory is included of N. lugens resistance donors available for breeding programs and a comprehensive survey of current work on gene maps, chromosomal locations, quantitative trait locus (QTL) detection and cloning as well as marker-assisted selection to introgress favorable alleles into chosen rice lines. A schematic view of the rice chromosomes on which N. lugens resistance QTLs and genes are positioned is included. The graphical gene locus of major resistance genes and QTL positions that have been detected on different chromosomes involved in N. lugens response is also presented. We highlight missing information that could help to design better N. lugens resistant varieties, and evaluate the significance of the data presented for the future of rice breeding. © 2013 Springer Science+Business Media Dordrecht.

Ahmed Z.U.,Cornell University | Panaullah G.M.,Uttara University | Gauch Jr. H.,Cornell University | McCouch S.R.,Cornell University | And 3 more authors.
Plant and Soil | Year: 2011

Genetic analysis of 38 rice varieties released by the Bangladesh Rice Research Institute (BRRI) identified 34 as indica, 2 as admixed between indica and aus, and 4 as belonging to the aromatic/Group V subpopulation. Indica varieties developed for the two major rice-growing seasons, the wet monsoon (aman) and the dry winter (boro), were not genetically differentiated. The Additive Main Effect and Multiplicative Interaction (AMMI) model was used to assess the effect of genotype (G), environment (E) and genotype-environment interaction (GEI) on grain arsenic (As) concentration when these rice varieties were grown at ten BRRI research stations located across diverse agro-ecological zones in Bangladesh. G, E and GEI, significantly influenced grain As concentration in both seasons. Overall, E accounted for 69%-80%, G 9%-10% and GEI 10%-21% of the observed variability in grain As. One site, Satkhira had the highest mean grain As concentration and the largest interaction principle component analysis (IPCA) scores in both seasons, indicating maximum interaction with genotypes. Site effects were more pronounced in the boro than in the aman season. The soil level of poorly crystalline Fe-oxide (AOFe), the ratio of AOFe to associated As, soil phosphate extractable As and soil pH were important sub-components of E controlling rice grain As concentration. Irrespective of environment, the mean grain As concentration was significantly higher in the boro (0.290 mg As kg-1) than in the aman (0.154 mg As kg-1) season (p < 0.0001), though the reasons for this are unclear. Based on mean grain As concentration and stability across environments, the variety BR3 is currently the best choice for the boro season, while BR 23 and BRRI dhan 38 are the best choices for the aman season. Popular varieties BR 11 (aman) and BRRI dhan 28 and 29 (boro) had grain As concentrations close to the mean value and were fairly stable across environments, while high-yielding, short-duration aman season varieties (BRRI dhan 32, 33 and 39) developed for intensified cropping had relatively high grain As concentrations. Results suggest that genetic approaches to reducing As in rice grain will require the introduction of novel genetic variation and must be accompanied by appropriate management strategies to reduce As availability and uptake by rice. © 2010 Springer Science+Business Media B.V.

Islam M.R.,Bangladesh Rice Research Institute | Gregorio G.B.,International Rice Research Institute
Sabrao Journal of Breeding and Genetics | Year: 2013

BR23, BRRI dhan40, BRRI dhan41, BRRI dhan53 and BRRI dhan54 possess salinity tolerance up to EC 8 dS m-1 in addition to high yield potential (> 4.0 t/ha), lodging tolerance and 10-38 days shorter growth duration over traditional rice varieties for the wet season. Development of BRRI dhan47, BINA dhan8, BRRI dhan53 and BRRI dhan55 for dry season was a major breakthrough for breeding salt tolerant rice in Bangladesh. BRRI dhan47 can tolerate EC 12 to 14 dS m-1 salt stress. The potential yield of the varieties ranged from 5.4 to 8.3 t ha-1 in different saline prone areas. Current efforts are to use advanced tools such as marker assisted selection (MAS) and marker assisted backcrossing (MABC) to introgress SalTol QTL into BR11. MABC for BRRI dhan28 was completed at IRRI. All of these introgressed lines are tested in the farmer's field in coastal regions. The principal focus was to pyramid multiple stress tolerant genes into mega-varieties of rice to ensure better adaptability in coastal salt affected areas. © Society for the Advancement of Breeding Research in Asia and Oceania (SABRAO) 2013.

Rashid M.H.,Bangladesh Rice Research Institute | Alam M.M.,International Rice Research Institute | Rao A.N.,IRRI India | Ladha J.K.,IRRI India
Field Crops Research | Year: 2012

