Directorate of Rice Research

Rajendranagar, India

Directorate of Rice Research

Rajendranagar, India
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Ladha J.K.,International Rice Research Institute | Reddy C.K.,Directorate of Rice Research | Padre A.T.,International Rice Research Institute | van Kessel C.,University of California at Davis
Journal of Environmental Quality | Year: 2011

Soil organic matter (SOM) is essential for sustaining food production and maintaining ecosystem services and is a vital resource base for storing C and N. Th e impact of long-term use of synthetic fertilizer N on SOM, however, has been questioned recently. Here we tested the hypothesis that long-term application of N results in a decrease in SOM. We used data from 135 studies of 114 long-term experiments located at 100 sites throughout the world over time scales of decades under a range of land-management and climate regimes to quantify changes in soil organic carbon (SOC) and soil organic nitrogen (SON). Published data of a total of 917 and 580 observations for SOC and SON, respectively, from control (unfertilized or zero N) and N-fertilized treatments (synthetic, organic, and combination) were analyzed using the SAS mixed model and by meta-analysis. Results demonstrate declines of 7 to 16% in SOC and 7 to 11% in SON with no N amendments. In soils receiving synthetic fertilizer N, the rate of SOM loss decreased. Th e time-fertilizer response ratio, which is based on changes in the paired comparisons, showed average increases of 8 and 12% for SOC and SON, respectively, following the application of synthetic fertilizer N. Addition of organic matter (i.e., manure) increased SOM, on average, by 37%. When cropping systems fl uctuated between fl ooding and drying, SOM decreased more than in continuous dryland or fl ooded systems. Flooded rice (Oryza sativa L.) soils show net accumulations of SOC and SON. Th is work shows a general decline in SOM for all long-term sites, with and without synthetic fertilizer N. However, our analysis also demonstrates that in addition to its role in improving crop productivity, synthetic fertilizer N signifi cantly reduces the rate at which SOM is declining in agricultural soils, worldwide. © 2011 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Rawat N.,Directorate of Rice Research | Neeraja C.N.,Directorate of Rice Research | Nair S.,International Center for Genetic Engineering and Biotechnology | Bentur J.S.,Directorate of Rice Research
Rice | Year: 2012

Background: A major pest of rice, the Asian rice gall midge (Orseolia oryzae Wood-Mason), causes significant yield losses in the rice growing regions throughout Asia. Feeding by the larvae induces susceptible plants to produce nutritive tissue to support growth and development. In order to identify molecular signatures during compatible interactions, genome wide transcriptional profiling was performed using SSH library and microarray technology. Results: Results revealed up-regulation of genes related to primary metabolism, nutrient relocation, cell organization and DNA synthesis. Concomitantly, defense, secondary metabolism and signaling genes were suppressed. Further, real-time PCR validation of a selected set of 20 genes, in three susceptible rice varieties (TN1, Kavya and Suraksha) during the interaction with the respective virulent gall midge biotypes, also revealed variation in gene expression in Kavya as compared to TN1 and Suraksha. Conclusions: These studies showed that virulent insects induced the plants to step up metabolism and transport nutrients to their feeding site and suppressed defense responses. But Kavya rice mounted an elevated defense response during early hours of virulent gall midge infestation, which was over-powered later, resulting in host plant susceptibility. © 2012 Rawat et al; licensee Springer.

Sultan S.M.,National Bureau of Plant Genetic Resources | Subba Rao L.V.,Directorate of Rice Research
International Journal of Conservation Science | Year: 2013

The aim of the present study was to know about past and present cultivation and status of rice landraces in Kashmir province of Indian Himalayan state of Jammu and Kashmir. Tremendous genetic diversity has existed in past in paddy fields throughout Kashmir especially in remote high altitude areas and more than 4 dozen named landraces have been recorded in the literature. Elderly farmers in their sixties and beyond still fondly remember these landraces and often recall quality attributes in many of these genetic resources. Most of the landraces have now disappeared from the local production system and only few are presently being cultivated and that too in a very small area. The reasons as to why farmers lost interest in these genetic resources and why few landraces are still popular in farmer fields have been discussed. Our study has revealed that variability in paddy fields has now been drastically reduced to few high altitude areas where also it is seriously endangered. We argue that collection of well adapted traditional varieties from these 'last remnants of rice genetic diversity' in Kashmir is an important task especially under prevailing uncertain social and climatic conditions to ensure a sustainable environment. 32 germplasm accessions of some landraces have been collected during our survey in these areas. These have been deposited in National Seed Gene Bank at NBPGR, New Delhi for conservation and characterization.

