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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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K.C. Bansal
National Bureau of Plant Genetic ResourcesPusa Campus, New Delhi – 110 012
www.nbpgr.ernet.in
National Genomic Resources Repository
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
De
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sCollection, 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 plantgenetic resources
Development and validation of new molecular marker systems in priority crops and molecular diagnostics for transgenes
National Genomic Resources Repository
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
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 aspecies, functional analysis of genes, comparative genomicsand plant and animal breeding
• It is necessary to maintain an efficient system forconservation and management of genomic resources
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
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
Plant DNA banks world-wideGenomic DNA ONLY
Plant DNA Bank in Korea (PDBK)Graduate School of Biotechnology, Korea University, Seoul, Korea.
Royal Botanic Gardens Kew DNA Bank22,000 samples of plant genomic DNA, all stored at -80°C.
The Australian Plant DNA BankAustralian native and other important crop plant species; also transgenic organisms developed through research
DNA Banking at the Missouri Botanical GardenTo promote phylogenetic research while easing the demand on herbarium specimens
DNA Bank Brazilian Flora SpeciesRio de Janeiro Botanical Garden, Brazil
DNA Bank at KirstenboschThe Leslie Hill Molecular Systematics Laboratory at Kirstenbosch, South Africa
Bank at the National Herbarium NederlandFor systematic treatments (Flora) in the National Herbarium of Netherland
cDNA clones, RFLP markers, PAC/BAC clones and YAC filters
NIAS DNA BankFor maintaining DNA materials and information that has been accumulated as part of the genome projects such as the
Rice Genome Research Program (RGP)
Other DNA banks world-wide …1Riken Bio-resource Center DNA Bank
Isolation, collection, preservation and distribution of cloned DNA and gene libraries (cDNA and genomelibraries) from human and other mammalian cells and from microorganisms (vectors and hosts). The RIKENDNA Bank undertakes research to ensure the authenticity of the materials in the collection and to improve andstandardize 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
Other DNA banks world-wide …2The 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
Source of genomic resources
A. Mega-projectsi. 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
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
i. Submission form and MTA
II. Modalities
ii. Request form and MTA
II. Modalities
iii. Research output form
II. Modalities
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
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)
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
Intellectual property and legal issues
• Material transfer agreement (MTA) by the beneficiary prior tothe shipment
• The MTAs regulate the intellectual property rights (IPR) of therequested material and related information, the conditions ofits use and distribution to third parties, as well as benefitsharing
• Existing MTAs can be specifically designed for the exchange ofgenomic resources, if desired
• DNA exchange through MTA: CATIE, Costa Rica; NIAS, Japan,the Missouri Botanical Garden, USA; and the Royal BotanicGardens, Kew
Genomic resources bank is a reality and a need of the hour
• The accelerated use of genomic technology inbiological research has fueled the need toestablish genomic resources bank
• Short-term collections, where newly obtainedmaterial is characterized and distributed basedon current goals
• Long-term collections, where samples are placedin safe-keeping
Facilities for research and generation of genomic resources at NBPGR
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
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
PGR conservation
at NBPGR
NABG
Genomics Platform
Genomics Resources Repository
Phenomics facility Allele mining
Other genomics projects
Marker assisted genetic
improvement
Repository and Utilization platform
High throughput Genomics platform
High throughput Transcriptomicsplatform
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
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
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
Thank you
Genomic resources bank is a reality and need of the hour