Skip to main content
SpringerLink
Log in

Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPs

  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Genetic diversity among 40 accessions (Coffea canephora) of robusta coffee genepool available in India was determined in comparison with 14 representative samples from a C. canephora core collection and three accessions of C. congensis, using amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Both these molecular approaches were able to generate unique fingerprints for each of the accessions analysed. All the 12 SSR primers used in the present study were found polymorphic, with an average of six alleles per primer pair. Comparative analysis revealed the higher amount of diversity in representatives from a core collection than in the Indian genepool. Moreover, a total of 205 polymorphic AFLP bands were scored in all the 57 accessions analysed. The genetic relationship among 57 accessions was compared on the basis of SSR and AFLP polymorphisms. Genetic similarity dendrograms showed high correlation between the two marker systems. This study clearly established the high amount of diversity present in core samples, which is not represented in Indian genepool. Furthermore, the three accessions of C. congensis did not exhibit any significant diversity from other robusta accessions supporting the school of thought that C. congensis forms a biotype of C. canephora. The potential use of SSRs and AFLP markers in genetic diversity analysis for better ex situ management and also for exploitation of diversity in breeding programmes is discussed.

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

  • C.O. Agwanda P. Lashermes P. Trouslot M.C. Combes A. Charrier (1997) ArticleTitleIdentification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee Euphytica 97 241–248 Occurrence Handle10.1023/A:1003097913349

    Article  Google Scholar 

  • InstitutionalAuthorNameAnonymous (1985) Coffee Guide Coffee Board Bangalore, India 200

    Google Scholar 

  • InstitutionalAuthorNameAnonymous (1998) Technical Bulletin on C × R Coffee Board Bangalore, India

    Google Scholar 

  • F. Anthony M.C. Combes C. Astorga B. Bertrand G Graziosi P. Lashermes (2002) ArticleTitleThe origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers Theor Appl. Genet. 104 894–900 Occurrence Handle10.1007/s00122-001-0798-8

    Article  Google Scholar 

  • J. Berthaud (1986) Les resources génétiques pour l’ amélioration des caféiers africains diploides ORSTOM, collection Travaux et documents Montpellier, France 379

    Google Scholar 

  • F. Berthou C. Mathieu F. Vedel (1983) ArticleTitleChloroplast and mitochondrial DNA variation as indicator of phylogenetic relationships in the genus Coffea Theor. Appl. Genet. 65 77–84 Occurrence Handle10.1007/BF00276268

    Article  Google Scholar 

  • D.M. Bridson B. Verdcourt (1988) Coffea & Psilanthus Balkema (Eds) Fl. Trop. East Africa: Rubiaceae (part 2) R.M. Polhill Rotterdam 703–727

    Google Scholar 

  • A. Charrier J. Berthaud (1985) Botanical classification of coffee M.N. Clifford K.C. Wilson (Eds) Coffee: Botany, Biochemistry and Production of Beans and Beverage. Croom Helm London 13–47

    Google Scholar 

  • M.C. Combes S. Andrzejewski F. Anthony B. Bertrand P. Rovelli G. Graziosi P. Lashermes (2000) ArticleTitleCharacterization of microsatellite loci in Coffea arabica and related coffee species Mol. Ecol. 9 1178–1180 Occurrence Handle10.1046/j.1365-294x.2000.00954-5.x Occurrence Handle10964241

    Article  PubMed  Google Scholar 

  • J. Cros M.C. Combes P. Trouslot F. Anthony S. Hamon A. Charrier P. Lashermes (1998) ArticleTitlePhylogenetic analysis of chloroplast DNA variation in Coffea L Mol. Phylogenet Evol. 9 109–117 Occurrence Handle10.1006/mpev.1997.0453 Occurrence Handle9479700

    Article  PubMed  Google Scholar 

  • S. Dussert P. Lashermes F. Anthony C. Montagnon P. Trouslot M.C. Combes J. Berthaud N. Noirot S. Hamon (1999) Le caféier, Coffea canephora P. Hamon M. Seguin X. Perrier J.C. Glaszmann (Eds) Diversité Génétique des Plantes Tropicales Cultivées. CIRAD Montpellier, France 175–194

    Google Scholar 

  • A. Garner W.F. Ludwig A.E. Melchinger (1994) ArticleTitleRelationships among European barley germplasm: II Comparisons of RFLP and pedigree data Crop. Sci. 34 1199–1205

    Google Scholar 

  • J.C. Herrera M.C. Combes F. Anthony A. Charrier P. Lashermes (2002) ArticleTitleIntrogression into the allotetraploid coffee (Coffea arabica L.): Segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid (C. arabica × C. canephora) Theor. Appl. Genet. 104 661–668 Occurrence Handle10.1007/s001220100747 Occurrence Handle12582671

    Article  PubMed  Google Scholar 

  • J. Jakse K. Kindlhofer B. Javornik (2001) ArticleTitleAssessment of genetic variation and differentiation of hop genotypes by microsatellite and AFLP markers Genome 44 773–782 Occurrence Handle10.1139/gen-44-5-773 Occurrence Handle11681600

    Article  PubMed  Google Scholar 

  • A. Karp K. Edwards M. Bruford B. Vosman M. Morgante O. Seberg A. Kremer P. Boursot P. Arctander D. Tautz G. Hewitt (1997) ArticleTitleNewer molecular technologies for biodiversity evaluation: Opportunities and challenges Nat Biotechnol. 15 625–628 Occurrence Handle10.1038/nbt0797-625 Occurrence Handle9219262

