Pigeonpea is an important legume crop and molecular breeding can help improve it faster than conventional methods. Researchers are developing a multiparent advanced generation inter-cross (MAGIC) population for pigeonpea using 8 parental lines. As a first step, 28 two-way crosses were made between parental lines. Whole genome resequencing of parental lines is underway to identify SNPs for mapping traits in the MAGIC population, which will be generated through eight-way crosses and advanced by selfing.

1. Pigeonpea is the sixth most important legume crop in the world and it is a rich source of proteins. Conventional
methods of breeding varieties with higher yield and inbuilt resistance are time consuming and cumbersome process.
Molecular breeding with the help of genome wide sequence information will be helpful in achieving the goal in less time with
high precision. With an aim to enhance genetic gains and to identify genomic regions responsible for economically important
traits in pigeonpea a first set of multiparent advanced generation inter-cross mapping population (MAGIC) is being
developed. Eight parental genotypes are being used for crossing and for assessment of marker polymorphism for testing
hybridity, of F1s. As a first step of development (two-way crosses) a total of 28 two-way cross have been developed in current
cropping season 2012 - 2013. Presently, re-sequencing of 8 parent lines is in under progress to identify the polymorphic SNP
between parental lines. In the subsequent year we will complete the 14 four-way crosses and 7 eight-way crosses. The lines
generated through eight way crosses will be advanced through single seed decent method to generate the 500 MAGIC lines.
These lines will be phenotyped for disease screening and yield and yield related traits under multi-location trials. The
phenotypic data together with genotypic data will be used to identify the marker trait associations (MTA) for the targeted
traits and can be further used in marker assisted selection for pigeonpea improvement.
Financial support from United States
Agency for International Development is gratefully acknowledged. The
authors thank Swathi Parulpalli and Kishan Patel (ICRISAT). ICRISAT is
a member of the CGIAR Consortium.
Abstract
Acknowledgements
Generation of F1s
Description of parents used in MAGIC
MAGIC Scheme
Whole genome re-sequencing of parental lines
Summary
Vikas K Singh1, Rachit K Saxena1, Vinay Kumar1, CV Sameer Kumar1, Suyash Patil1,
Mayank Kaashyap1, V Suryanarayana1, K B Saxena1, Rajeev K Varshney1,2,*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
2Generation Challenge Programme, CIMMYT, Mexico, DF, Mexico, *Address for correspondence: r.k.varshney@cgiar.org
Development of First Multiparent Advanced
Generation Inter-cross (MAGIC) Population in
Pigeonpea (Cajanus cajan)
Genotypes Features
ICP 7426 High pod numbers, medium duration
HPL 24 High protein content, medium duration, compact,
susceptible to FW and resistant to SMD, inter-specific
derivative
ICP 11605 Early flowering, germplasm line
ICP 14209 High number of pods, germplasm line
ICP 14486 Early flowering, germplasm line
ICP 5529 Medium duration, obcordate leaves, compact plant,
poor yielding, modified flower
ICP 7035 Medium duration, SMD resistant to both Patancheru and
Bangalore races, large purple seed, high sugar content
ICP 8863 Erect, mid late, highly resistant to FW and susceptible
to SMD, an extensively grown variety in Northern
Karnataka and Maharashtra region of India, red seeded
genotype
ICP
7426
HPL
24
ICP
11605
ICP
14209
ICP
14486
ICP
5529
ICP
7035
ICP
8863
ICP 7426
HPL 24 24
ICP 11605 45 37
ICP 14209 60 32 30
ICP 14486 45 20 34 45
ICP 5529 20 10 10 15 16
ICP 7035 50 26 30 70 50 20
ICP 8863 32 35 30 20 27 10 80
Developed MAGIC lines will be used for phenotyping to identify the
marker trait association (MTA) for target traits.
Total of 28 two way
crosses were
attempted in the net
house conditions.
Numbers of F1s seed generated (28 combination)
Identification of polymorphic SSR between parents
 DNA libraries of all eight MAGIC parental lines for whole genome re-sequencing on
MiSeq platform have been constructed. Sequencing of samples is performed at
minimum of 5X coverage. Whole genome re-sequencing for one parental lines ICP
8863 has been completed successfully on MiSeq platform being used using 2 X150
bp pair-end sequencing. Re-sequencing of rest seven parental lines is in under
progress.
 SNPs and haplotypes will be identified among parental lines.
Genomic DNA
1 2 3 4 5 6 7 8
Before size selection After size selection
Bioanalyzer profile of
DNA library of selected
sample showed average
size of 450 bp.
1 ICP 7426
2 HPL 24
3 ICP 11605
4 ICP 14209
5 ICP 14486
6 ICP 5529
7 ICP 7035
8 ICP 8863
L 1 2 3 4 L 5 6 7 8 L L 1 2 3 4 L 5 6 7 8 L
Sequencing of sample on MiSeq platform
A A BB C C DD E E F F H HXX X G G X
AB X CD EF X GH
ABCD EFGH
ABCDEFGH
CS-1
CS-2
CS-3
CS-4CS-5CS-n
Half di-allele mating of 8 founder MAGIC line
Selfing n cycle through single seed decent
method
Generation of 14, 4-way crosses (AEGH, AHCE…..)
Generation of 7, 8-way crosses, (ADGHFGCE, AFGCDBEH……….)
Selfing to generate F2 Population (500 plants ≈
72 plants from each 8 way crosses)
Generation of 500 MAGIC Lines
Generation of 28, 2-way crosses (AB, AC, AD, AE, AF, AG, AH…..)
M 1 2 3 4 5 6 7 8 M 1 2 3 4 5 6 7 8
M: 100 bp DNA ladder; 1: ICP7426; 2: HPL24; 3: ICP 11605; 4: ICP 14209; 5: ICP14486; 6: ICP5529; 7: ICP7035; 8: ICP8863
CcM306 CcM602
DNA Library preparation for Pair-end sequencing on MiSeq platform