plant genomic resources - nbpgr · 2012-03-23 · national genomic resources repository de novo...
TRANSCRIPT
Plant Genomic Resources
Scope and relevance
K C BANSAL
National Bureau of Plant Genetic Resources
Pusa Campus
New Delhi – 110012
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.
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
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