Trilochan Mohapatra

Central Rice Research Institute, Каттаке, Odisha, India

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Publications (90)274.3 Total impact

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    ABSTRACT: Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
    DNA Research 01/2015; DOI:10.1093/dnares/dsu046 · 4.43 Impact Factor
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    ABSTRACT: Halomonas salina strain CIFRI1 is an extremely salt-stress-tolerant bacterium isolated from the salt crystals of the east coast of India. Here we report the annotated 3.45-Mb draft genome sequence of strain CIFRI1 having 86 contigs with 3,139 protein coding loci, including 62 RNA genes.
    Genome Announcements 01/2015; 3(1):e01321-14. DOI:10.1128/genomeA.01321-14
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    ABSTRACT: Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize using a high-density marker set under water stress. Out of 61 significant SNPs (11 were false-discovery-rate-corrected associations), identified across agronomic traits, models, and locations by subjecting the accessions to water stress at flowering stage, 48% were associated with drought-tolerant genes. Maize gene models revealed that SNPs mapped for agronomic traits were in fact associated with number of functional traits as follows: stomatal closure, 28; flowering, 15; root development, 5; detoxification, 4; and reduced water potential, 2. Interactions of these SNPS through the functional traits could lead to drought tolerance. The SNPs associated with ABA-dependent signalling pathways played a major role in the plant's response to stress by regulating a series of functions including flowering, root development, auxin metabolism, guard cell functions, and scavenging reactive oxygen species (ROS). ABA signalling genes regulate flowering through epigenetic changes in stress-responsive genes. ROS generated by ABA signalling are reduced by the interplay between ethylene, ABA, and detoxification signalling transductions. Integration of ABA-signalling genes with auxin-inducible genes regulates root development which in turn, maintains the water balance by regulating electrochemical gradient in plant. Several genes are directly or indirectly involved in the functioning of agronomic traits related to water stress. Genes involved in these crucial biological functions interacted significantly in order to maintain the primary as well as exclusive functions related to coping with water stress. SNPs associated with drought-tolerant genes involved in strategic biological functions will be useful to understand the mechanisms of drought tolerance in subtropical maize.
    BMC Genomics 12/2014; 15(1):1182. DOI:10.1186/1471-2164-15-1182 · 4.04 Impact Factor
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    ABSTRACT: Determination of maintainer and restorer status of germplasm collections is a prerequisite for their use in development of hybrid employing CMS system. In the present study, restorer and maintainer status of 372 Indian genotypes was determined using fertility restoration (Rf) linked microsatellite marker RM6100. A total of seven alleles for the marker locus, including four novel and three known, were identified in the study material. Maximum frequency was observed for the 144bp allele (44.89%) while minimum frequency was for 138bp allele (0.27%). Though most of the novel alleles were minor, occurring in less than 5% frequency, cumulatively they accounted for 9.2% frequency in the study material. Of the known alleles, which were found in 90.8% (338 genotypes) of the tested rice genotypes, 36% had maintainer type allele (132bp allele similar to Pusa 6B) while the rest had restorer type (144 or 150 bp) alleles. The spikelet fertility data generated on a subset of the study material agreed well with the established associations for the already reported alleles. Of the novel alleles, two (141 and 147 bp) were represented in the spikelet fertility dataset, both of which restored fertility, though their representation was low. This allelic information would be useful in selection of parental lines for development of hybrids in rice.
