Plant Genomic Resources - NBPGR · 2012-03-23 · National Genomic Resources Repository De novo sequencing, Re-sequencing, High throughput genotyping and Development of QTLs and markers

Plant Genomic Resources

Scope and relevance

K C BANSAL

National Bureau of Plant Genetic Resources

Pusa Campus

New Delhi – 110012

[email protected]

2

INDIA - A GENE RICH CENTRE OF

AGROBIODIVERSITY Possesses 11.9% of world flora

250,000 species of plants

17,500 species of higher plants

356 crop plant species cultivated

168 crop plant species of Hindustani

centre

334 wild species of crop plant relatives

1,000 wild edible plant species occur,

which includes: 145 species of roots and tubers

521 of leafy vegetables

101 of buds and flowers

647 of fruits

118 of seeds and nuts

NETWORK COLLABORATORS

Indian Council of Agricultural Research

(The Umbrella Organization)

NBPGR and

its 10

Regional

Stations

57 National Active

Germplasm Sites (NAGS)

comprising ICAR institutes,

Project Directorates, NRCs,

AICRIPs, SAUs

Other National

Stakeholders

International

Collaborators

NBPGR (The Nodal Institute)

Plant Genetic Resources Management System

Germplasm exploration and collection

• Collection of 2, 57,432 accessions of

more than 2,000 species in 2,467

explorations

• 25% share of germplasm collection:

wild species and relatives

• National Herbarium of Cultivated Plants

has 20,478 herbarium specimens

• Biosystematics in native crop taxa such

as Vigna, Macrotyloma, Trichosanthes,

Allium, Luffa, etc.

Germplasm introduction and exchange

• Exchange of PGR facilitated from more

than 105 countries and International

Agricultural Research Centres

• Every year over 20,000 accessions of

germplasm and 50,000 samples of trial

material received for utilization

• More than 420,000 accessions supplied

to different indenters for use in national

programmes

Plant quarantine

• 3,139,542 samples of various crops

processed for quarantine clearance

• Infestation/ infection/ contamination

detected in 161,723 samples of

which 161,501 salvaged

• Several new techniques/ treatments

developed/ standardized for

detection of pests and salvaging of

infested/ infected/contaminated PGR

Germplasm conservation in Genebank

• The National Seed Genebank

holds 385,150 accessions of

over 1500 crop species

• Initiatives for permafrost

conditions

• Ultra-desiccation as a cost-

effective seed storage

strategy being developed

• 897 germplasm accessions

/genetic stocks of 137 crop

species registered

Crop groups Accessions

Cereals 150721

Millets and forages 55581

Pseudo Cereals 6682

Grain Legumes 57387

Oilseeds 56158

Fibre Crops 11543

Vegetables 24478

Fruits 530

Medicinal & Aromatic Plants 6421

Spices & Condiments 2972

Agro-forestry 2442

Duplicate Safety Samples 10235

Total 385150

In vitro conservation and cryopreservation

• Cryopreservation protocols developed in species of

Allium, Bacopa, Dioscorea, Picrorhiza, Pyrus, Rubus,

Morus and Musa

• Genetic stability studies using morphological and/or

molecular markers carried out in in vitro conserved and

cryopreserved accessions of Allium tuberosum, Bacopa

sp., banana, ginger, mulberry and turmeric

• In vitro cryobanking of germplasm initiated in apple,

banana, blackberry, garlic and yams; about 40

accessions cryopreserved

Crop group Species Accessions

Tropical Fruits 14 416

Temperate and Minor Fruits 41 318

Tuber Crops 12 594

Bulbous and other Crops 11 171

Medicinal and Aromatic

Plants

28 170

Spices and Industrial Crops 27 380

Total 133 2049

DNA Fingerprinting

• DNA fingerprinting protocols developed in

33 crops of national importance; 2,215

varieties in these crops fingerprinted; new

microsatellite markers developed in

chillies, mungbean, pigeonpea and

sesame for cultivar identification and

diversity analysis

• Molecular phylogeny and evolution in

Sesamum species and spatial distribution

of genetic diversity has been studied in

banana, sesame, horsegram, mungbean,

cashew nut, mango, neem and others.

