Skip to main content
SpringerLink
Log in

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

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ali MA, Seyal MT, Awan SI, Niaz S, Ali S, Abbas A (2008) Hybrid authentication in upland cotton through RAPD analysis. Aust J Crop Sci 2:141–149

    CAS  Google Scholar 

  • Anderson JA, Churchill GA, Sutrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    Article  CAS  PubMed  Google Scholar 

  • Asif M, Rahman MU, Zafar Y (2006) Genotyping analysis of six maize (Zea mays L.) hybrid using DNA fingerprinting technology. Pakistan J Bot 38:1425–1430

    Google Scholar 

  • Barbosa AMM, Geraldi IO, Benchimol LL, Garcia AAF, Souza CL Jr, Souza AP (2003) Relationship of intra- and inter-population tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers. Euphytica 130:87–99

    Article  CAS  Google Scholar 

  • Bohn M, Friedrich Utz H, Melchinger AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs and SSRs and their use for predicting progeny variance. Crop Sci 39:228–237

    CAS  Google Scholar 

  • Burns MJ, Edwards KJ, Newbury HJ, Ford-Lloyd BV, Baggott CD (2001) Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan). Mol Ecol Notes 1:283–285

    Article  CAS  Google Scholar 

  • Chowdari KV, Venkatachalam SR, Davierwala AP, Gupta VS, Ranjekar PK, Govila OP (1998) Hybrid performance and genetic distance as revealed by the (GATA)4 microsatellite and RAPD markers in pearl millet. Theor Appl Genet 97:163–169

    Article  CAS  Google Scholar 

  • Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:55

    Article  PubMed  CAS  Google Scholar 

  • Ferguson ME, Burow MD, Schultz SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A hypogaea L.). Theor Appl Genet 108:1064–1070

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Hashemi SH, Sayyed Mirmohammadi-Maibody AM, Nematzadeh GA, Arzani A (2009) Identification of rice hybrids using microsatellite and RAPD markers. Afr J Biotechnol 8:2094–2101

    CAS  Google Scholar 

  • He G, Meng R, Newman M, Gao GM, Pittman RN, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 3:3

    Article  PubMed  Google Scholar 

  • Jena KK, Pandey SK (1999) DNA markers for purification of A and B lines for hybrid rice improvement. Hybrid Rice News Lett 2:13–14

    Google Scholar 

  • Jordan D, Tao Y, Godwin I, Henzell R, Cooper M, McIntyre C (2003) Prediction of hybrid performance in grain sorghum using RFLP markers. Theor Appl Genet 106:559–567

    CAS  PubMed  Google Scholar 

  • Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT, Howarth CJ (2008) Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breed 127:33–37

    CAS  Google Scholar 

  • Kidwell KK, Hartweck LM, Yandell BS, Crump PM, Brummer JE, Moutray J, Osborn TC (1999) Forage yields of alfalfa populations derived from parents selected on the basis of molecular marker diversity. Crop Sci 39:223–227

    Article  Google Scholar 

  • Kwon SJ, Ha WG, Wang HG, Yang SJ, Choi HC, Moon HP, Ahn SN (2002) Relationship between heterosis and genetic divergence in ‘Tongil’-type rice. Plant Breed 121:487–492

    Article  Google Scholar 

  • Lanza LLB, Souza CL Jr, Ottoboni LMM, Vieira MLC, Souza AP (1997) Genetic distance of inbred lines and prediction of maize single-cross performance using RAPD markers. Theor Appl Genet 94:1023–1030

    Article  CAS  Google Scholar 

  • Mishra GP, Singh RK, Mohapatra T, Singh AK, Prabhu KV, Zaman FU, Sharma RK (2003) Molecular mapping of gene for fertility restoration of wild abortive (WA) cytoplasmic male sterility using a basmati rice restorer line. J Plant Biochem Biotech 12:37–42

    CAS  Google Scholar 

  • Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SCM, Gimanes MA, Martin WS, Valls JFM, Grattapaglia D, Bertioli D (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111:1060–1071

    Article  CAS  PubMed  Google Scholar 

  • Nandakumar N, Singh AK, Sharma RK, Mohapatra T, Prabhu KV, Zaman FU (2004) Molecular fingerprinting of hybrids and assessment of genetic purity of hybrid seeds in rice using microsatellite markers. Euphytica 136:257–264

    Article  CAS  Google Scholar 

  • Naresh V, Yamini KN, Rajendrakumar P, Dinesh KV (2009) EST-SSR marker-based assay for the genetic purity assessment of safflower hybrids. Euphytica 170:347–353

    Article  CAS  Google Scholar 

  • Odeny DA, Jayashree B, Ferguson M, Hoisington D, Crouch J, Gebhardt C (2007) Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed 126:130–137

    Article  CAS  Google Scholar 

  • Odeny DA, Jayashree B, Gebhardt C, Crouch J (2009) New microsatellite markers for pigeonpea (cajanus cajan (L.) millsp.). BMC Res Notes 2:35