    Indian Journal of Genetics and Plant Breeding 12/2014; 74(4):409-413. DOI:10.5958/0975-6906.2014.00863.3 · 0.19 Impact Factor
  • 11/2014; 80(1):163. DOI:10.16943/ptinsa/2014/v80i1/55094
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    ABSTRACT: Dwarf plant height and tillering ability are two of the most important agronomic traits that determine the plant architecture, and have profound influence on grain yield in rice. To understand the molecular mechanism controlling these two traits, an EMS-induced recessive dwarf and increased tillering1 (dit1) mutant was characterized. The mutant showed proportionate reduction in each internode as compared to wild type revealing that it belonged to the category of dn-type of dwarf mutants. Besides, exogenous application of GA3 and 24-epibrassinolide, did not have any effect on the phenotype of the mutant. The gene was mapped on the long arm of chromosome 4, identified through positional candidate approach and verified by cosegregation analysis. It was found to encode carotenoid cleavage dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant, and thus formation of a truncated protein, unlike amino acid substitution event in htd1. The new allele will facilitate further functional characterization of this gene, which may lead to unfolding of newer signalling pathways involving plant development and architecture.. 2014 A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice. J. Genet. 93, xx–xx]
    Journal of Genetics 08/2014; 93(2). DOI:10.1007/s12041-014-0389-5 · 1.01 Impact Factor
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    ABSTRACT: Moth bean (Vigna aconitifolia (Jacq.) Marechal), an important grain-legume crop grown in hot desert regions of Thar, under scorching sun rays, was investigated for heat tolerance at molecular level. In the present study, we constructed a forward suppression subtractive hybridization (SSH) cDNA library of heat tolerant genotype RMO-40 to identify genes expressing under delayed response to elevated temperature. Heat induction was carried out by exposing 14-day-old seedlings to elevated temperature of 42 °C for 30 min. A total of 125 unigenes (33 contigs and 92 singletons) were derived by cluster assembly and sequence alignment of 200 ESTs; out of 125 unigenes, 21 (16 %) were found to be novel to moth bean. Gene ontology functional classification terms were retrieved for 98 (78.4 %) unigenes of which 73 (58.4 %) ESTs were functionally annotated (GO consensus) where 19 unigenes were annotated with 11 enzyme commission (EC) codes and were mapped to 25 different KEGG pathways. We have identified a majority of heat-shock proteins (constituting 35 % of the present library) aiding heat stress tolerance to moth bean. An expression level of 22 ESTs generated from the above SSH cDNA library was studied through semiquantitative RT-PCR assay simultaneously under 5 and 30 min of heat stress at 42 °C.
    Applied Biochemistry and Biotechnology 06/2014; 173(8). DOI:10.1007/s12010-014-1011-2 · 1.69 Impact Factor
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    ABSTRACT: Rice (Oryza sativa) is the staple food of more than half of the world‟s population. The International Rice Genome Sequencing Project (IRGSP) generated very high quality sequences that were used to predict the number and type of genes, and the non-genic regions containing repeats and mobile genetic elements. Concerted efforts are required to understand the function of individual genes, and their interactions among themselves as well as with environment in relation to variation in traits for a directed genetic manipulation of this important crop for the benefit of the mankind. One of the approaches to determine functions of genes employs natural mutants available in the germplasm or those induced by physical, chemical or biological agents. Mutants facilitate unveiling the causal relationships between coding/regulatory sequences and plant performance, and also cloning of the corresponding genes. Therefore a number of international efforts are underway for generation, collection and characterization of mutants for providing technological platform for functional genomics. In an indigenous effort funded by the Department of Biotechnology (DBT), Government of India, a set of 22, 292 EMS mutagenised lines have been generated in the background of an upland rice variety Nagina-22. EMS was chosen since it gives high point mutation densities by base substitution either in the transcribed regions or in the regulatory elements of a gene that might alter gene function leading to creation of a series of alleles of a gene. The uniqueness of this national effort is phenotyping for a range of traits. Elaborate phenotyping by different partner institutions has led to identification of mutants for plant growth and architecture, flowering, maturity, grain number, shape and size, yield, resistance to blast and bacterial leaf blight diseases, phosphorus use efficiency, and tolerance to herbicide, drought and salinity. Inheritance of selected mutants has been carried out using F2 populations developed from the cross of the mutants with wild type Nagina22. Mutant loci for seed size and plant height have been mapped using SSR markers on chromosomes 5 and 4, respectively. Transcriptome profiling using rice microarrays has revealed altered expression of only a limited set of genes in these mutants. In contrast, hundreds of genes were found differentially regulated in a gain-offunction mutant having higher level of tolerance to moisture deficit stress. This mutant also showed longer roots and more of partially closed stomata under stress. Two of the mutants, one for plant height and the other for seed size were characterized in detail. The dwarf mutant showed proportionate reduction in each of the internodes as compared to wild type. The gene, identified through positional candidate approach and verified by co-segregation analysis, was found to encode Carotenoid Cleavage Dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant. The short grain mutant had shorter, narrower, and lesser cells in as compared to the wild type. The candidate gene region on the short arm of chromosome 5 includes srs3, which was already reported to control grain size in rice. It encodes kinesin 13 family proteins with a major role in mediation of microtubule organisation during mitosis. Sequencing of 11kb srs3 gene region revealed a substitution of C to T in the coding region of the mutant leading to creation of a stop codon. Sequencing of the kinesin motor domain region of the gene did not reveal presence of this mutation in 96 germplasm lines having significant grain size variation. Results suggested utility of the mutant resource in rice functional genomics including discovery of new genes for traits agronomic importance and allele mining.
