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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

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. Source

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

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. Source

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

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. Source

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

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. Source

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

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. Source

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