Field experiments were conducted for two years during 2005-2006 and 2006-2007 in farmers' fields at Sorajgonj Village in Sadar Upazila of Chuadanga District in Bangladesh. The objective was to evaluate the comparative efficacy of hand weeding and pretilachlor applied at different days after seeding (DAS) rice in effectively and economically controlling weeds and improving the productivity of rice wet-seeded using a drum seeder, during the aman and boro seasons. Three application timings of pretilachlor and five weed control treatments, including (a) pretilachlor 0.500kgha -1, (b) pretilachlor 0.375kgha -1, (c) pretilachlor 0.250kgha -1, (d) hand weeding thrice, and (e) unweeded (check), were tested. The reduction in grassy weeds due to different rates of pretilachlor and hand weeding thrice was inconsistent due to less efficacy of pretilachlor against Cynodon dactylon and incomplete removal of the same weed by hand weeding. The density and biomass of sedges and broad-leaved weeds at different pretilachlor rates were lower than or similar to those of hand weeding thrice during both seasons. On average, rice yield loss due to uncontrolled weeds was 43% and 51% in aman and boro seasons, respectively. Economic analysis revealed that the net income with pretilachlor application was equivalent to that obtained with hand weeding thrice in the boro season and higher than with hand weeding thrice in the aman season, in spite of getting slightly lesser rice yield with pretilachlor usage than with hand weeding thrice. Results of the study revealed that, for effectively controlling associated weeds and attaining optimal wet-seeded rice productivity and net returns, pretilachlor 0.250kga.i.ha -1 or 0.375kga.i.ha -1 application at 3 or 5 DAS in aman and at 7 or 9 DAS in boro season can be used as an alternative to hand weeding thrice, during the times of labor scarcity in Bangladesh. © 2011 Elsevier B.V.

Ali M.P.,Bangladesh Rice Research Institute | Huang D.,University of Chinese Academy of Sciences | Nachman G.,Copenhagen University | Ahmed N.,Bangladesh Rice Research Institute | And 2 more authors.
PLoS ONE | Year: 2014

Recently, planthoppers outbreaks have intensified across Asia resulting in heavy rice yield losses. The problem has been widely reported as being induced by insecticides while other factors such as global warming that could be potential drivers have been neglected. Here, we speculate that global warming may increase outbreak risk of brown planthopper (Nilaparvata lugens Stål.). We present data that demonstrate the relationship between climate variables (air temperature and precipitation) and the abundance of brown planthopper (BPH) during 1998-2007. Data show that BPH has become significantly more abundant in April over the 10-year period, but our data do not indicate that this is due to a change in climate, as no significant time trends in temperature and precipitation could be demonstrated. The abundance of BPH varied considerably between months within a year which is attributed to seasonal factors, including the availability of suitable host plants. On the other hand, the variation within months is attributed to fluctuations in monthly temperature and precipitation among years. The effects of these weather variables on BPH abundance were analyzed statistically by a general linear model. The statistical model shows that the expected effect of increasing temperatures is ambiguous and interacts with the amount of rainfall. According to the model, months or areas characterized by a climate that is either cold and dry or hot and wet are likely to experience higher levels of BPH due to climate change, whereas other combinations of temperature and rainfall may reduce the abundance of BPH. The analysis indicates that global warming may have contributed to the recent outbreaks of BPH in some rice growing areas of Asia, and that the severity of such outbreaks is likely to increase if climate change exaggerates. Our study highlights the need to consider climate change when designing strategies to manage planthoppers outbreaks. © 2014 Ali et al.

Gumma M.K.,International Rice Research Institute | Gumma M.K.,Indian International Crops Research Institute for the Semi Arid Tropics | Thenkabail P.S.,U.S. Geological Survey | Maunahan A.,International Rice Research Institute | And 3 more authors.
ISPRS Journal of Photogrammetry and Remote Sensing | Year: 2014

Rice is the most consumed staple food in the world and a key crop for food security. Much of the world's rice is produced and consumed in Asia where cropping intensity is often greater than 100% (more than one crop per year), yet this intensity is not sufficiently represented in many land use products. Agricultural practices and investments vary by season due to the different challenges faced, such as drought, salinity, or flooding, and the different requirements such as varietal choice, water source, inputs, and crop establishment methods. Thus, spatial and temporal information on the seasonal extent of rice is an important input to decision making related to increased agricultural productivity and the sustainable use of limited natural resources. The goal of this study was to demonstrate that hyper temporal moderate-resolution imaging spectroradiometer (MODIS) data can be used to map the spatial distribution of the seasonal rice crop extent and area. The study was conducted in Bangladesh where rice can be cropped once, twice, or three times a year.MODIS normalized difference vegetation index (NDVI) maximum value composite (MVC) data at 500m resolution along with seasonal field-plot information from year 2010 were used to map rice crop extent and area for three seasons, boro (December/January-April), aus (April/May-June/July), and aman (July/August-November/December), in Bangladesh. A subset of the field-plot information was used to assess the pixel-level accuracy of the MODIS-derived rice area. Seasonal district-level rice area statistics were used to assess the accuracy of the rice area estimates. When compared to field-plot data, the maps of rice versus non-rice exceeded 90% accuracy in all three seasons and the accuracy of the five rice classes varied from 78% to 90% across the three seasons. On average, the MODIS-derived rice area estimates were 6% higher than the sub-national statistics during boro, 7% higher during aus, and 3% higher during the aman season. The MODIS-derived sub-national areas explained (R2 values) 96%, 93%, and 96% of the variability at the district level for boro, aus, and aman seasons, respectively.The results demonstrated that the methods we applied for analysing and interpreting moderate spatial and high temporal resolution imagery can accurately capture the seasonal variability in rice crop extent and area. We discuss the robustness of the approach and highlight issues that must be addressed before similar methods are used across other areas of Asia where a mix of rainfed, irrigated, or supplemental irrigation permits single, double, and triple cropping in a single calendar year. © 2014 International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS).

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