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Deploying genome
sequence information for
pigeonpea improvement
Rachit Saxena
ICRISAT
Pigeonpea
(Cajanus cajan L. Millsp)
 Food legume with diversified uses
such as food, feed, fodder and fuel
 India : Larg...
Constrains in pigeonpea
production
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
1950-60 1961-70 1971-1980 1981-1990 1991-2...
Use specialized
genetic stock
+
Re-sequencing
+
Phenotyping
NAM: 11 crossing parental genotypes
 Fusarium wilt
 Sterility mosaic
10 Bi-parental mapping populations
Multi-parental...
Specialized genetic stocks
 Parental lines of mapping populations : 20
(RILs, MAGIC and NAM)
 Parental lines of hybrids ...
Re-sequencing
Whole genome re-sequencing (WGRS) of 416 lines generated
~3 Tb data with the coverage ranging from 5X to 16X...
Sequence variations….
 Large variation
reduction in the
cultivated gene pool
First-generation HapMap in
Cajanus spp.
Plant Biotechnol. J., doi: 10.1111/pbi.12528 (2016)
Unique accession signatures
Understanding relationships
between re-sequencing data
and hybrid performance
Prediction of better yielding
hybrids/defi...
Data on hybrid performance
 Data available on 82
hybrids
 54 hybrids data from
single location
 28 hybrids data from
mu...
7 1
2
35
6
4
 104
parental
lines
clustered
in 7 groups
(0.43; -9.8)
(0.37; -22.94)
(0.40; 45.39)
(0.38; 14.6)
(0.38; 56)
...
Towards defining heterotic pools
Selection of diverse parental lines (A and R)
Generation of
test crosses
Genotyping of
pa...
Harnessing alleles from germplasm
Early Flowering gene
 C.cajan_22378 a homolog of ELF3 on CcLG09
Source: BMC Plant Biol...
Marker trait associations from
reference set
100 seed weight
Days to flowering
 Evaluated for yield related traits:
two y...
Summary: harvesting genetic gains
 Genome sequence has facilitated cataloguing
genetic diversity in Cajanus spp.
 Allele...
Many thanks…
Merci
Rajeev K Varshney
CV Sameer Kumar
Abhishek Rathore
KB Saxena
Hari D Upadhyaya
Mamta Sharma
Aamir Khan
V...
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Deploying genome sequence information for pigeonpea improvement

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Oral Presentation 08 by Rachit K Saxena at the International Conference on Pulses in Marrakesh, Morocco, 18-20 April 2016.

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Deploying genome sequence information for pigeonpea improvement

  1. 1. Deploying genome sequence information for pigeonpea improvement Rachit Saxena ICRISAT
  2. 2. Pigeonpea (Cajanus cajan L. Millsp)  Food legume with diversified uses such as food, feed, fodder and fuel  India : Largest producer, consumer, importer  Commodity crop Myanmar Tanzania Kenya Malawi Uganda Mozambique
  3. 3. Constrains in pigeonpea production 0.00 0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 1950-60 1961-70 1971-1980 1981-1990 1991-2000 2001-2007 Years Area (M ha) Production (M tonnes) Productivity (tonnes/ha) Sterility mosaic disease (SMD) Fusarium wilt (FW) BioticStresses Abiotic Stresses LossofGeneticDiversity
  4. 4. Use specialized genetic stock + Re-sequencing + Phenotyping
  5. 5. NAM: 11 crossing parental genotypes  Fusarium wilt  Sterility mosaic 10 Bi-parental mapping populations Multi-parental mapping populations MAGIC: 8 crossing parental genotypes  Elite breeding lines with unique preferred traits  Protein content  Yield elated traits Developing specialized genetic stocks: Mapping populations/ genetic resources  Fertility restoration  Terminal drought  Bringing diversity from landraces  Yield related traits
  6. 6. Specialized genetic stocks  Parental lines of mapping populations : 20 (RILs, MAGIC and NAM)  Parental lines of hybrids : 104 (all available cytoplasmic-male sterile (A-), maintainer (B-) and fertility restorer (R-) lines in hybrid breeding program)  Harnessing alleles from germplasm : reference set 300 (Landraces, Breeding lines and Wild species accessions)
  7. 7. Re-sequencing Whole genome re-sequencing (WGRS) of 416 lines generated ~3 Tb data with the coverage ranging from 5X to 16X Reference set (292 samples): 2.15 Tb Parental lines of hybrids (104 samples): 511 Gb Parental lines of mapping populations (20 samples) generated 200 Gb data with the coverage ranging from 7X to 16X
  8. 8. Sequence variations….  Large variation reduction in the cultivated gene pool
  9. 9. First-generation HapMap in Cajanus spp. Plant Biotechnol. J., doi: 10.1111/pbi.12528 (2016) Unique accession signatures
  10. 10. Understanding relationships between re-sequencing data and hybrid performance Prediction of better yielding hybrids/defining the heterotic pools Re-sequencing parental lines of hybrids
  11. 11. Data on hybrid performance  Data available on 82 hybrids  54 hybrids data from single location  28 hybrids data from multiple locations (2 to 5 years)
  12. 12. 7 1 2 35 6 4  104 parental lines clustered in 7 groups (0.43; -9.8) (0.37; -22.94) (0.40; 45.39) (0.38; 14.6) (0.38; 56) (0.55; 24.01)
  13. 13. Towards defining heterotic pools Selection of diverse parental lines (A and R) Generation of test crosses Genotyping of parental lines Test cross evaluation GS model prediction Applying GS for selection of parents Phenotyping of new hybrids Large scale seed production
  14. 14. Harnessing alleles from germplasm Early Flowering gene  C.cajan_22378 a homolog of ELF3 on CcLG09 Source: BMC Plant Biology201515:197 Landrace C C A T A Breeding Line C C A T A Wild species A A G G G  Mutations in ELF3 gene have produced early flowering plants SHATTERING gene: C.cajan_24676 Landrace G A A Breeding Line G A A Wild species C G G Landrace A G TGGCGGCGGCGGCGG Breeding Line A G TGGCGGCGGCGGCGG Wild species G T TGGCGGCGGCGG LIGULELESS1 gene: C.cajan_43701
  15. 15. Marker trait associations from reference set 100 seed weight Days to flowering  Evaluated for yield related traits: two years @ three locations  Consistent MTAs identified for: Days to flowering, days to maturity, plant height, secondary branches per plant, 100 seed weight
  16. 16. Summary: harvesting genetic gains  Genome sequence has facilitated cataloguing genetic diversity in Cajanus spp.  Alleles and haplotype information available for candidate genes  MTAs have been identified and initiated MABC program in pigeonpea for traits improvement Novel genetic stock and improved lines developed  Breeders-friendly genome and marker database
  17. 17. Many thanks… Merci Rajeev K Varshney CV Sameer Kumar Abhishek Rathore KB Saxena Hari D Upadhyaya Mamta Sharma Aamir Khan Vinay Kumar Vikas Singh KN Yamini G Anuradha S Muniswamy Obarley Yu Changhoon Kim Dong Seon Jihun Kim Shaun An Wei Zhang Bellbull Kim

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