Genetic Resources and Crop Evolution

, Volume 60, Issue 3, pp 1021–1036 | Cite as

An assessment of the genetic integrity of ex situ germplasm collections of three endangered species of Coffea from Madagascar: implications for the management of field germplasm collections

  • Sarada KrishnanEmail author
  • Tom A. Ranker
  • Aaron P. Davis
  • Jean Jacques Rakotomalala
Research Article


Madagascar has 59 species of Coffea, of which 42 are listed as Critically Endangered, Endangered, or Vulnerable by criteria of the Red List Category system of the World Conservation Union. In an attempt to assess the conservation value of ex situ collections of Malagasy coffee species, a study was undertaken using the field genebank collections maintained at the Kianjavato Coffee Research Station. Three species were selected for this purpose, C. kianjavatensis, C. montis-sacri, and C. vatovavyensis, and for comparative purposes extant, in situ populations of the same species were studied. Parentage analyses of ex situ propagated offspring of C. kianjavatensis and C. montis-sacri were performed to assess if crossing with other Coffea species maintained in the field genebank is compromising the genetic integrity of the collection. For these three species, higher genetic diversity was observed in the ex situ populations compared to the in situ populations, highlighting the importance of preserving the plants currently in ex situ collections. Parentage analyses of seed-propagated offspring of C. kianjavatensis and C. montis-sacri revealed that cross contamination with pollen from other Coffea species in the ex situ field genebank is occurring. These results have significant implications for the conservation management of wild Coffea species and for the management of ex situ genebanks.


Coffea kianjavatensis Coffea montis-sacri Coffea vatovavyensis Ex situ germplasm Madagascar Microsatellite markers 



This work was supported by grants to S. Krishnan from the Association of Zoological Horticulture Conservation, the University of Colorado Museum of Natural History, Department of Ecology and Evolutionary Biology, and Beverly Sears program of the Graduate Division. We thank the FOFIFA team, RBG Kew Madagascar (Kew Madagascar Conservation Center, KMCC) team, Ueshima Coffee Corporation and Dr. Franck Rakotonasolo for their valuable collaboration and field support.


