(ii) Varshney
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Transcript (ii) Varshney
Towards utilization of genome
sequence information for
pigeonpea improvement
By
ICAR institutes, SAUs and ICRISAT
Pigeonpea
(Cajanus cajan L. Millsp)
Belongs to family Leguminosae
with chromosome no. 2n=22
and genome size of ~833 Mbp
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
Climate change!
Pigeonpea – production trends
(last five decades)
4.00
3.50
3.00
2.50
Area (M ha)
2.00
Production (M tonnes)
1.50
Productivity (tonnes/ha)
1.00
0.50
0.00
1950-60
1961-70
1971-1980
1981-1990
1991-2000
2001-2007
Years
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
Some constraints in
pigeonpea production
Sterility mosaic disease (SMD)
Fusarium wilt (FW)
A route developed and taken by
breeders: From germplasm to
variety/hybrid
Germplasm
Superior variety
Genomics-assisted breeding:
Predicting the phenotype
Genotype
Genetic Mapping
Physical Mapping
EST Sequencing
Genome Sequencing
Map-based Cloning
Gene(s)
Genetic
Resources
Genetic Mapping
Association Mapping
QTL Mapping
Trait Correlations
Improved
germplasm
Trait/QTL
Transcriptomics
Proteomics
Metabolomics
TILLING
EcoTILLING
Phenotype
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
X
Swarna:
Non-tolerant
IR49830-7:
Marker-assisted backcrossing tolerant
• Target gene selection
• Recombinant selection
• Background selection
Sub1
Swarna-Sub1
Courtesy of David Mackill, IRRI
BC2
or BC3
New Sub1 lines (in yellow) and recurrent
parents (in white) after 17 days
submergence in field at IRRI, 2007DS
IR64-Sub1
Samba-Sub1
Samba
IR49830 (Sub1)
Samba
IR64
IR42
IR42
IR64
IR49830 (Sub1)
IR49830 (Sub1)
IR64-Sub1
IR64
Samba
Samba-Sub1
IR64-Sub1
IR42
IR49830 (Sub1)
IR42
IR64-Sub1
Samba
Samba-Sub1
IR64
Courtesy of David Mackill, IRRI
IR49830 (Sub1)
Swarna-Sub1 in U.P.
(Faizabad area)
Courtesy of David Mackill, IRRI, The Philippines
Challenges in genomicsassisted 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
Germplasm
Superior variety
Developing infrastructures and
sign posts for providing directions
(Indo-US AKI, CGIAR-GCP, US-NSF)
Gene/transcriptomic/
SNP resources
Resource
SSRs
Pigeonpea
29,000
SNPs
GoldenGate
35,000
768 SNPs
KASPar assays
1,616 SNPs
DArT arrays
15,360
Sanger ESTs
454 /FLX reads
TUSs
~20,000
496,705
21,432
Illumina reads
(million reads)
>160
(14 parents)
CMS and mt genome
sequencing of pigeonpea
Production 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
From Orphan crop- genomic resources rich crop
Phylogenetic analysis of Cajanus
spp. using KASPar assays
Cluster-I
Cluster-II
Cluster-III
How to use this genome information…
Objectives
Molecular mapping of resistance to biotic and
abiotic stresses
- Mapping populations available
and Rf
- Genotyping and phenotyping
- Marker trait association for resistance to FW, SMD
Enhancing the genetic base of pigeonpea
genepool by developing multi-parents populations
- MAGIC population (2000 lines) developed using 8 parents
lines
at
- NAM population (50 crosses-1000 lines) with 50 parents
- High density genotyping or genotyping by sequencing of 3000
- Phenotyping of MAGIC and NAM populations (each population
least in 3 environments)
Genome wide association studies based on resequencing and phenotyping of germplasm set
- Germplasm set of 300-500 lines assembled
different
- Genotyping-by-sequencing of the germplasm set
- Precise phenotyping of the germplasm set by
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
resistance
- Mining of superior allleles/haplotypes for disease
Validation and characterization of ca. 200
abiotic stress tolerance genes
-
traits
Genetic mapping of abiotic stress tolerance genes
- Association of genes with abiotic stress tolerance
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
Possible partners
NRCPB, New Delhi
NBPGR, New Delhi
IIPR, Kanpur
IARI, New Delhi
Uni Agril Sciences- Bangalore
Banaras Hindu University
ANGRAU- Hyderabad