• 2,614 lines of 132 imported transgenic

planting materials comprising 12 different

crops have been tested

Germplasm characterization and evaluation

• 181,325 accessions of different crops

characterized and evaluated

• Multi-location evaluation for tolerance to

biotic/abiotic stresses and quality traits in

rice, wheat, pigeon pea and chickpea,

maize, rapeseed-mustard, brinjal, okra,

lentil and Giloe

• Core sets in okra, mungbean, sesame

and brinjal

• 80 crop catalogues on characterization

and evaluation of different crops

PGR management: Thrust areas

• Detailed evaluation of conserved germplasm

• Pre-breeding/germplasm enhancement

• Utilization of ex situ conserved germplasm

• Promoting on-farm conservation of plant germplasm

• Bio-prospecting plant germplasm

• Bio-safety and PGR management

• Genomic resource generation and conservation

• National PGR database

Total conserved germplasm

(1584 species, 385150 accn)

15 Priority crops

for XII plan

(56% of total

holding)

11 Crop groups (585 crops)

Rice

Wheat

Maize

Finger millet

Pearl millet

Sorghum

Chickpea

Pigeonpea

Rapeseed mustard

Brinjal

Okra

Cucumber/Melons

Mango

Citrus

Banana

XII Plan priority crops

Functional

Genomics

Germplasm

Structural

Genomics

Learn what

genes do

Identify Genes

Crop

Varieties with

useful Genes

Transgenic

Development

Breeding

Enhancement

Genomics Engine

Biotechnological Approaches for Crop

Improvement

• Genetic Engineering

• Molecular markers and marker-assisted selection

• Functional Genomics

Limited availability of the most appropriate genes for genetic engineering

Plant Genomic Resources

Sequencing

Mapping

Microarray Proteomics

Deciphering pathways

A HISTORY OF DNA

• Discovery of the DNA double helix

A. Frederick Griffith – Discovers that a factor in diseased bacteria can transform harmless bacteria into deadly bacteria (1928)

B. Rosalind Franklin - X-ray photo of DNA.

(1952)

C. Watson and Crick - described the DNA molecule from Franklin’s X-ray.

(1953)

Genetic Diversity…

• Different

arrangements of

NUCLEOTIDES in a

nucleic acid (DNA)

provides the key to

DIVERSITY among

living organisms.

Fine structure of a gene

mRNA

Protein

Metabolite

P H E N O T Y P E

Genomic and Related Resources in Plants

Mochida K , Shinozaki K Plant Cell Physiol 2010;51:497-523

Mochida K , Shinozaki K Plant Cell Physiol 2010;51:497-523

Genomic and Related Resources in Plants

Mochida K , Shinozaki K Plant Cell Physiol 2010;51:497-523

Genomic and Related Resources in Plants

Application of Genomic Resources

DETAILED UNDERSTANDING OF PLANT BIOLOGY

Plant architecture

Reproductive biology

Vernalisation

Photosynthesis and partitioning

Stress tolerance/resistance

Nutrient metabolism

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

DNA genotyping and sequencing as integral

components for conservation of

plant genetic resources

The Genomics Platform

An open platform to be created at NBPGR,

New Delhi and integrated in the XII plan of

the ICAR

Expected to create, and provide counseling

and access to the state of the art

infrastructure in genomics workbench (wet

lab and bioinformatics)

Rationale

• To act as a centralized platform for genomics

research in ICAR across commodities

• To provide technical back-stopping to

ICAR researchers in genomics

• To facilitate intensive genomics

research related to agriculture by inter-

linking ICAR institutes and state

agricultural universities with diverse

capabilities and requirements (across

commodities)

Objectives

Generate genomic resources for every

prioritised crops

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

• High throughput Genomics (Sequencing,

expression analyses and genotyping)

• Bioinformatics (Servers, software,

pipelines, databases,

capabilities)

• Proteomics and Metabolomics

Major facilities

Capacity Building

• Specialized trainings for core staff

• Consultants/outsourcing

• Organizing trainings for partners

• Post-doc and research students

IPs

NABG

Genomics Platform

Genomics Resources Repository

Phenomics

facility Allele mining

Other genomics

projects

Marker assisted

genetic

improvement

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