Manimaran P.,Directorate of Rice Research | Ramkumar G.,Directorate of Rice Research | Sakthivel K.,Tamilnadu Agricultural University | Sundaram R.M.,Directorate of Rice Research | And 2 more authors.
Biotechnology Advances | Year: 2011

Genetically modified crops are one of the prudent options for enhancing the production and productivity of crop plants by safeguarding from the losses due to biotic and abiotic stresses. Agrobacterium-mediated and biolistic transformation methods are used to develop transgenic crop plants in which selectable marker genes (SMG) are generally deployed to identify 'true' transformants. The commonly used SMG obtained from prokaryotic sources when employed in transgenic plants pose risks due to their lethal nature during selection process. In the recent past, some non-lethal SMGs have been identified and used for selection of transformants with increased precision and high selection efficiency. Considering the concerns related to bio-safety of the environment, it is desirable to remove the SMG in order to maximize the commercial success through wide adoption and public acceptance of genetically modified (GM) food crops. In this review, we examine the availability, and the suitability of wide range of non-lethal selection markers and elimination of SMG methods to develop marker-free transgenics for achieving global food security. As the strategies for marker-free plants are still in proof-of-concept stage, adaptation of new genomics tools for identification of novel non-lethal marker systems and its application for developing marker-free transgenics would further strengthen the crop improvement program. © 2011 Elsevier Inc.

Manimaran P.,Directorate of Rice Research
GM crops | Year: 2011

Bacillus thuringiensis (Bt), a gram positive soil bacteria was first identified and named by Japanese microbiologist Shigetane Ishiwata in 1901. During sporulation Bt produces proteinaceous parasporal crystal proteins called δ-endotoxins, or Cry proteins, which are insecticidal. Numerous Cry proteins have been isolated and characterized from different Bt strains with activity against insects, mites and nematodes. Sprayable formulations containing these Cry proteins as active ingredients have contributed significantly in the field of insect pest management. Since the first cloning of cry genes from Bt,1 scientists have successively demonstrated that plants could be genetically engineered to express these cry genes for the control of dreadful insect pests. Eventually, the first transgenic crop expressing Btcry1Ac gene in cotton was approved in 1996 for commercial cultivation in the USA to manage bollworms.

Andow D.A.,University of Minnesota | Bentur J.S.,Directorate of Rice Research
Entomologia Experimentalis et Applicata | Year: 2010

Monitoring changes in rare, recessive allele frequencies in natural populations can be accomplished using pedigreed individuals sampled from these populations. A pedigree keeps track of and limits the mating of sampled individuals, to preserve information about the genotype of the sampled individual in the phenotypes of its descendents. To estimate allele frequencies in a natural population using pedigreed crosses, four relations must be specified: a method to determine whether the pedigreed line carries the desired allele; a method to estimate the phenotypic frequency of the trait among the pedigreed lines and a credibility limit for the estimate; (the genetic relation between the phenotype frequency among the lines and the allele frequency in the natural population; and a method to estimate the probability that the first method did not detect the trait, assuming that the allele was present in the sampled individual. Knowledge about the segregation patterns of the allele enables specification of andBayesian statistics were used to estimate the phenotypic frequency of the trait among the pedigreed lines. The method determining whether the pedigreed line carries the desired allele will vary with the species and trait of concern. We focused on monitoring of vGm1, a recessive autosomal allele, and vGm2, a recessive sex-linked allele, which provide virulence against certain rice resistance genes in rice gall midge, Orseolia oryzae (Wood-Mason) (Diptera: Cecidomyiidae). We show how three pedigrees can be used to estimate these allele frequencies. An F1 field screen challenges the F1 offspring of sampled individuals on the rice differentials. A P1 test-cross mates the sampled individual with a homozygous lab colony for the allele of interest, and evaluates their offspring on the rice differentials. A conditional F1 test-cross takes the offspring from pedigrees that were negative in an F1 field screen, and test-crosses these offspring with the homozygous laboratory colony. We also indicate how to test for independent assortment when a double (or multiple) homozygote laboratory colony is used in a test-cross, how to test for differences among samples, and how to pool data to produce a single estimate based on a larger number of pedigreed lines. These methods may encourage the development of a variety of pedigreed monitoring strategies that could improve and prolong the use of scarce plant resistance alleles in rice and other plants. © 2010 The Authors. Journal compilation © 2010 The Netherlands Entomological Society.

Himabindu K.,Directorate of Rice Research | Suneetha K.,Directorate of Rice Research | Sama V.S.A.K.,Directorate of Rice Research | Bentur J.S.,Directorate of Rice Research
Euphytica | Year: 2010