    4th NGGIBCI, ICRISAT, Hyderabad, India; 02/2014
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    ABSTRACT: Development of a representative and well-diversified core with minimum duplicate accessions and maximum diversity from a larger population of germplasm is highly essential for breeders involved in crop improvement programmes. Most of the existing methodologies for the identification of a core set are either based on qualitative or quantitative data. In this study, an approach to the identification of a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data was proposed. For this purpose, six different combined distance measures, three for quantitative data and two for qualitative data, were proposed and evaluated. The combined distance matrices were used as inputs to seven different clustering procedures for classifying the population of germplasm into homogeneous groups. Subsequently, an optimum number of clusters based on all clustering methodologies using different combined distance measures were identified on a consensus basis. Average cluster robustness values across all the identified optimum number of clusters under each clustering methodology were calculated. Overall, three different allocation methods were applied to sample the accessions that were selected from the clusters identified under each clustering methodology, with the highest average cluster robustness value being used to formulate a core set. Furthermore, an index was proposed for the evaluation of diversity in the core set. The results reveal that the combined distance measure A 1 B 2 – the distance based on the average of the range-standardized absolute difference for quantitative data with the rescaled distance based on the average absolute difference for qualitative data – from which three clusters that were identified by using the k-means clustering algorithm along with the proportional allocation method was suitable for the identification of a core set from a collection of rice germplasm.
    Plant Genetic Resources 01/2014; DOI:10.1017/S1479262114000732 · 1.06 Impact Factor
  • Journal of Genetics 01/2014; 93(1):e8-e16. DOI:10.1007/s12041-014-0333-8 · 0.88 Impact Factor
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    ABSTRACT: Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome. We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200-300 Kb) at r2 <= 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36. The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.
    BMC Genomics 12/2013; 14(1):877. DOI:10.1186/1471-2164-14-877 · 4.04 Impact Factor
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    ABSTRACT: Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-á-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.
    Journal of Genetics 12/2013; 92(3):545-57. DOI:10.1007/s12041-013-0312-5 · 0.88 Impact Factor
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    ABSTRACT: Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.
    Euphytica 12/2013; DOI:10.1007/s10681-013-0964-5 · 1.69 Impact Factor
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    ABSTRACT: The present investigation was carried out with an objective of evaluating genetic diversity in brinjal (Solanum melongena) using DNA markers. A total of 38 brinjal accessions including one wild-species, Solanum sisymbrifolium were characterized using random amplified polymorphic DNA (RAP D) and amplified fragment length polymorphism (AFLP) techniques. Out of 45 primers employed to generate RAPD profiles, reproducible patterns were obtained with 32 primers and 30 (93.7%) of these detected polymorphism. A total of 149 bands were obtained, out of which 108 (72.4%) were polymorphic. AFLP analysis was carried out using four primer combinations. Each of these primers was highly polymorphic. Out of 253 fragments amplified from these four primer combinations, 237 (93.6%) were polymorphic. The extent of pair-wise similarity ranged from 0.264 to 0.946 with a mean of 0.787 in RAPD, in contrast to a range of 0.103 to 0.847 with a mean of 0.434 in AFLP. The wild species clustered separately from the brinjal genotypes. In the dendrogram constructed separately using RAPD and AFLP markers, the brinjal genotypes were grouped into clusters and sub-clusters, and the varieties released by IARI remained together on both the dendrograms. All the 30 RAPD primers in combination and each of the four primer pairs in AFLP could distinguish the brinjal accessions from each other. AFLP was thus found to be more efficient than RAPD in estimation of genetic diversity and differentiation of varieties in brinjal.
    Journal of Plant Biochemistry and Biotechnology 01/2013; 15(1). DOI:10.1007/BF03321895 · 0.81 Impact Factor
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    ABSTRACT: Plant height and flowering time are two of the important traits that affect plant architecture. Efforts were made in this study to characterize morphologically the-EMS-induced dwarf and early flowering mutants of rice variety Nagina22 and to study their mode of inheritance. Nine true breeding mutants generated earlier by EMS treatment were analysed for differences in their phenotypic characteristics recorded according to the national guidelines for Distinctness, Uniformity and Stability (DUS). The mutants exhibited variation from Nagina22 for maximum of 11 DUS characteristics to a minimum of 4 DUS descriptors, while retaining majority of the wild type features. Plant height of the dwarf mutants ranged from 69 to 101cm, while tiller number was in the range of 9 to 60. The early flowering mutants were weak in their plant stature, but flowered approximately 20-25 days earlier than Nagina22. Significant correlation among various traits of the selected mutants was observed. The mutant traits exhibited monogenic inheritance giving 3:1 phenotypic segregation ratio in F2 generation. These mutants have potential usage in functional analysis of the traits and in rice improvement programs.
