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Barnwal M.K.,Birsa Agricultural University | Magculia N.,International Rice Research Institute | Magculia N.,Kobe University | Mukherjee P.K.,Bhabha Atomic Research Center | And 9 more authors.
European Journal of Plant Pathology | Year: 2013

Rice brown spot (BS) is a chronic disease that affects millions of hectares of rice every growing season, grown by some of the most resource-poor farmers. Despite its widespread occurrence and impact, much still needs to be understood about BS. Reported yield losses in relative terms vary widely from 4 to 52 %. However, accurate, systematic estimates are lacking. BS is conventionally perceived as a secondary problem that reflects rice crops that experience physiological stresses, e. g. drought and poor soil fertility, rather than a true infectious disease. Much remains to be understood about the mechanisms leading to epidemics and crop losses. Quantitative and qualitative knowledge gaps exist in our understanding of the epidemiological processes, sources of resistance and biocontrol methods. In this review we identify several of these gaps, which if filled, could lead to a strong impact on the management of brown spot. We also use the architecture of a simulation model to position and prioritize these knowledge gaps, assess the epidemiological consequences of disease management options on BS monocyclic processes and explore the impact changing production situations on this important disease. © 2013 The Author(s).


Singh P.K.,Indian Agricultural Research Institute | Singh P.K.,Banasthali University | Thakur S.,Indian Agricultural Research Institute | Rathour R.,CSK Himachal Pradesh Agricultural University | And 7 more authors.
Functional and Integrative Genomics | Year: 2014

Magnaporthe oryzae causes rice blast that is one of the most devastating diseases of rice worldwide. Highly variable nature of this fungus has evolved itself against major resistance genes in newly released rice varieties. Understanding the population structure of this fungus is essential for proper utilization of the rice blast resistance genes in rice crop plants. In the present study, we analyzed 133 isolates of M. oryzae from ten countries to find the allelic variation of Avr-Pita gene that is triggering Pita-mediated resistance in rice plant. The diversity analysis of these alleles showed higher level of nucleotide variation in the coding regions than the noncoding regions. Evolutionary analysis of these alleles indicates that Avr-Pita gene is under purifying selection to favor its major alleles in 133 isolates analyzed in this study. We hypothesize that the selection of favorable Avr-Pita allele in these isolates may occur through a genetic mechanism known as recurrent selective sweeps. A total of 22 functional Avr-Pita protein variants were identified in this study. Insertion of Pot3 transposable element into the promoter of Avr-Pita gene was identified in virulent isolates and was suggested that mobility of repeat elements in avirulence genes of M. oryzae seems to help in emergence of new virulent types of the pathogen. Allele-specific markers developed in this study will be helpful to identify a particular type of Avr-Pita allele from M. oryzae population which can form the basis for the deployment of Pita gene in different epidemiological regions. © 2014 Springer-Verlag.


Henry A.,International Rice Research Institute | Dixit S.,International Rice Research Institute | Mandal N.P.,Central Rainfed Upland Rice Research Station | Anantha M.S.,Central Rainfed Upland Rice Research Station | And 2 more authors.
Functional Plant Biology | Year: 2014

To improve yield in upland conditions, near-isogenic lines (NILs) of the major-effect drought yield quantitative trait locus qDTY12.1 in rice (Oryza sativa L.) were developed in the background of the upland variety Vandana. These NILs have shown greater water uptake a larger proportion of lateral roots, and higher transpiration efficiency under drought than Vandana, and one NIL (481-B) was selected as having the highest yield. In this study, the NILs were assessed in two greenhouse and 18 upland field trials for their response to drought and different soil textures. Performance of qDTY12.1 NILs was not affected by soil texture but showed a notable response to drought stress severity. The yield advantage of 481-B over Vandana was highest in field trials with intermittent drought stress, in which the mean trial yield was greater than 0.5tha-1, and in the least favourable well watered trial. The effects of qDTY12.1 on water uptake were most apparent under mild to moderate stress but not in very severe drought or well watered treatments, whereas the lateral root and transpiration efficiency responses were observed under a range of conditions. These results highlight the varying response of qDTY12.1 across upland environments and the complexity of multiple mechanisms acting together to confer an effect on rice yield under drought. © CSIRO 2014.


