This document discusses the deployment of genome sequencing information to improve pigeonpea, an important food legume crop. It outlines constraints on pigeonpea production including diseases and loss of genetic diversity. The author details efforts to use specialized genetic stocks, whole genome resequencing, and phenotyping to understand genetic diversity and identify alleles controlling traits like flowering time, shattering, and ligule development. Marker-trait associations have been found that can enable marker-assisted breeding to improve yield and other important traits. Overall, harnessing genetic diversity and the genome sequence is facilitating genetic gains in pigeonpea.

1. Deploying genome
sequence information for
pigeonpea improvement
Rachit Saxena
ICRISAT

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. 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. Use specialized
genetic stock
+
Re-sequencing
+
Phenotyping

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. 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. 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. Sequence variations….
 Large variation
reduction in the
cultivated gene pool

9. First-generation HapMap in
Cajanus spp.
Plant Biotechnol. J., doi: 10.1111/pbi.12528 (2016)
Unique accession signatures

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. 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. 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. 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. 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. 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. 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. 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