IFPRI - NAIP - National Genomic Resources Repository - K C Bansal

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National Agricultural Innovation Project (NAIP), ICAR and the International Food Policy Research Institute (IFPRI) organized a two day workshop on ‘Impact of capacity building programs under NAIP’ on June 6-7, 2014 at AP Shinde Auditorium, NASC Complex, Pusa, New Delhi. The main purpose of the workshop was to present and discuss the findings of the impact evaluation study on capacity building programs under NAIP by IFPRI. The scientists from ICAR and agricultural universities were sent abroad to receive training in specialized research techniques. Post-training, scientists were expected to work on collaborative projects within the ICAR, which would further enrich their knowledge and skills, expand their research network and stimulate them’ to improve their productivity, creativity and quality of their research. The ICAR commissioned with IFPRI (International Food Policy Research Institute) to undertake an evaluation of these capacity building programs under NAIP in July 2012. The workshop shared the findings on the impact of capacity building programs under NAIP and evolve strategies for future capacity building programs

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IFPRI - NAIP - National Genomic Resources Repository - K C Bansal

  1. 1. K.C. Bansal National Bureau of Plant Genetic Resources Pusa Campus, New Delhi – 110 012 www.nbpgr.ernet.in National Genomic Resources Repository
  2. 2. PGR Utilization and Preparedness for future PGR Collection, Conservation, Exchange and Quarantine PGR Informatics & IP Protection Genomics and National Genomic Resources Repository PGR Characterization and Evaluation (phenotypic and genotypic) NBPGR major activities
  3. 3. Developmentandconservationof genomicresources Collection, validation and conservation of genomic resources Basic and supportive research in genomics and bioinformatics Gene discovery and allele mining for specific traits (biotic & abiotic stresses, quality) from plant genetic resources Development and validation of new molecular marker systems in priority crops and molecular diagnostics for transgenes National Genomic Resources Repository
  4. 4. Plant Genetic Resources / FirstView Article pp 1-10 Copyright © NIAB 2014 DOI: Published online: 20 February 2014 Research Article Next-generation genebanking: plant genetic resources management and utilization in the sequencing era Rob van Treurena1 c1 and Theo J. L. van Hintuma1 a1 Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, PO Box 16, NL-6700 AA Wageningen, The Netherlands DNA sequencing as an integral component for generation and conservation of plant genetic resources
  5. 5. Why conserve genomic resources? • Current research generates a lot of genomic resources ▫ Routine cloning experiments ▫ Genome sequencing projects • The genome resources are indispensable tools for post- genomic research ▫ Physiological and morphological characterization of a species, functional analysis of genes, comparative genomics and plant and animal breeding • It is necessary to maintain an efficient system for conservation and management of genomic resources
  6. 6. Salient Points I. Types of genomic resources II. Modalities of operation III. Documentation and Database IV. Infrastructure, space and human resources V. Storage methodologies VI. Research component VII. Policy issues
  7. 7. I. Types of genomic resources • Cloning vectors, expression vectors, binary vectors, RFLP probes • Cloned genes, promoters fused to reporter genes • Sub-genomic, cDNA , EST, repeat enriched libraries • BAC, YAC, PAC clone set from sequencing projects • Genomic, mitochondrial or chloroplast DNA • Cloned DNA from wild and weedy species produced exclusively for the repository
  8. 8. Plant DNA banks world-wide Genomic DNA ONLY Plant DNA Bank in Korea (PDBK) Graduate School of Biotechnology, Korea University, Seoul, Korea. Royal Botanic Gardens Kew DNA Bank 22,000 samples of plant genomic DNA, all stored at -80°C. The Australian Plant DNA Bank Australian native and other important crop plant species; also transgenic organisms developed through research DNA Banking at the Missouri Botanical Garden To promote phylogenetic research while easing the demand on herbarium specimens DNA Bank Brazilian Flora Species Rio de Janeiro Botanical Garden, Brazil DNA Bank at Kirstenbosch The Leslie Hill Molecular Systematics Laboratory at Kirstenbosch, South Africa Bank at the National Herbarium Nederland For systematic treatments (Flora) in the National Herbarium of Netherland cDNA clones, RFLP markers, PAC/BAC clones and YAC filters NIAS DNA Bank For maintaining DNA materials and information that has been accumulated as part of the genome projects such as the Rice Genome Research Program (RGP)
  9. 9. Other DNA banks world-wide …1 Riken Bio-resource Center DNA Bank Isolation, collection, preservation and distribution of cloned DNA and gene libraries (cDNA and genome libraries) from human and other mammalian cells and from microorganisms (vectors and hosts). The RIKEN DNA Bank undertakes research to ensure the authenticity of the materials in the collection and to improve and standardize the methods of characterization, maintenance, preservation and distribution of genetic resources San Francisco Zoo DNA Bank The Zoo maintains a bank with hair, feather or other tissue samples The Frozen Ark The mission of the Frozen Ark Project is to collect, preserve and store DNA and viable cells from animals in danger of extinction The Ambrose Monell Cryo Collection, New York In the American Museum of Natural History; approximately one million frozen tissue samples representing the DNA of a wide range of species