Thakur S.,Indian Agricultural Research Institute | Thakur S.,Himachal Pradesh University | Gupta Y.K.,Indian Agricultural Research Institute | Singh P.K.,Indian Agricultural Research Institute | And 9 more authors.
Functional and Integrative Genomics | Year: 2013

Rice blast is one of the important diseases of rice which can be effectively managed by the deployment of resistance genes. Pi-ta is one of the major blast resistant genes effective against pathogen populations in different parts of India. We analysed allelic variants of Pi-ta from 48 rice lines selected after phenotyping of 529 rice landraces across three eco-geographical blast hot spot regions. Besides, Pi-ta orthologue sequences of 220 rice accessions belonging to wild and cultivated species of rice were also included in the study for a better evo-devo perspective of the diversity present in the gene and the selection pressures acting on this locus. We obtained high nucleotide variations (SNPs and insertion-deletions) in the intronic region. We also identified 64 haplotypes based on nucleotide polymorphism in these alleles. Pi-ta orthologues of Indian landraces were scattered in eight major haplotypes indicating its heterogenous nature. We identified a total of 47 different Pi-ta protein variants on the basis of deduced amino acid residues amongst the orthologues. Five unique and novel Pi-ta variants were identified for the first time in rice landraces exhibiting different reaction types against the Magnaporthe oryzae population. A high value of Pinon/syn was observed only in the leucine-rich domain of the alleles cloned from Indian landraces, indicating strong selective forces acting on this region. The detailed molecular analysis of the Pi-ta orthologues provides insights to a high degree of inter- and intraspecific relationships amongst the Oryza species. We identified rice landraces possessing the effective alleles of this resistance gene which can be used in future blast resistance breeding programmes. © 2013 Springer-Verlag Berlin Heidelberg.


Henry A.,International Rice Research Institute | Swamy B.P.M.,International Rice Research Institute | Dixit S.,International Rice Research Institute | Torres R.D.,International Rice Research Institute | And 5 more authors.
Journal of Experimental Botany | Year: 2015

Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs - as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY 2.2 + qDTY 4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY 2.2 and qDTY 4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.


PubMed | International Rice Research Institute and Central Rainfed Upland Rice Research Station
Type: Journal Article | Journal: Journal of experimental botany | Year: 2015

Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs-as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY 2.2 + qDTY 4.1 ) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY 2.2 and qDTY 4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.


Akhtar J.,Birsa Agricultural University | Lal H.C.,Birsa Agricultural University | Kumar Y.,Central Rainfed Upland Rice Research Station | Kumar Y.,Birsa Agricultural University | And 5 more authors.
Legume Research | Year: 2014

Field screening conducted during Kharif, 2008 and 2009 revealed that out of 31 genotypes of greengram, only 1 genotype ML 1299 and out of 14 genotypes of blackgram, only 3 genotypes viz, BS 2-3, IPU 02-43 and B 3-8-8 showed resistant or highly resistant response against multiple diseases including Cercospora leaf spot, web blight and powdery mildew. In another trial conducted for management of foliar diseases of greengram and blackgram through chemical revealed that two foliar sprays of propiconazole @ 0.1% at an interval of 8-10 days was most effective as it reduced severity of Cercospra leaf spot (85.77 and 80.10 %), web blight (77.87 and 85.29 %) and powdery mildew (100.00 % each) with average yield of 9.08 and 8.83q/ha of greengram and blackgram, respectively.


