National Bureau of Plant Genetic Resources NBPGR

Delhi, India

National Bureau of Plant Genetic Resources NBPGR

Delhi, India
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Teixeira da Silva J.A.,Kagawa University | Rana T.S.,CSIR - Central Electrochemical Research Institute | Narzary D.,Gauhati University | Verma N.,National Bureau of Plant Genetic Resources NBPGR | And 2 more authors.
Scientia Horticulturae | Year: 2013

Pomegranate (Punica granatum L.) is one of the oldest known edible fruit tree species, originating in Central Asia, but with a wide geographical global distribution, reflecting its adaptation to a wide range of climatic conditions. It is important for its nutritional, medicinal and ornamental properties and its high consumption and industrial value. In a bid to better utilize and improve the current genetic resources, there is a need to understand and appreciate studies related to the use, centre of origin and diversity, as well as the characterization, evaluation and conservation, taxonomy and systematics of the genus Punica. In addition to understanding the basic biology of the plant, how biotechnological tools, including cell and tissue culture and micropropagation (i.e. somatic embryogenesis, organogenesis, synthetic seeds, somaclonal variation, mutagenesis, haploidy, and in vitro conservation), genetic transformation and marker technology, have been used to improve pomegranate germplasm are all topics that have been covered in this review. © 2013 Elsevier B.V.

Saxena M.S.,National Institute of Plant Genome Research NIPGR | Bajaj D.,National Institute of Plant Genome Research NIPGR | Das S.,National Institute of Plant Genome Research NIPGR | Kujur A.,National Institute of Plant Genome Research NIPGR | And 5 more authors.
DNA Research | Year: 2014

The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6-39.8% R2 at 4.2-15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea. © 2014 The Author.

Saxena M.S.,National Institute of Plant Genome Research NIPGR | Bajaj D.,National Institute of Plant Genome Research NIPGR | Kujur A.,National Institute of Plant Genome Research NIPGR | Das S.,National Institute of Plant Genome Research NIPGR | And 6 more authors.
PLoS ONE | Year: 2014

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. © 2014 Saxena et al.

Bhatt K.C.,National Bureau of Plant Genetic Resources NBPGR | Saha D.,Indian Central Arid Zone Research Institute
Indian Journal of Natural Products and Resources | Year: 2014

Indigenous knowledge plays a vital role in assessing the trend of evolution of human civilization; hence documentation of local uses of plants and traditional practices developed through use of human intellect now has become an important activity due to implementation of various issues related to Convention on Biological Diversity (CBD), Intellectual Property Rights (IPR), etc. Keeping this in view, an attempt has been made to document indigenous knowledge on fibre extraction of sunnhemp still practiced in some pockets among the tribal communities of Bundelkhand region, reflecting to preserve the age old tradition of farming communities residing there.

Kandan A.,National Bureau of Plant Genetic Resources NBPGR | Kandan A.,Tamil Nadu Agricultural University
Vegetos | Year: 2013

Basal stem rot (BSR) is an important disease caused by Ganoderma lucidum in economically important palms and forest trees. Thirty-five isolates were collected from all over India under different agroclimatic zones from different hosts and these isolates were characterized for cultural, phenotypical and molecular variations. The colony colour range from white to pale yellow or yellow. The aerial mycelium consist mostly thin walled, branched hyphae with clamp connections. Some isolates showed sparse mycelial growth and chlamydospore formation on the PDA medium. Amongst the three liquid media tested for growth of G. lucidum, the potato dextrose broth was significantly superior to other Waksman media and Glucose special media in the order of importance. Lignin degrading enzyme laccase activity was observed higher on fast growing isolates followed by medium and slow growing G. lucidum isolates. Molecular variability studies were also done with six random primers after preliminary screening with thirty random primers to group the G. lucidum isolates. All the slow growing isolates and few medium growing G. lucidum isolates were grouped in cluster A, but all the fast growing isolates were grouped in cluster B to G.

Aravindaram K.,National Bureau of Plant Genetic Resources NBPGR | Wang P.-H.,National Bureau of Plant Genetic Resources NBPGR | Yin S.-Y.,Academia Sinica, Taiwan | Yang N.-S.,Academia Sinica, Taiwan
Gene Therapy | Year: 2014

