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

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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