Gall midge is the third most destructive insect pests of rice after stem borers and planthoppers. Host plant resistance has been recognized as the most effective and economic, means for gall midge management. With the characterization of a new gall midge biotype (GMB) 4M, unique feature of gall midge resistance in the breeding line CR57-MR1523 was highlighted. Multi-location evaluation of F3 families derived from the cross TN1 × CR57-MR1523 against different gall midge biotypes helped to identify a new dominant gene conferring resistance against GMB4. This gene has been designated as Gm11t. Though CR57-MR1523 has been extensively used in breeding gall midge resistant rice varieties like Suraksha, neither the genetics of resistance nor chromosomal location of the resistance gene(s) is known. In the present study we have tagged and mapped the new gall midge resistance gene, Gm11t, on chromosome 12, using SSR markers. To map the gene locus, 466 F10 generation Recurrent Inbred Lines (RILs), from the cross of TN1 × CR57-MR1523 were used. Of the 471 SSR markers spread across the rice genome, 56 markers showed polymorphism and were used to screen a subset of the mapping population consisting of 10 resistant (R) and 10 susceptible (S) F10 RILs. Six SSR markers, RM28706, RM235, RM17, RM28784, RM28574 and RM28564 on chromosome 12 were initially found to be associated with resistance and susceptibility. Based on the linkage analysis in selected 158 RILs, we were able to map the locus between two flanking SSR markers, RM28574 and RM28706, on chromosome 12 within 4.4 and 3.8 cM, respectively. Further, two NILs with 99% genetic similarity, were identified from the RILs which differed in gall midge resistance. The tightly linked flanking SSR markers will facilitate marker-assisted gene pyramiding and map-based cloning of the resistant gene. NILs would be valuable materials for functional analysis of the identified candidate gene. © 2009 Springer Science+Business Media B.V.

Anuradha K.,Directorate of Rice Research | Agarwal S.,Directorate of Rice Research | Rao Y.V.,Directorate of Rice Research | Rao K.V.,Directorate of Rice Research | And 2 more authors.
Gene | Year: 2012

Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. 168 F 7 RILs derived from Madhukar×Swarna were used to map QTLs for iron and zinc concentrations in unpolished rice grains. Iron ranged from 0.2 to 224ppm and zinc ranged from 0.4 to 104ppm. Genome wide mapping using 101 SSRs and 9 gene specific markers showed 5 QTLs on chromosomes 1, 3, 5, 7 and 12 significantly linked to iron, zinc or both. In all, 14 QTLs were identified for these two traits. QTLs for iron were co-located with QTLs for zinc on chromosomes 7 and 12. In all, ten candidate genes known for iron and zinc homeostasis underlie 12 of the 14 QTLs. Another 6 candidate genes were close to QTLs on chromosomes 3, 5 and 7. Thus the high priority candidate genes for high Fe and Zn in seeds are OsYSL1 and OsMTP1 for iron, OsARD2, OsIRT1, OsNAS1, OsNAS2 for zinc and OsNAS3, OsNRAMP1, Heavy metal ion transport and APRT for both iron and zinc together based on our genetic mapping studies as these genes strictly underlie QTLs. Several elite lines with high Fe, high Zn and both were identified. © 2012 Elsevier B.V.

Swamy B.P.M.,Directorate of Rice Research | Swamy B.P.M.,International Rice Research Institute | Sarla N.,Directorate of Rice Research
Plant Molecular Biology Reporter | Year: 2011

Several reports on mapping and introgression of quantitative trait loci (QTLs) for yield and related traits from wild species showed their importance in yield improvement. The aim of this study was to locate common major effect, consistent and precise yield QTLs across the wild species of rice by applying genome-wide QTL meta-analysis for their use in marker-aided selection (MAS) and candidate gene identification. Seventy-six yield QTLs reported in 11 studies involving inter-specific crosses were projected on a consensus map consisting of 699 markers. The integration of 11 maps resulted in a consensuses map of 1,676 cM. The number of markers ranged from 32 on chromosome 12 to 96 on chromosome 1. The order of markers between consensus map and original map was generally consistent. Meta-analysis of 68 yield QTLs resulted in 23 independent meta-QTLs on ten different chromosomes. Eight meta-QTLs were less than 1.3 Mb. The smallest confidence interval of a meta-QTL (MQTL) was 179.6 kb. Four MQTLs were around 500 kb and two of these correspond to a reasonably small genetic distance 4.6 and 5.2 cM, respectively, and suitable for MAS. MQTL8. 2 was 326-kb long with a 35-cM interval indicating it was in a recombination hot spot and suitable for fine mapping. Our results demonstrate the narrowing down of initial yield QTLs by Meta-analysis and thus enabling short listing of QTLs worthy of MAS or fine mapping. The candidate genes shortlisted are useful in validating their function either by loss of function or over expression. © 2010 Springer-Verlag.

Kumar G.R.,Directorate of Rice Research | Sakthivel K.,Directorate of Rice Research | Sundaram R.M.,Directorate of Rice Research | Neeraja C.N.,Directorate of Rice Research | And 4 more authors.
Biotechnology Advances | Year: 2010

Enormous sequence information is available in public databases as a result of sequencing of diverse crop genomes. It is important to use this genomic information for the identification and isolation of novel and superior alleles of agronomically important genes from crop gene pools to suitably deploy for the development of improved cultivars. Allele mining is a promising approach to dissect naturally occurring allelic variation at candidate genes controlling key agronomic traits which has potential applications in crop improvement programs. It helps in tracing the evolution of alleles, identification of new haplotypes and development of allele-specific markers for use in marker-assisted selection. Realizing the immense potential of allele mining, concerted allele mining efforts are underway in many international crop research institutes. This review examines the concepts, approaches and applications of allele mining along with the challenges associated while emphasizing the need for more refined 'mining' strategies for accelerating the process of allele discovery and its utilization in molecular breeding. © 2010 Elsevier Inc.

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