  10. 10. Other DNA banks world-wide …2 The Animal Gene Storage Resource Centre of Australia To preserve reproductive cells, (semen, embryos, ovaries et cetera) and genetic material in a frozen state, at - 196°C in liquid nitrogen Conservation Genome Resource Bank for Korean Wildlife Tissues, blood, DNA, somatic and germ cells, and semen from mammals, birds, amphibians, and reptiles including endangered species of Korea San Diego Zoo Conservation by DNA Barcoding for identifying species from unrecognizable samples of blood, bone, meat, hair, feathers, or feces. Austrian DNA Bank for Farm Animal Genetic Resources To secure preservation-worthy farm animal races National Plant, Fungi and Animal DNA Bank, Poland Initiative of five Polish scientific institutions using DNA barcoding for researching as well as for many practical purposes
  11. 11. Source of genomic resources A. Mega-projects i. Genome sequencing ii. Allele mining and bio-prospecting B. On-going projects in NARS on gene isolation/cloning/ expression, etc. C. On-going projects in CSIR/DBT/University/others D. Material originating outside India
  12. 12. II. Modalities of operation i. Submission form and MTA ii. Request form and MTA iii. Research output form iv. Quality and quantity of the material v. Minimum data accompanying the material
  13. 13. i. Submission form and MTA II. Modalities
  14. 14. ii. Request form and MTA II. Modalities
  15. 15. iii. Research output form II. Modalities
  16. 16. iv. Quality and quantity of the material • Genomic DNA ▫ A260/A280=1.7-2.0; A260/A230>1.5 ▫ Agarose gel electrophoresis photo with  ▫ >50ng/, > 10, 10 replications • Library ▫ <5% empty vectors ▫ Free from all sorts of contaminations ▫ 384 well plate (BACs), 96 well plate (cDNA, shotgun, EST) ▫ 1 library  192 plates or  one filter (36,884 spots) ▫ Amplified library  1010 pfu/ml; at least 106 pfu/ml II. Modalities
  17. 17. v. Accompanying data II. Modalities Genomic DNA Name of the plant Genus species common name Family TaxID Genebank Accn. No. Extraction procedure DNA dissolved in Concentration (ng per microL) Importance of the plant Reasons for the choice of the variety/landrace/accession Source of the biological material Clear from MTA for plant material? Any ITK Any publications? (pl. attach a copy) Cloned DNA Name of the plant common name Family TaxID Genebank Accn. No. Vector, antibiotic marker Cloning sites, fragment size (range) Bacterial strain, transformation method Culture conditions, Storage conditions Importance of the plant Reasons for the choice of the variety/landrace/accession Source of the biological material Clear from MTA for plant material? Any ITK Any publications? (pl. attach a copy)
  18. 18. RT 4°C -20°C -80°C -196°C Research output form MTA Request form Information Accession No. Submission form Agreement, benefit sharing MTA Reposition (quality, quantity, purity, data) Distribution Aliquot Replicate Recipient Donor
  19. 19. Intellectual property and legal issues • Material transfer agreement (MTA) by the beneficiary prior to the shipment • The MTAs regulate the intellectual property rights (IPR) of the requested material and related information, the conditions of its use and distribution to third parties, as well as benefit sharing • Existing MTAs can be specifically designed for the exchange of genomic resources, if desired • DNA exchange through MTA: CATIE, Costa Rica; NIAS, Japan, the Missouri Botanical Garden, USA; and the Royal Botanic Gardens, Kew
  20. 20. Genomic resources bank is a reality and a need of the hour • The accelerated use of genomic technology in biological research has fueled the need to establish genomic resources bank • Short-term collections, where newly obtained material is characterized and distributed based on current goals • Long-term collections, where samples are placed in safe-keeping
  21. 21. Facilities for research and generation of genomic resources at NBPGR
  22. 22. Status of Genomic Resources holdings at NBPGR S. No. Category 2010 -11 2011 -12 2012 -13 2013 -14 31.5. 2014 1 DNA Fingerprinting 0 20 20 66 2281 2 Genomic Resources A Markers 68 0 4247 40 4355 B Genomic DNA Varieties 0 55 90 375 3692 C BAC Clones 0 0 0 0 386000 D Trait/gene specific clones 0 0 0 0 48 3 Utilization of Genomic resources- markers 0 1256 40 13 1269
  23. 23. Genomics Platform: Objectives  Generate genomic resources for every prioritised crop  Develop computational biology tools  Advance plant systems biology  Translate basic discovery to the field  Capacity building, HRD and trainings  Develop plant genome database  Strengthen Repository of Genomic Resources
  24. 24. PGR conservation at NBPGR NABG Genomics Platform Genomics Resources Repository Phenomics facility Allele mining Other genomics projects Marker assisted genetic improvement
  25. 25. Repository and Utilization platform High throughput Genomics platform High throughput Transcriptomics platform Bioinformatics platform National Genomic Resources Repository Generation of genomic resources by de novo sequencing, targeted re-sequencing of indigenous genetic resources Gene discovery, allele mining and bio- prospecting in indigenous genetic resources Single window system for assemblage, conservation, exchange and IPR issues Computational systems, tools and expertise for assembly, analysis, mining, comparative studies
  26. 26. Utilisation of Genomic Resources CROP IMPROVEMENT  Markers: Molecular Breeding  Genes: Transgenic development  Allele mining and mutant generation  Assessing plant diversity  Comparative genomics  Understanding epigenomes  Genotyping
  27. 27. ICAR Genomics Platform Fish GR Insect GR Plant GR Animal GR Microbe GR National Genomic Resources Repository De novo sequencing, Re-sequencing, High throughput genotyping and Development of QTLs and markers for priority traits (Genes, ESTs, cDNAs, Markers, Gene constructs) Value added genomic resources for molecular breeding New genes and constructs for genetic engineering
  28. 28. Thank you Genomic resources bank is a reality and need of the hour

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