Dendritic cell (DC)-based vaccine approaches are being actively evaluated for developing immunotherapeutic agents against cancers. In this study, we investigated the use of engineered DCs expressing transgenic tumor-associated antigen hgp100 and the regulatory cytokine interleukin-21, namely DC-hgp100/mIL-21, as a therapeutic vaccine against melanoma. Tumor-bearing mice were injected intratumorally with transgenic DCs followed by three booster injections. Transgenic DC-hgp100/mIL-21 showed significant reduction in primary tumor growth and metastasis compared with DC-hgp100 alone and DC-MIL-21 alone. In vivo depletion of specific immune cell types (CD8+T, CD4 +T and Natural killer (NK)-1.1+cells) effectively blocked the protective effect of this combinational vaccine. In adoptive transfer experiments, a survival rate of nearly 90% was observed at 60 days post-tumor inoculation for the combinational vaccine group. In contrast, all mice in the DC-hgp100 and DC-MIL-21-only groups died within 43-46 days after tumor challenge. Considerably increased levels of interferon (IFN)-γ, tumor necrosis factor (TNF)-, granulocyte macrophage colony-stimulating factor (GM-CSF) and cytotoxic T lymphocytes (CTLs) were detected with the combination vaccine group compared with other individual treatment groups. In comparison with the DC-hgp100 or mIL-21 groups, the combinational DC-hgp100/mIL-21 vaccine also drastically suppressed the myeloid-derived suppressor cells (MDSCs) and T-regulatory (Treg) cell populations. Our findings suggest that a combinational DC- and gene-based hgp100 and mIL-21 vaccine therapy strategy warrants further evaluation as a clinically relevant cancer vaccine approach for human melanoma patients. © 2014 Macmillan Publishers Limited.

PubMed | National Institute of Plant Genome Research NIPGR, National Bureau of Plant Genetic Resources Regional Station and National Bureau of Plant Genetic Resources NBPGR
Type: Journal Article | Journal: DNA research : an international journal for rapid publication of reports on genes and genomes | Year: 2016

The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 ILWC 46 and Pusa 256 ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (Caq(a)PN4.1: 867.8 kb and Caq(a)PN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (Caq(b)PN4.1: 637.5 kb and Caq(b)PN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.

Sharma S.,Guru Nanak Dev University | Singh N.,Guru Nanak Dev University | Virdi A.S.,Guru Nanak Dev University | Rana J.C.,National Bureau of Plant Genetic Resources NBPGR
Food Chemistry | Year: 2014

The grain and flour characteristics of different field pea (FP) accessions were evaluated. Accessions with higher grain weight had less compact structure with a greater proportion of large-sized starch granules. Accessions with higher protein content had lower starch content, blue value and λmax whereas accessions with higher amylose showed higher resistant starch (RS) and final viscosity and lower rapidly digestible starch (RDS). Ca, Zn, K and Fe content vary significantly amongst different accessions and creamish green and white seeds accessions showed higher Fe and Zn content. Yellow coloured accessions (1.36-3.71%) showed lower antioxidant activity as compared to brownish and green coloured accessions (4.06-9.30%). Out of 21 major polypeptides observed (9-100 kDa), 11 showed differential trypsin inhibitory activity (TIA) under non-reducing conditions. Polypeptides of 68, 46, 33 and 22 kDa showed prominent TIA. © 2014 Published by Elsevier Ltd.

Kumar M.N.,Indian National Remote Sensing Centre | Seshasai M.V.R.,Indian National Remote Sensing Centre | Vara Prasad K.S.,National Bureau of Plant Genetic Resources NBPGR | Kamala V.,National Bureau of Plant Genetic Resources NBPGR | And 3 more authors.
International Journal of Remote Sensing | Year: 2011

The reflectance spectrum of species in a hyperspectral data can be modelled as an n-dimensional vector. A spectral angle mapper (SAM) computes the angle between the vectors that is used to discriminate the species. Spectral information divergence (SID) models the data as a probability distribution so that the spectral variability between the bands can be extracted using stochastic measures. The hybrid approach of the SAM and SID is found to be a better discriminator than the SAM or SID on their own. The spectral correlation angle (SCA) is computed as a cosine of the angle of the Pearsonian correlation coefficient between the vectors. The SCA is a better measure than the SAM as it considers only standardized values of the vector rather than the absolute values of the vector. In the present article, we propose a new hybrid measure based on the SCA and the SID. The proposed method has been compared with the hybrid approach of the SID and SAM for discriminating species belonging to Vigna genus using measures such as relative spectral discriminatory power, relative discriminatory probability and relative discriminatory entropy in different spectral regions. Experimental results using the laboratory spectra show that the proposed method gives higher relative discriminatory power in the 400-700 nm spectral region. © 2011 Taylor & Francis.

Banerjee A.,ICAR Research Complex for NEH Region | Dutta R.,ICAR Research Complex for NEH Region | Roy S.,National Bureau of Plant Genetic Resources NBPGR | Ngachan S.V.,ICAR Research Complex for NEH Region
VirusDisease | Year: 2014

The present study confirms the occurrence of Chilli veinal mottle virus (ChiVMV) under the genus Potyvirus in Naga chilli (Capsicum chinense) in Meghalaya based on mechanical transmission assay, transmission electron microscopy, RT-PCR and sequence analysis. This is the first record of Chivmv in Naga chilli in North-East India. © 2013, Indian Virological Society.

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