    Article  PubMed  Google Scholar 

  • P. Lashermes M.C. Combes P. Trouslot A. Charrier (1997) ArticleTitlePhylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA Theor Appl. Genet. 94 947–955 Occurrence Handle10.1007/s001220050500

    Article  Google Scholar 

  • P. Lashermes S. Andrzejewski B. Bertrand M.C. Combes S. Dussert G. Graziosi P. Trouslot F. Anthony (2000) ArticleTitleMolecular analysis of introgressive breeding in coffee (Coffea arabica L.) Theor. Appl. Genet. 100 139–146 Occurrence Handle10.1007/s001220050019

    Article  Google Scholar 

  • T. Leroy C. Montagnon E.B. Eskes A. Charrier (1993) ArticleTitleReciprocal recurrent selection applied to Coffea canephora Pierre. 1. Characterisation and evaluation of breeding populations and value of intergroup hybrids Euphytica 67 113–125 Occurrence Handle10.1007/BF00022734

    Article  Google Scholar 

  • T.L. Maguire R. Peakall P. Saenger (2002) ArticleTitleComparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs Theor. Appl. Genet. 104 338–398 Occurrence Handle10.1007/s001220100724 Occurrence Handle12582706

    Article  PubMed  Google Scholar 

  • N. Mantel (1967) ArticleTitleThe detection of disease clustering and a generalized regression approach Cancer Res. 27 209–220 Occurrence Handle6018555

    PubMed  Google Scholar 

  • Montagnon C., Leroy T. and Yapo A. (1992). Etude complémentaire de la diversité génotypique et phénotypique des caféiers de l’ espéce C. canephora en collection en Cote d’ Ivorie. In: XIVe colleque scientifique international sur le café, Paris, France, ASIC, pp. 444–450

  • C. Montagnon T. Leroy E.B. Eskes (1998) ArticleTitleAmélioration variétale de Coffea canephora. 2. Les programmes de sélection et leurs résultas Plantation, Recherche, Dépveloppement 5 89–98

    Google Scholar 

  • I. Pejic P. Ajmone-Marson M. Morgante V. Kozumplick P. Castiglioni G. Taramino M. Motto (1998) ArticleTitleComparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs Theor Appl. Genet. 97 1248–1255 Occurrence Handle10.1007/s001220051017

    Article  Google Scholar 

  • W. Powell M. Morgante C. Andre M. Hanafey J. Vogel S. Tingey A. Rafalski (1996) ArticleTitleThe comparison of RFLP, RAPD, AFLP, and SSR (microsatellite) markers for germplasm analysis Mol. Breed. 2 225–238 Occurrence Handle10.1007/BF00564200

    Article  Google Scholar 

  • N.S. Prakash M.C. Combes K.S. Naveen P Lashermes (2002) ArticleTitleAFLP analysis of introgression in coffee cultivars of (Coffea arabica L.) derived from a natural interspecific hybrid Euphytica 124 265–271 Occurrence Handle10.1023/A:1015736220358

    Article  Google Scholar 

  • A.S. Ram M.S. Sreenivasan R. Naidu (1994) ArticleTitleExploitation of coffee germplasm in India – II Diploid species J. Coffee Res 24 107–114

    Google Scholar 

  • P. Rovelli R. Mettulio F. Anthony F. Anzueto P. Lashermes G. Graziosi (2000) Microsatellites in Coffea arabica L Sera. Soccol. Pandey. Roussos. (Eds) Coffee Biotechnology and Quality. Kluwer Academic Publisher Dordrecht 123–133

    Google Scholar 

  • J.R. Russel J.D. Fuller M. Macaulay B.G. Hatz A. Jahoor W. Powell R. Waugh (1997) ArticleTitleDirect comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs Theor. Appl. Genet. 95 714–722 Occurrence Handle10.1007/s001220050617

    Article  Google Scholar 

  • B. Teulat C. Aldam R. Trehin P. Lebrun J.H.A. Barker G.M. Arnold A. Karp L. Baudouin F. Rognon (2000) ArticleTitleAn analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequencetagged microsatellites (SSRs) and AFLPs Theor. Appl Genet. 100 764–771 Occurrence Handle10.1007/s001220051350

    Article  Google Scholar 

  • Y. Peer ParticleVan de R. Wachter ParticleDe (1994) ArticleTitleTREECOM for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment Comput Appl. Biosci. 10 569–570

    Google Scholar 

  • P. Vos R. Hogers M. Bleeker M. Reijans T. Lee ParticleVan der M. Hornes A. Frijters J. Pot J. Peleman M. Kuiper M. Zabeau (1995) ArticleTitleAFLP: A new technique for DNA fingerprinting Nucleic Acids Res. 23 4407–4414 Occurrence Handle7501463

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Regional Coffee Research Station, Coffee Board, R.V. Nagar, 531 133, Visakhapatnam Dt, Andhra Pradesh, India

    Nayani Surya Prakash

  2. Institut de Recherche pour le déeveloppement, GeneTrop, 911 Avenue Agropolis, B.P. 64501, 34394, Montpellier Cedex 5, France

    Marie-Christine Combes, Stéphane Dussert & Philippe Lashermes

  3. Biotechnology Centre, Coffee Board, Manasagangotri, Mysore, 570 006, Karnataka, India

    Somanna Naveen

Authors
  1. Nayani Surya Prakash
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marie-Christine Combes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stéphane Dussert
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Somanna Naveen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Philippe Lashermes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Philippe Lashermes.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Prakash, N.S., Combes, MC., Dussert, S. et al. Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPs. Genet Resour Crop Evol 52, 333–343 (2005). https://doi.org/10.1007/s10722-003-2125-5

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-003-2125-5

Keywords

Search

Navigation