  1. Anthony F, Dussert S, Dulloo E (2007a) Coffee genetic resources. In: Engelmann F, Dulloo ME, Astorga C, Dussert S, Anthony F (eds) Conserving coffee genetic resources: complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources. A case study in CATIE, Costa Rica. Bioversity International, Rome, pp 12–22Google Scholar
  2. Anthony F, Astorga C, Avendaño J, Dulloo E (2007b) Conservation of coffee genetic resources in the CATIE field genebank. In: Engelmann F, Dulloo ME, Astorga C, Dussert S, Anthony F (eds) Conserving coffee genetic resources: complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources. A case study in CATIE, Costa Rica. Bioversity International, Rome, pp 23–34Google Scholar
  3. Chase MW, Hillis HH (1991) Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40:215–220CrossRefGoogle Scholar
  4. Combes MC, Andrzejewski S, Anthony F, Bertrand B, Rovelli P, Graziosi G, Lashermes P (2000) Characterization of microsatellite loci in Coffea arabica and related coffee species. Mol Ecol 9:1178–1180PubMedCrossRefGoogle Scholar
  5. Coulibaly I, Revol B, Noirot M, Poncet V, Lorieux M, Carasco-Lacombe C, Minier J, Dufour M, Hamon P (2003) AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [(C. heterocalyx × C. canephora) × C. canephora]. Theor Appl Genet 107:1148–1155PubMedCrossRefGoogle Scholar
  6. Cubry P, Musoli P, Legnate H, Pot D, de Bellis F, Poncet V, Anthony F, Dufour M, Leroy T (2008) Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome 51:50–63PubMedCrossRefGoogle Scholar
  7. Davis AP (2010) Six species of Psilanthus transferred to Coffea (Coffeeae, Rubiaceae). Phytotaxa 10:41–45Google Scholar
  8. Davis AP (2011) Psilanthus mannii, the type species of Psilanthus transferred to Coffea. Nordic J Bot 29:471–472CrossRefGoogle Scholar
  9. Davis AP, Rakotonasolo F (2008) A taxonomic revision of the baracoffea alliance: nine remarkable Coffea species from western Madagascar. Bot J Linn Soc 158:355–390CrossRefGoogle Scholar
  10. Davis AP, Govaerts R, Bridson DM, Stoffelen P (2006) An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152:465–512CrossRefGoogle Scholar
  11. Davis AP, Tosh J, Ruch N, Fay MF (2011) Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data: implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc 167:357–377CrossRefGoogle Scholar
  12. Dawson IK, Waugh R, Simons AJ, Powell W (1997) Simple sequence repeats provide a direct estimate of pollen-mediated gene dispersal in a tropical tree Gliricidia sepium. Mol Ecol 6:179–183CrossRefGoogle Scholar
  13. Duchesne P, Castric T, Bernatchez L (2005) PASOS (parental allocation of singles in open systems): a computer program for individual parental allocation with missing parents. Mol Ecol Notes 5:701–704CrossRefGoogle Scholar
  14. Dulloo ME, Guarino L, Maxted N, Newbury JH, Attere F, Ford-Lloyd BV (1998) Complementary conservation strategies for the genus Coffea: a case study of Mascarene Coffea species. Genet Resour Crop Evol 45:565–579CrossRefGoogle Scholar
  15. Dulloo ME, Ebert AW, Dussert S, Gotor E, Astorga C, Vasquez N, Rakotomalala JJ, Rabemiafara A, Eira M, Bellachew B, Omondi C, Engelmann F, Anthony F, Watts J, Qamar Z, Snook L (2009) Cost efficiency of cryopreservation as a long-term conservation method for coffee genetic resources. Crop Sci 49:2123–2138CrossRefGoogle Scholar
  16. Engelmann F, Dulloo E (2007) Introduction. In: Engelmann F, Dulloo ME, Astorga C, Dussert S, Anthony F (eds) Conserving coffee genetic resources: complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources. A case study in CATIE, Costa Rica. Bioversity International, Rome, pp 1–11Google Scholar
  17. Etisham-Ul-Haq M, Allnutt TR, Smith-Ramirez C, Gardner MF, Armesto JJ, Newton AC (2001) Patterns of genetic variation in in situ and ex situ populations of the threatened Chilean vine Berberidopsis coralline, detected using RAPD markers. Ann Bot 87:813–821CrossRefGoogle Scholar
  18. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedGoogle Scholar
  19. Frankel OH (1984) Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P (eds) Genetic manipulation: impact on man and society. Cambridge University Press, Cambridge, pp 161–170Google Scholar
  20. Hein L, Gatzweiler F (2005) The economic value of coffee (Coffea arabica) genetic resources. Ecol Econ 60:176–185CrossRefGoogle Scholar
  21. Holmgren PK, Holmgren NH, Barnett LC (1990) Index herbariorum. In: Part 1: The herbaria of the world, 8th edn. Regnum Vegetabile. New York Botanical Garden, New YorkGoogle Scholar
  22. International Coffee Organization (2012) Breakdown of exports of green Arabica and green robusta for countries exporting significant volumes of both types of coffee. Accessed 05 May 2012
