Towards utilization of genome sequence information forpigeonpea improvement
By ICAR institutes, SAUs and ICRISAT
A major source of protein to about 20% of the world population (Thu
et al., 2003) An abundant source of minerals and vitamins (Saxena et al., 2002)
Most versatile food legume with diversified uses such as food, feed,
fodder and fuel It is hardy, widely adaptable crop with better tolerance to
drought and high temperature
Belongs to family
Leguminosae with
chromosome no. 2n=22
and genome size of ~833
Mbp
Pigeonpea (Cajanus cajan L. Millsp)
Pigeonpea – production trends
(last five decades)
Unfortunately, no increase has been witnessed in its productivity (yield kg ha-1), which in the past five decades has remained stagnant at around 700 kg ha-1
Unfortunately, no increase has been witnessed in its productivity (yield kg ha-1), which in the past five decades has remained stagnant at around 700 kg ha-1
A route developed and taken by breeders: From germplasm to
variety/hybrid
Germplasm
Superior variety
Genomics-assisted breeding: Predicting the phenotype
Genotype
Gene(s)
Trait/QTL
Phenotype
TranscriptomicsProteomicsMetabolomicsTILLINGEcoTILLING
EST SequencingGenome SequencingMap-based Cloning
Genetic MappingPhysical Mapping
Genetic MappingAssociation MappingQTL MappingTrait Correlations
Genetic Resources
Improved germplasm
Trends Pl Science 2005;Trends Biotech 2006
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 genome-wide several loci that confer tolerance/resistance/ superiority to traits of interest
using GEBVs based on genome-wide marker profiling
Example of development of a submergence tolerant version of
Swarna, a widely grown variety, in 2½ years
Marker-assisted backcrossingIR49830-7:tolerant
Swarna-Sub1
Swarna:Non-tolerant
Sub1• Target gene selectionTarget gene selection• Recombinant selectionRecombinant selection• Background selectionBackground selection
BC2or BC3
X
Courtesy of David Mackill, IRRI
New Sub1 lines (in yellow) and recurrent parents (in white) after 17 days submergence in field at IRRI, 2007DS
New Sub1 lines (in yellow) and recurrent parents (in white) after 17 days submergence in field at IRRI, 2007DS
Samba
Samba-Sub1
Samba-Sub1
IR64-Sub1IR49830 (Sub1)IR6
4IR42 IR6
4IR64-Sub1
Samba-Sub1
IR49830 (Sub1)
Samba
IR64
IR64-Sub1
IR49830 (Sub1)
IR42
IR64-Sub1
IR64
IR49830 (Sub1)
IR49830 (Sub1)
IR42
Samba
IR42
Samba
Courtesy of David Mackill, IRRI
Swarna-Sub1 in U.P. (Faizabad area)
Swarna-Sub1 in U.P. (Faizabad area)
Courtesy of David Mackill, IRRI, The Philippines
Challenges in genomics-assisted crop improvement
Narrow genetic base in the primary gene pool
Very few molecular (SSR) markers
Non-availability of appropriate germplasm such as mapping populations
Intraspecific genetic map with low marker density
Non-availability of trait-associated markers in breeding
Issues of costs and expertise in molecular breeding
Resource Pigeonpea
SSRs 29,000
SNPs 35,000
GoldenGate 768 SNPs
KASPar assays 1,616 SNPs
DArT arrays 15,360
Sanger ESTs ~20,000
454 /FLX reads 496,705
TUSs 21,432
Illumina reads(million reads)
>160 (14 parents)
Gene/transcriptomic/ SNP resources
CMS and mt genome sequencing of pigeonpeaProduction
of A- line seeds
Production of hybrid seeds for commercial crop Commercial pigeonpea hybrids production
ICPA 2039, ICPB 2039, ICPH 2433 & ICPW 29 sequenced using 454 technology
Objectives Molecular mapping of resistance to biotic
and abiotic stresses- Mapping populations available
- Genotyping and phenotyping- Marker trait association for resistance to FW,
SMD and Rf
Enhancing the genetic base of pigeonpea genepool by developing multi-parents populations
- MAGIC population (2000 lines) developed using 8 parents
- NAM population (50 crosses-1000 lines) with 50 parents
- High density genotyping or genotyping by sequencing of 3000 lines
- Phenotyping of MAGIC and NAM populations (each population at least in 3 environments)
- Marker trait association analysis for traits of interest
Genome wide association studies based on re-sequencing and phenotyping of germplasm set
- Germplasm set of 300-500 lines assembled
- Genotyping-by-sequencing of the germplasm set
- Precise phenotyping of the germplasm set by different partners
- Fine mapping of traits of interest for breeders
Bioinformatics analysis to improve the quality of
draft genome- Two genome assemblies need to be merged
- Defining a consensus genes set- Breeders-friendly genome databases
Validation and characterization of 1213 disease resistance genes
- Genetic mapping of disease resistance genes
- Association of genes with disease resistance traits
- Functional validation of selected set of candidate genes
- Mining of superior allleles/haplotypes for disease resistance
Validation and characterization of ca. 200 abiotic stress tolerance genes
- Genetic mapping of abiotic stress tolerance genes
- Association of genes with abiotic stress tolerance traits
- Functional validation of selected set of candidate genes
- Mining of superior allleles/haplotypes for abiotic stress tolerance genes
Possible outcomes
Superior breeding lines for traits of interest with enhanced genetic diversity
Molecular markers associated with resistance to
biotic stresses and tolerance to abiotic stresses
Alleles and haplotype information available on germplasm set so that breeders can use informative lines
Set of well characterized disease resistance and
abiotic stress tolerance genes Breeder-friendly genome database of
pigeonpea
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