Molecular Breeding

, Volume 26, Issue 2, pp 371–380

Application of SSR markers for molecular characterization of hybrid parents and purity assessment of ICPH 2438 hybrid of pigeonpea [Cajanus cajan (L.) Millspaugh]

  • Rachit K. Saxena
  • Kulbhushan Saxena
  • Rajeev K. Varshney


With an objective of achieving a breakthrough in the productivity of pigeonpea, a hybrid breeding technology based on elements of the cytoplasmic-nuclear male-sterility (CMS) system and partial natural out-crossing has recently been developed. However, there is no molecular diversity information available on parental lines of hybrids being generated at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). This study deals with the use of 148 simple sequence repeat (SSR) markers, including 32 novel markers reported here for the first time, on 159 A (cytoplasmic male sterile), B (maintainer) and R (fertility restorer) lines. In total, 41 (27.7%) markers showed polymorphism with 2 to 6 (average 2.6) alleles and 0.01 to 0.81 (average 0.34) polymorphism information content (PIC) value. Of these polymorphic markers, 22 SSR markers showed polymorphism between A (ICPA 2039) and R (ICPR 2438) lines of the commercial hybrid (ICPH 2438); however, only 21 of these SSR markers showed the same profile between A (ICPA 2039) and B (ICPB 2039) lines. Finally, two SSR markers, CCB4 and CCttc006, were found most suitable for purity assessment of hybrid seeds of the ICPH 2438 hybrid. The utility of these two diagnostic SSR markers has been demonstrated by using seed lots of this hybrid from two sources, ICRISAT and Mahabeej. It is anticipated that molecular diversity information generated on parental lines of hybrids under development, and identification of the two most suitable markers for testing the purity of hybrid seeds of ICPH 2438, will facilitate the pigeonpea hybrid breeding programme.


Cajanus cajan Microsatellite markers Grow out test Cytoplasmic male sterility 

Supplementary material

11032_2010_9459_MOESM1_ESM.doc (190 kb)
Supplementary material 1 (DOC 190 kb)
11032_2010_9459_MOESM2_ESM.doc (345 kb)
Supplementary material 2 (DOC 345 kb)
11032_2010_9459_MOESM3_ESM.doc (81 kb)
Supplementary material 3 (DOC 81 kb)

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Rachit K. Saxena
    • 1
  • Kulbhushan Saxena
    • 2
  • Rajeev K. Varshney
    • 1
    • 3
  1. 1.Centre of Excellence in Genomics (CEG)International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, Greater HyderabadIndia
  2. 2.Global Theme–Crop ImprovementInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, Greater HyderabadIndia
  3. 3.Genomics towards Gene Discovery Sub Programme, Generation Challenge ProgrammeMexico, DFMexico

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