Thakur S.,Indian Agricultural Research Institute | Thakur S.,Himachal Pradesh University | Singh P.K.,Indian Agricultural Research Institute | Rathour R.,CSK Himachal Pradesh Agricultural University | And 7 more authors.
Journal of Plant Interactions | Year: 2013

Allelic variants of the broad-spectrum blast resistance gene, Piz-t, have been analyzed in 48 rice lines selected after phenotyping across three blast hot-spot regions of India. Single Nucleotide Polymorhisms in the form of transitions were more frequent than the transversions in the alleles. On the basis of nucleotide polymorphism, 46 haplotypes have been identified, with major haplotypes forming three main haplogroups. The Piz-t alleles formed mostly region-specific clusters. Resistant and susceptible Piz-t alleles were grouped into separate sub-clusters. The value of Tajima's D was negative indicating positive selection on Piz-t locus. Sequence variations were more abundant in the leucine rich repeats (LRR) region than in the NB-ARC (nucleotide-binding adaptor shared by APAF-1,R proteins, and CED-4) region, indicating that the LRR region has played a more important role in the evolution of this allele. The detailed molecular analysis of the Piz-t locus provide insights to high degree of inter-and intra-specific relationship among the Indian land races of rice which will help in the selection of better alleles for future rice breeding programs. © 2013 Copyright Taylor and Francis Group, LLC.


Karan A.K.,Indian Institute of Technology Kharagpur | Kar S.,Indian Institute of Technology Kharagpur | Singh V.K.,Indian Institute of Technology Kharagpur | Singh C.Y.,Central Rainfed Upland Rice Research Station
International Journal of Soil Science | Year: 2014

The productivity of wetland rice is constrained by the reduced availability of Sulfur (S) and micronutrients in acid alluvial and laterite soils of West Bengal, India. In an attempt to increase the soil and plant availability of S and micronutrients; the effects of liming1 and soil moisture regimes were assessed on the time changes of soil pH and Eh, soil and plant availability of S and micronutrients. The acid alluvial and laterite soils were deficient in B but had toxic concentration of Fe Mn and AL. Prolonged submergence of soils increased pH and reduced Eh which in turn decreased the availability of S, B, Cu and Zn in these acid soils. Liming of these acid soils significantly reduced the availability of S, Cu, Zn, Fe, Mn and AL but increased B availability, irrespective of soil moisture regime. Continuous flooding during rice growing season decreased the plant availability of S, Cu, Zn and AL but increased that of B, Fe and Mn. Alternate Flooding and Drying (AFD) was more beneficial to rice than continuous flooding as it significantly increased the plant availability of S, B, Cu, Zn and decreased that of Fe and Mn. © 2014 Academic Journals Inc.


Arif M.,Govind Ballabh Pant University of Agriculture & Technology | Chawla S.,Texas Tech University | Zaidi N.W.,Govind Ballabh Pant University of Agriculture & Technology | Rayar J.K.,Govind Ballabh Pant University of Agriculture & Technology | And 2 more authors.
African Journal of Biotechnology | Year: 2012

Detection of Fusarium solani causal agent of wilt and rots in many plant species are difficult if based only on morphological characteristics. Beside this, morphological discrimination requires special skill and the expertise of taxonomists or specialists. To simplify the detection and discrimination of F. solani from other Fusarium species, end-point polymerase chain reaction (PCR) assays were developed. Consensus sequences obtained from multiple alignments of target genes, internal transcribed spacer (ITS), rDNA and transcription elongation factor (TEF-1α), were used to design the primers for rapid detection of genus Fusarium (amplified product 420 and 466) and F. solani (amplified product 658, 595 and 485). BLASTn was used for in silico specificity. No cross reactivity was observed when primers were checked against the near-neighbor plant pathogens. The described primer sets allowed accurate identification and discrimination of genus Fusarium and F. solani. All tests have multiple applications including screening of infected plants, breeding programs and disease diagnosis. © 2012 Academic Journals.

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