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CFA- Molecular Breeding @
ICRISAT
Rajeev Varshney
Center of Excellence in Genomics
ICRISAT
Genomics-assisted breeding: Predicting the phenotype
Genotype
Gene(s)
Trait/QTL
Phenotype
Transcriptomics Proteomics Metabolomics TILLING EcoTILLING
EST Sequencing Genome Sequencing Map-based Cloning
Genetic Mapping Physical Mapping
Genetic Mapping Association Mapping QTL Mapping Trait Correlations
Genetic Resources
Improved germplasm
Trends Pl Science 2005; Trends Biotech 2006
MABC, MARS and GS approaches seem to most
promising for crop improvement
Need to have genomic resources and cost-effective
genotyping platforms
Precise phenotyping platforms required
Breeders-friendly pipelines and decision support tools required for prediction of phenotype
Modern breeding approaches for increasing genetic gains
A route developed and taken by breeders: From germplasm to
variety/hybrid
Germplasm
Superior variety
A variety of approaches (cars)
• MAS: MARKER-ASSISTED SELECTION - Plants are selected for one or more (up to 8-10) alleles
• MABC: MARKER-ASSISTED BACKCROSSING
– One or more (up to 6-8) donor alleles are transferred to an elite line
• MARS: MARKER-ASSISTED RECURRENT SELECTION – Selection for several (up to 20-30) mapped QTLs relies
on index (genetic) values computed for each individual based on its haplotype at target QTLs
• GWS: GENOME-WIDE SELECTION
– Selection of lines based on genome-wide marker data for tolerance/resistance/ superiority to traits of interest using GEBVs
Germplasm
Superior variety
Developing infrastructures and sign posts for providing directions
The sorghum genome
98% of genes were placed in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information.
Genetic recombination is
largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice.
Retrotransposon accumulation
in recombinationally recalcitrant heterochromatin explains the 75% larger genome size of sorghum compared with rice.
Illumina sequencing tech used to generate 237.2 Gb
72.7% (605.78 Mb) of the total pigeonpea genome assembled into scaffolds
Genome analysis predicted 48,680 genes
High levels of synteny observed between the pigeonpea and soybean
>50,000 SSR and SNP markers identified
Higher abundance of drought tolerance genes
The pigeonpea genome
The chickpea genome
• Illumina sequencing used to generate 153.01 Gb
• 73.8% of the genome is captured in scaffolds
• Genome analysis predicted 28,269 genes
• High levels of synteny observed between chickpea and Medicago
• > 81,845 SSRs and 4.4
million variants (SNPs and INDELs)
Center of Excellence in Genomics (CEG)
SSR genotyping
DArT genotyping
SNP genotyping
High-throughput Sequencing
CEG facilities
Genotyping services extended
0
100000
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500000
600000
700000
800000
2008 2009 2010 2011 2012
ICRISAT National partners Overseas
Create a new Project, Study
Start a new experiment
LIMS
Plate File Generated by LIMS System that servers as an input to the ABI Sequencer used (Sample file is for ABI Sequencer 3700)
LIMS
• Assemble & Align Raw Reads
• Mine SNPs • Generate Marker Matrix • Automated Visualize in
TABLET and FLAPJACK • Developing genotyping
assays • Export in FLAT Files
ISMU V1
Raw Reads
Reference
Assemble & Align Raw Reads Mine SNPs Generate Marker Matrix Visualize in TABLET and FLAPJACK Export in FLAT Files
ISMU
GDMS
GDMS
GDMS
1. Accession List
3. QTL Maps
4. Linkage Map
5. Heat Maps
6. Creation of Target Genotype
2. Subset
7. Similarity Matrix
MBDT- Molecular Breeding Design Tool
Information System for Marker-Assisted Backcrossing
(ISMAB)
Complete data management of breeding, including
management of segregating material, planting plans, analysis of data, data reporting and making field books
Using a single software package to manage variety and pedigree information, design trials, aid in field operations, and analyze and store data eliminates the time lost from transferring data between applications
Good software and user support provided
Breeding data management
First generation molecular breeding products for root traits in chickpea and leaf rust in groundnut
MABC products in fields
GWS
MARS
ISMU V2
Raw Reads
Reference
Assemble & Align Raw Reads Mine SNPs Generate Marker Matrix Visualize in TABLET and FLAPJACK Export in FLAT Files
GDMS
Genotypic Matrix & QTLs
Select lines for further crossing in MARS & GWS
External Genotyping Platforms
Called SNPs
ISMU version 2.0
Summary
State-of-art genotyping facilities are available Bioinformatics and molecular breeding pipeline
becoming available Regular monthly meeting being held (including
scientists from different disciplines) Efforts have initiated to implement GS in breeding
programme Working in close collaboration with Integrated
Breeding Platform of GCP
Linking with “Enhancing Genetic Gain” and “Digital Design for Agriculture” initiatives of Gates Foundation
Safe driving!
Genomics
Crop improvement
In context of Strategic Plan-2020
& CGIAR Research Programmes…
Crop improvement
Taking crop improvement to more heights
(higher genetic gains)