Skip to main content
SpringerLink
Log in

Cross-genera amplification of informative microsatellite markers from common bean and lentil for the assessment of genetic diversity in pigeonpea

  • Research Article
  • Published:
Physiology and Molecular Biology of Plants Aims and scope Submit manuscript

Abstract

A total of 24 pigeonpea (Cajanus cajan L. Millspaugh) cultivars representing different maturity groups were evaluated for genetic diversity analysis using 10 pigeonpea specific and 66 cross-genera microsatellite markers. Of the cross-genera microsatellite markers, only 12 showed amplification. A total of 45 alleles were amplified by the 22 markers. Nine markers showed 100 % polymorphism. Markers Lc 14, BMd 48 and CCB 9 amplified maximum number (5) of alleles each. One genotype specific unique band in Pusa 9 was generated by markers CCB 8. Maximum genetic diversity (74 %) was observed between cultivars MA 3 and CO 6, while the minimum diversity (12 %) was observed between NDA 1 and DA 11. The average diversity among the cultivars was estimated to be 45.6 %. SSR primers from pigeonpea were found to be more polymorphic (37 %) as compared to common bean and lentil markers. The arithmetic mean heterozygosity (Hav) and marker index (MI) were found to be 0.014 and 0.03, respectively, indicating the potential of common bean and lentil microsatellite markers for genetic mapping, diversity analysis and genotyping in Cajanus.

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

Similar content being viewed by others

References

  • Abdelnoor RV, Barros EG and Moreira MA (1995). Determination of genetic diversity within Brazilian soybean germplasm using random amplified DNA amplification techniques and comparative analysis with pedigree data. Braz. J. Genet. 18: 265–273

    CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Barrett BA, Kidwell KK and Fox PN (1998). Comparison of AFLP and pedigree based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Sci. 38: 1271–1278

    Article  CAS  Google Scholar 

  • Blair MW, Pedraza F, Buendia HF, Gaitan-Solis E, Beebe SE, Gepts P and Tohme J (2003). Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris). Theor. Appl. Genet. 107: 1362–1374

    Article  CAS  PubMed  Google Scholar 

  • Burns MJ, Edwards KJ, Newburg HJ, Ford Lloyd BV and 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 4: 283–285

    Article  Google Scholar 

  • Choi HK, Mun JH, Kin DJ, Zhu H, Baek JM, Mudjge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND and Cook DR (2004). Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. 101: 15289–15294

    Article  CAS  PubMed  Google Scholar 

  • Choudhary S, Sethy NK, Shokeen B and Bhatia S (2009). Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet. 118: 591–608

    Article  CAS  PubMed  Google Scholar 

  • Choumane W, Winter P, Weigand F and Kahl G (2004). Conservation of microsatellite flanking sequences in different taxa of leguminosae. Euphytica 138: 239–245

    Article  CAS  Google Scholar 

  • Datta S, Kaashyap M and Kumar S (2009). Amplification of chickpea-specific SSR primers in Cajanus species and their validity in diversity analysis. Plant Breed. doi 10.1111/j.1439-0523.2009.01678.x

  • DeWoody JA, Honeycutt RL and Skow LC (1995). Microsatellite markers in white-tailed deer. J. Hered. 86: 317–319

    CAS  PubMed  Google Scholar 

  • Doldi ML, Vollmann J and Lelley T (1997). Genetic diversity in soybean as determined by RAPD and microsatellite analysis. Plant Breed. 116: 331–335

    Article  Google Scholar 

  • Ford R, Le Roux K, Itman C, Brouwer JB and Taylor PWJ (2002). Diversity analysis and genotyping in Pisum with sequence tagged microsatellite site (STMS) primers. Euphytica 124: 397–405

    Article  CAS  Google Scholar 

  • Gupta SC, Reddy LJ, Sharma D, Green JM, Murthi AN and Saxena KB (1980). Maintenance of pigeonpea cultivars. In: Proceedings of International Workshop on Pigeonpea, (Eds. Nene Y.L.), Vol 2, ICRISAT, Patancheru, India, pp 295–301.

    Google Scholar 

  • Gutierrez MV, Vaz Patto MC, Huguet T, Cubero JI, Moreno MT and Torres AM (2005). Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor. Appl. Genet. 110: 1210–1217

    Article  CAS  PubMed  Google Scholar 

  • Hamwieh A, Udupa SM, Choumane W, Sarker A, Dreyer F, Jung C and Baum M (2005). A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance. Theor. Appl. Genet. 110: 669–677

    Article  CAS  PubMed  Google Scholar 

  • Hamwieh A, Udupa SM, Sarker A, Jung C and Baum M (2009). Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breed. Sci. 59: 77–86

    Article  CAS  Google Scholar 

  • Jaccard P (1908), Nouvelle recherches sur La distribution florale. Bulletin Bull. Soc. Vaud. Sci. Nat. 44: 223–270

    Google Scholar 

  • Kumar S and Ali M (2006). GE interaction and its breeding implications in pulses. The Botanica 56: 31–36