  23. IUCN (2001) IUCN red list categories, Version 3.1. IUCN Species Survival Commission, Gland/CambridgeGoogle Scholar
  24. Krishnan S (2011) Conservation genetics of wild coffee (Coffea spp.) in Madagascar. Dissertation, University of Colorado, Boulder, COGoogle Scholar
  25. Lashermes P, Combes MC, Robert J, Trouslot P, D’Hont A, Anthony F, Charrier A (1999) Molecular characterization and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266PubMedCrossRefGoogle Scholar
  26. Maunder M, Hughes C, Hawkins JA, Culham A (2003) Hybridization in ex situ plant collections: conservation concerns, liabilities, and opportunities. In: Guerrant EO, Havens K, Maunder M (eds) Ex situ plant conservation: supporting species survival in the wild. Island Press, Washington DC, USA, pp 325–364Google Scholar
  27. Musloi P, Cubry P, Aluka P, Billot C, Dufour M, De Bellis T, Pot D, Bieysse D, Charrier A, Leroy T (2009) Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 52:634–646CrossRefGoogle Scholar
  28. Nowak MD, Davis AP, Anthony F, Yoder AD (2011) Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae). PLoS ONE 6(6):1–11e21019Google Scholar
  29. Pearl HM, Nagai C, Moore PH, Steiger DL, Osgood RV, Ming R (2004) Construction of a genetic map for arabica coffee. Theor Appl Genet 108:829–835PubMedCrossRefGoogle Scholar
  30. Pendergrast M (2009) Coffee second only to oil? Tea Coffee Trade Journal April:38–41Google Scholar
  31. Poncet V, Hamon P, Minier J, Carasco C, Hamon S, Noirot M (2004) SSR cross-amplification and variation within coffee trees (Coffea spp.). Genome 47:1071–1081PubMedCrossRefGoogle Scholar
  32. Rousset F (2008) GENEPOP’007: a complete reimplementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106PubMedCrossRefGoogle Scholar
  33. Rovelli P, Mettulio R, Anthony F, Anzueto F, Lashermes P, Graziosi G (2000) Microsatellites in Coffea arabica L. In: Sera T, Soccol CR, Pandey A, Roussos S (eds) Coffee biotechnology and quality. Kluwer Academic Publishers, Netherlands, pp 123–133Google Scholar
  34. Schneider S, Roessli D, Excoffier L (2000) Arlequin: A software for population genetics data analysis. Ver 2.000. Genetics and Biometry Lab, Dept. of Anthropology, University of GenevaGoogle Scholar
  35. Silvestrini M, Junqueira MG, Favarin AC, Guerreiro-Filho O, Maluf MP, Silvarolla MB, Colombo CA (2007) Genetic diversity and structure of Ethiopian, Yemen and Brazilian Coffea arabica L. accessions using microsatellite markers. Genet Resour Crop Evol 54:1367–1379CrossRefGoogle Scholar
  36. Suso MJ, Gilsanz S, Duc G, Marget P, Moreno MT (2006) Germplasm management of faba bean (Vicia faba L.): monitoring intercrossing between accessions with inter-plot barriers. Genet Resour Crop Evol 53:1427–1439CrossRefGoogle Scholar
  37. Van Hintum TJL, Brown AHD, Spillane C, Hodgkin T (2000) Core collections of plant genetic resources. IPGRI Tech Bull 3:5–48Google Scholar
  38. Vega F, Rosenquist E, Collins W (2003) Global project needed to tackle coffee crisis. Nature 425:343PubMedCrossRefGoogle Scholar
  39. Vega FE, Ebert AW, Ming R (2008) Coffee germplasm resources, genomics, and breeding. In: Janick J (ed) Plant breeding reviews, vol 30. Wiley, New York, pp 415–447CrossRefGoogle Scholar
  40. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370CrossRefGoogle Scholar
  41. Ye QG, Yao X-H, Zhang S-J, Kang M, Huang H-W (2006) Potential risk of hybridization in ex situ collections of two endangered species of Sinojackia Hu (Styracaceae). J Integr Plant Biol 48(7):867–872CrossRefGoogle Scholar
  42. Zhang D, Mischke S, Johnson ES, Phillips-Mora W, Meinhardt L (2009) Molecular characterization of an international cacao collection using microsatellite markers. Tree Genet Genomes 5:1–10CrossRefGoogle Scholar
  43. Zhang J-J, Ye Q-G, Yao X-H, Huang H-W (2010) Spontaneous interspecific hybridization and patterns of pollen dispersal in ex situ populations of a tree species (Sinojackia xylocarpa) that is extinct in the wild. Conserv Biol 24(1):246–255PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Sarada Krishnan
    • 1
    • 2
    Email author
  • Tom A. Ranker
    • 3
  • Aaron P. Davis
    • 4
  • Jean Jacques Rakotomalala
    • 5
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderUSA
  2. 2.Denver Botanic GardensDenverUSA
  3. 3.Division of Environmental BiologyNational Science FoundationArlingtonUSA
  4. 4.The Herbarium, Library, Art and Archives, Royal Botanic Gardens, KewRichmond, SurreyUK
  5. 5.FOFIFA-DRAAntananarivoMadagascar

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