    Article  CAS  PubMed  Google Scholar 

  • Panguluri SK, Janaiah K, Govil JN, Kumar PA, Sharma PC (2006) AFLP fingerprinting in pigeonpea (Cajanus cajan (L.) Millsp.) and its wild relatives. Genet Resourc Crop Evol 53:523–531

    Article  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier, pp 43–76

    Google Scholar 

  • Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592

    CAS  Google Scholar 

  • Saxena KB (2008) Genetic improvement of pigeonpea—a review. Tropical Plant Biol 1:159–178

    Article  Google Scholar 

  • Saxena KB, Kumar RV, Srivastava N, Shiying B (2005) A cytoplsmic-nuclear male sterility system derived from a cross between Cajanus cajanifolius and Cajanus cajan. Euphytica 145:289–294

    Article  Google Scholar 

  • Saxena RK, Prathima C, Saxena KB, Hoisington DA, Singh NK, Varshney RK (2010a) Novel SSR markers for polymorphism detection in pigeonpea (Cajanus spp.). Plant Breed 129:142–148

    Article  CAS  Google Scholar 

  • Saxena RK, Saxena KB, Kumar RV, Hoisington DA, Varshney RK (2010b) SSR-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance to Fusarium wilt and sterility mosaic disease. Plant Breed 129:135–141

    Article  CAS  Google Scholar 

  • Smith JSC, Register JC III (1998) Genetic purity and testing technologies for seed quality: a company perspective. Seed Sci Res 8:285–293

    Article  CAS  Google Scholar 

  • Souframanien J, Manjaya JG, Krishna TG, Pawar SE (2003) Random amplified polymorphic DNA analyses of cytoplasmic male sterile and male fertile pigeonpea (Cajanus cajan (L.) Millsp.). Euphytica 129:293–299

    Article  CAS  Google Scholar 

  • Sundaram RM, Naveenkumar B, Biradar SK, Balachandran SM, Mishra B, IlyasAhmed M, Viraktamath BC, Ramesha MS, Sharma NP (2008) Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica 163:215–224

    Article  Google Scholar 

  • Thudi M, Senthilvel S, Bottley A, Hash CT, Reddy AR, Feltus AF, Paterson AH, Hoisington DA, Varshney RK (2010) A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica. doi 10.1007/s10681-010-0148-5

  • Varshney RK, Penmetsa RV, Dutta S, Kulwal PL, Saxena RK, Datta S, Sharma TR, Rosen B, Carrasquilla-Garcia N, Farmer AD, Dubey A, Saxena KB, Gao J, Fakrudin B, Singh MN, Singh BP, Wanjari KB, Yuan M, Srivastava RK, Kilian A, Upadhyaya HD, Mallikarjuna N, Town CD, Bruening GE, He G, May GD, McCombie R, Jackson SA, Singh NK, Cook DR (2010) Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breed. doi 10.1007/s11032-009-9327-2

  • Weber JL (1990) Informativeness of human (cC-dA)n (dG-dT)n polymorphisms. Genomics 7:524–530

    Article  CAS  PubMed  Google Scholar 

  • Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong X, Kilian A (2006) Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor Appl Genet 113:585–595

    Article  CAS  PubMed  Google Scholar 

  • Yashitola J, Thirumurugan T, Sundaram RM, Naseerullah MK, Ramesha MS, Sarma NP, Stone RV (2002) Assessment of purity of rice hybrids using microsatellite and STS markers. Crop Sci 42:1369–1373

    Article  CAS  Google Scholar 

  • Zhang Q, Gao YL, Yang SH, Ragab R, Saghai-Maroof MA, Li ZB (1994) A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsattelites. Theor Appl Genet 89:185–192

    Article  Google Scholar 

Download references

Acknowledgments

The study was funded by the Pigeonpea Genomics Initiative of the Indian Council of Agricultural Research (ICAR) under the framework of Indo-US Agricultural Knowledge Initiative (AKI), Generation Challenge Programme (www.generationcp.org) and Tropical Legume II (TL II) of Bill and Melinda Gates Foundation (BMGF).

Author information

Authors and Affiliations

  1. Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, AP, India

    Rachit K. Saxena & Rajeev K. Varshney

  2. Global Theme–Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, AP, India

    Kulbhushan Saxena

  3. Genomics towards Gene Discovery Sub Programme, Generation Challenge Programme, c/o CIMMYT, Int APDO Postal 6-641, 06600, Mexico, DF, Mexico

    Rajeev K. Varshney

Authors
  1. Rachit K. Saxena
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kulbhushan Saxena
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajeev K. Varshney
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rajeev K. Varshney.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Saxena, R.K., Saxena, K. & Varshney, R.K. Application of SSR markers for molecular characterization of hybrid parents and purity assessment of ICPH 2438 hybrid of pigeonpea [Cajanus cajan (L.) Millspaugh]. Mol Breeding 26, 371–380 (2010). https://doi.org/10.1007/s11032-010-9459-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-010-9459-4

Keywords

Search

Navigation