    Google Scholar 

  • L’taief B, Horres R, Jungmann R, Molina C, Sifi B, Lachaal M, Winter P and Kahl G (2008). Locus-specific microsatellite markers in common bean (Phaseolus vulgaris L.) isolation and characterization. Euphytica 162: 301–310

    Article  Google Scholar 

  • Nadimpalli RG, Jarret RL, Phatak SC and Kochert G (1992). Phylogenetic relationships of the pigeonpea (Cajanus cajan) based on nuclear restriction fragment length polymorphisms. Genome 36: 216–223

    Article  Google Scholar 

  • Nei M and Li WH (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. 79: 5269–5273

    Article  Google Scholar 

  • Odeny DA, Jayashree B, Ferguson M, Hoisngton D, Crouch J and Gebhardt C (2007). Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed. 126:130–136

    Article  CAS  Google Scholar 

  • Odeny DA, Jayashree B, Gebhardt C and Crouch J (2009). New microsatellite markers for pigeonpea (Cajanus cajan (L) millsp.) BMC Res. Notes 2: 35. doi:10.1186/1756-0500-2-35

    Article  CAS  PubMed  Google Scholar 

  • Pandian A, Ford R and Paul WJ (2000). Transferability of sequence tagged microsatellite site (STMS) primers across four major pulses. Plant Mol. Biol. Rep. 18:395a–395h

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Peakall R, Gilmore S, Keys W, Morgante M and Rafalski A (1998). Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera; Implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15: 1275–1287

    CAS  PubMed  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey V, Vogel T, Tingey S and Rafalski JA (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 3: 225–238

    Article  Google Scholar 

  • Roa A, P Chavarriaga-Agguirre, Duque MC, Maya MM, Bonier-bale MW, Iglesias C and Tohme J (2000). Crosss-pecies amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellite: allelic polymorphism and degree of relationship. Am. J. of Bot. 87: 1647–1655

    Article  CAS  Google Scholar 

  • Ratnaparkhe MB, Gupta VS, Ven Meurthy MR and Ranjekar PK (1995). Genetic fingerprinting of Pigeonpea (Cajanus cajan L. Millsp) and wild relatives using RAPD markers. Theor. Appl. Genet. 91: 893–898

    Article  CAS  Google Scholar 

  • Rohlf FJ (1998). NTSYS-PC Numerical taxonomy and Multivariate analysis system Version 2.1, Exeter Software, Applied Biostatistics, New York, USA

    Google Scholar 

  • Sethy NK, Shokeen B, Edwards KJ and Bhatia S (2006). Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 112: 1416–1428

    Article  CAS  PubMed  Google Scholar 

  • Singh F, Kumar S and Majumder ND (2006). Genetic base of pigeonpea varieties released in India. Indian J. Pulses Res. 19: 179–183

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Stepien L, Mohler V, Bocianowski and Koczyk G (2004). Assessing genetic diversity of Polish wheat (Triticum aestivum) varieties using microsatellite markers. Genet. Res. Crop. Evol. 54: 1499–1506

    Article  Google Scholar 

  • Tautz D (1989). Hyper variability of simple sequences as a general source of polymorphism DNA markers. Nucl. Ac. Res. 17: 6463–6471

    Article  CAS  Google Scholar 

  • Tautz D and Renz M (1984). Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl. Ac. Res. 12: 4127–4137

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Reddy KN, Gowda CLL and Singh S (2007). Phenotypic diversity in the pigeonpea core collection. Genet. Resour. Crop. Evol. 54: 1167–1184

    Article  Google Scholar 

  • Varshney RK, Garner A and Sorell ME (2005). Genic microsatellite markers in plants: Features and application. Trends Biotech. 23: 48–55

    Article  CAS  Google Scholar 

  • Wilde J, Waugh JR and Powell W (1992). Genetic fingerprinting of Theobroma clones using RAPD markers. Theor. Appl. Genet. 83:871–877

    Article  CAS  Google Scholar 

  • Zeng L, Kwon TR, Liu X, Wilson C, Grieve CM and Gregorio GB (2006) Genetic diversity analyzed by microsatellite markers among rice genotypes with different adaptation to saline soil. Plant Sci. 166: 1275–1285

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, 208 024, India

    Subhojit Datta, Sahil Mahfooz, Pallavi Singh, A. K. Choudhary, Farindra Singh & Shiv Kumar

  2. International Center for Agricultural Research in the Dry Areas, Aleppo, Syria

    Shiv Kumar

Authors
  1. Subhojit Datta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sahil Mahfooz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pallavi Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. K. Choudhary
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Farindra Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shiv Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Subhojit Datta.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Datta, S., Mahfooz, S., Singh, P. et al. Cross-genera amplification of informative microsatellite markers from common bean and lentil for the assessment of genetic diversity in pigeonpea. Physiol Mol Biol Plants 16, 123–134 (2010). https://doi.org/10.1007/s12298-010-0014-x

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12298-010-0014-x

Keywords

Search

Navigation