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    ABSTRACT: Genetic improvement of sugar content in sugarcane would benefit from the availability of sufficient DNA markers and a genetic map. Genetic linkage maps were constructed to identify quantitative trait loci (QTLs) for seedling brix (SB), brix (B), sucrose percent in juice (SUC), stalk number (SN), stalk length (SL), stalk diameter (SD), internodes (INT), number of green leaves (NGL), at three crop cycles across seven environments in a segregating population with 207 individuals derived from a bi-parental cross of sugarcane elite cultivars. Linkage analysis led to the construction of eight linkage groups (LGs) for Co86011 and sixteen LGs for CoH70. The combined length of the two linkage maps was 2606.77 cM distributed over 24 LGs. 31 QTLs were identified: 2 for SB, 7 for B, 6 for SUC, 4 for SN, 1 for SL, 3 for SD, 6 for INT and 2 for NGL at LOD scores ranging from 2.69 to 4.75. 7 QTLs (22 %) had stable effect across crop year and locations. Markers from parents were found to be associated with both positive and negative effect on all of the traits analyzed. The most important QTLs intervals identified in this study using single-dose marker, were qB2, qSUC2, qINT2 and qB2, qSUC2, qSL2, qINT2 located between SSR markers UGSM31548 and UGSM31649. These QTLs could be put into use in marker assisted breeding.
    Euphytica 12/2012; 191(3). DOI:10.1007/s10681-012-0841-7 · 1.69 Impact Factor
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    ABSTRACT: Moth bean ( Vigna aconitifolia (Jacq.) Marechal) is an important grain legume crop grown in rain fed areas of hot desert regions of Thar, India, under scorching sun rays with very little supplementation of water. An SSH cDNA library was generated from leaf tissues of V. aconitifolia var. RMO-40 exposed to an elevated temperature of 42 °C for 5 min to identify early-induced genes. A total of 488 unigenes (114 contigs and 374 singletons) were derived by cluster assembly and sequence alignment of 738 ESTs; out of 206 ESTs (28%) of unknown proteins, 160 ESTs (14%) were found to be novel to moth bean. Only 578 ESTs (78%) showed significant BLASTX similarity (<1 × 10(-6)) in the NCBI non-redundant database. Gene ontology functional classification terms were retrieved for 479 (65%) sequences, and 339 sequences were annotated with 165 EC codes and mapped to 68 different KEGG pathways. Four hundred and fifty-two ESTs were further annotated with InterProScan (IPS), and no IPS was assigned to 153 ESTs. In addition, the expression level of 27 ESTs in response to heat stress was evaluated through semiquantitative RT-PCR assay. Approximately 20 different signaling genes and 16 different transcription factors have been shown to be associated with heat stress in moth bean for the first time.
    Genome 11/2012; 55(11):783-96. DOI:10.1139/g2012-064 · 1.56 Impact Factor
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    ABSTRACT: Background Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.
    BMC Genomics 08/2012; 13(1):426. DOI:10.1186/1471-2164-13-426 · 4.04 Impact Factor

Publication Stats

2k Citations
274.30 Total Impact Points


  • 2012–2015
    • Central Rice Research Institute
      Каттаке, Odisha, India
    • Chaudhary Charan Singh University
      • Department of Genetics and Plant Breeding
      Merath, Uttar Pradesh, India
  • 2014
    • Swami Keshwanand Rajasthan Agricultural University - Bikaner
      Bîkâner, Rajasthan, India
  • 2013
    • Punjab Agricultural University
      Ludhiana, Punjab, India
  • 2004–2013
    • Indian Agricultural Research Institute
      • • National Research Centre on Plant Biotechnology (NRCPB)
      • • Division of Genetics
      • • Division of Vegetable Science
      New Dilli, NCT, India
  • 2002–2013
    • National Research Centre on Plant Biotechnology
      Old Delhi, NCT, India
  • 2010
    • Jaypee University of Information Technology
      Solon, Himachal Pradesh, India
  • 2008
    • National Bureau of Plant Genetic Resources
      New Dilli, NCT, India
  • 2006
    • Central Research Institute for Jute and Allied Fibres
      Chennai, Tamil Nadu, India
  • 2005
    • Sugarcane Breeding Institute
      Koyambattūr, Tamil Nadu, India