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Nad7a_del marker for A4 derived

CMS lines

Infusing genomics in hybrid breeding program

of pigeonpea (Cajanus cajan)Saxena RK, Sameerkumar CV, Saxena KB, Lekha PT, Sinha P, Singh VK, Katta MAVSK, Kumar V, Hingane A,

Srikanth S, Kulshreshtha A, Krishnamurthy L, Varshney RK *

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

*Address for correspondence: [email protected]

Pigeonpea is an important pulse crop, well-suited for rainfed and semi-arid cropping system. The released draft genome sequence and

commercial cytoplasmic nuclear male sterility (CMS)-based hybrids has been the significant contributions of ICRISAT. The pigeonpea hybrids- ICPH

2671, ICPH 2740 and ICPH 3762 have become popular by outperforming the local varieties with 30-40% higher yield in Asia under rainfed ecosystem.

Breeding heterotic hybrids conventionally for different niches is a herculean task. Genomic approaches have been initiated to accelerate the hybrid

breeding programs. With the large scale commercial hybrid seed production, ensuring the quality of F1 seed is of utmost importance. Towards this,

marker based hybrid purity assessment kit has been developed for ICPH 2671. Identification of potential restorers, marker based purity assessment

for hybrids, CMS (A-) and their maintainer (B-) lines derived from A4 systems are being carried out. In this regard, mitochondrial genomes of wild

species (C. cajanifolius), the source of CMS, hybrid, A- and B-line have been sequenced and candidate genes (nad4l and nad7a) identified. In

addition, a heterotic pool is also being generated using whole genome re-sequencing of parental lines of hybrids which will assist the existing hybrid

breeding efforts. The advantage of two line hybrid breeding system has encouraged the evaluation and characterization of a temperature-sensitive

male sterile line for its potential use. Various studies are being carried out at the molecular and cellular level to identify putative candidate genes that

will help elucidate the underlying molecular mechanism. These efforts promise accelerated hybrid breeding program in Asia and other regions of the

semi arid tropics.

Abstract

Performance of ICPH 2671 at

multi-locations over 4 years

Advantages of Hybrids

More vigour

More yield

44% greater shoot mass

40-50% greater root mass

Greater drought tolerance

Ideal for inter-croppingLocal check

Pigeonpea Hybrid Breeding- ICPH 2671, ICPH 2740 and ICPH 3762

Genomic Initiative in Pigeonpea Hybrid Breeding

Hybrid purity test kitMitochondrial genome sequencing

9 rearrangements: ICPW 29 v/s ICPA 2039

22 rearrangements: ICPA 2039 v/s ICPB 2039

1 rearrangement: ICPA 2433 v/s ICPH 2039

Identification of putative candidate genes for A4 derived CMS lines: nad7a and nad4l

nad7a

51 genes identified• 34 protein-coding

• 3 rRNA genes• 14 tRNA genes

Defining heterotic pool

EGMS line for 2-line hybrid system

Male sterile Male fertile

Expression profilingStructural variation identificationnad4l