Comparative Genomics for Marker Development in Cassava
1. Comparative Genomics for Marker Development
in Cassava
Melaku Gedil
IITA R4D Week
November 23, 2009
Ibadan, Nigeria
International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
13. PCR Amplification with degenerate primers
Amplification with degenerate primers 50F-470RL was considered for
derived from At-NBS-LRR further analysis. Four DNA
Three forward and 7 reverse primers templates (TME3, TME7, and
(a total of 21 pairs) were tested TME117-a, TME-117-b) were
on the TME3 clone (Fig. x). amplified (Fig. xx). Amplicon
Different primer pairs yielded
size ranged from 200 – 900
different pattern of banding with
fragment sizes ranging from 500- bp.
1500 bp.
16. Sequence Analysis
Sequences edited
Sequences assembled
Sequence Clustered, identity matrix,
Similarity search in Genbank – BLAST
STS primers for resequencing
Marker development for MAS
37. Work in progress
• Sequence analysis and characterization
• Search on cassava and castor genome
• Re-sequencing primers from candidate
sequences (STS) for marker discovery
– in a panel of R and S cultivars
– BSA analysis of potential primers
– Develop PCR-based markers
* Allele Specific-PCR
* CAPS marker
38. Applications
1. Molecular markers (SNP, STS)
2. Gene discovery
3. Physical mapping (Qiu 2007 leaf rust R in wheat)
4. NBS profiling of genetic diversity – a modification
of AFLP (Mantovani 2006)
5. Host-pathogen interaction/pathways e.g. ATP-
binding or hydrolysis
6. Genome wide survey of Resistance genes
(Arabidopsis, Rice, poplar, Grape, papaya)
39. Advantages
1.Protocol is adaptable to other crops….e.g.
yam, cowpea
2.All resistance genes – insights to the
structure & organization
3.Starting material for comparative
genomics based data mining of R genes
4.Easy and cost-effective to generate data
5.Markers are gene-based (not random
association)
40. Application of Markers in Breeding
1. Gene mining in genetic resources (germplasm
evaluation)
• Selection of parents (diversity analysis/heterotic
group)
• Cultivar identity (‘branding’), hybrid validation
2. Introgression: minimizes linkage drag, saves time
(e.g. AB-QTL)
3. Pyramiding – traits from multiple parents
4. New approaches such as
• Marker-assisted Recurrent selection (MARS)
• Genome-wide selection (GWS)
Melaku Gedil
41. Key issues in implementation of MAB
1. Availability of genomic resources
2. Cost-effective genotyping systems
• Declining cost of genotyping and a choice of genotyping
technologies and markers
• Capital costs not necessary, (subcontract to service providers -
GCP)
3. Multienvironment phenotyping (GxE, epistasis)
• Genotyping no longer an issue
4. Accurate Marker-trait association methods (LD, QTL)
• Begin with less complex traits
• Advances in genomics (structural, functional) and other -omics,
and other disciplines, will elucidate the genetic mechanism of
complex traits of economic importance.
Melaku Gedil