, Volume 142, Issue 3, pp 185–199 | Cite as

Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora

  • Thierry LeroyEmail author
  • Fabien De Bellis
  • Hyacinthe Legnate
  • Pascal Musoli
  • Adrien Kalonji
  • Rey Gastón Loor Solórzano
  • Philippe Cubry


The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum-Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.


Coffea canephora SSR markers Genetic diversity Core collection Association study 



The plant material came from the Centre National de la Recherche Agronomique (CNRA), Divo, the Ivory Coast; from the Coffee Research Center (COREC), Mukono, Uganda; from the Institut National pour l’Etude et la Recherche Agronomiques (INERA) Luki, the Democratic Republic of the Congo; from the Centre de coopération International en Recherche Agronomique pour le Développement (CIRAD), Sinnamary, French Guyana; from the Instituto Agronomico do Parana (IAPAR), Londrina, Brazil; from the Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Pichilinge, Ecuador; and from the Institut de Recherche pour le Développement (IRD), Montpellier, France. We thank Dr. Le Cunff (UMR AGAP, IFV, Montpellier, France) and JP Labouisse (UMR AGAP, Montpellier, France) for helpful comments on the manuscript.

Supplementary material

10709_2014_9766_MOESM1_ESM.docx (16 kb)
Description of the collections and origin of the genotypes that were used in this study. (DOCX 15 kb)
10709_2014_9766_MOESM2_ESM.xlsx (22 kb)
This file consists of several tabs and describes the group-nested core collections: Summary tab: statistics and effectiveness of known diversity groups and group-nested core collections. The size of the optimal core collection within each group was assessed using redundancy curves as described in the materials and methods for the whole sample. Group tabs: composition (genotypes) of each group-nested core collection. (XLSX 21 kb)


  1. Anthony F (1992) Les ressources génétiques des caféiers : collecte, gestion d’un conservatoire et évaluation de la diversité génétique. Collection Travaux and Documents Microfichés n°81, ORSTOM (now IRD), ParisGoogle Scholar
  2. Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275PubMedCrossRefGoogle Scholar
  3. Barnaud A, Lacombe T, Doligez A (2006) Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. TheorAppl Genet 112:708–716CrossRefGoogle Scholar
  4. Belaj A, Dominguez-GarcíaMdC AS, Urdíroz NM, De la Rosa R, Satovic Z, Martín A, Kilian A, Trujillo I, Valpuesta V, Del Río C (2012) Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits. Tree GenetGenomes 8:365–378CrossRefGoogle Scholar
  5. Berthaud J (1986) Les ressources génétiques pour l’amélioration des caféiers africains diploïdes. Evaluation de la richesse génétique des populations sylvestres et de ses mécanismes organisateurs. Conséquences pour l’application, Paris (FRA), ORSTOM, 379 ppGoogle Scholar
  6. Berthaud J, Charrier A (1988) Genetic resources of Coffea. In: Clarke RJ and Macrae R (eds) Coffee, vol. 4 Agronomy, London: Elsevier Applied Science, pp. 1–42Google Scholar
  7. Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824CrossRefGoogle Scholar
  8. 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
  9. Crouzillat D, Rigoreau M, Lefebvre-Pautigny F, Priyono, Broun P, Lambot C (2013) A coffee high density genetic map for quantitative trait loci analysis on agronomical, technological and biochemical characteristics in robusta and arabica. In: ASIC 24th International Conference on Coffee Science (ASIC Costa Rica 2012), 11–16 Nov 2012, San José, Costa Rica, 6 pGoogle Scholar
  10. Cubry P (2008b) Structuration de la diversité génétique et analyse des patrons de déséquilibre de liaison de l’espèce Coffeacanephora Pierre ex Froehner. Thèse de doctorat de l’Université Montpellier II, Montpellier.
  11. Cubry P, Musoli P, Legnaté 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
  12. Cubry P, De Bellis F, Pot D, Musoli P, Leroy T (2013a) Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects. Genet Resour Crop Evol 60(2):483–501. doi: 10.1007/s10722-012-9851-5 CrossRefGoogle Scholar
  13. Cubry P, De Bellis F, Avia K, Bouchet S, Pot D, Dufour M, Legnate H, Leroy T (2013b) An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis. BMC Genom 14:10. doi: 10.1186/1471-2164-14-10 CrossRefGoogle Scholar
  14. 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 167:357–377. doi: 10.1111/j.1095-8339.2011.01177.x CrossRefGoogle Scholar
  15. Dussert D, Lashermes P, Anthony F, Montagnon C, Trouslot P, Combes MC, Berthaud J, Noirot M, Hamon S (1999) Le caféier, Coffea canephora. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Diversité génétique des plantes tropicales cultivées. CIRAD, Montpellier, pp 175–194Google Scholar
  16. El Bakkali A, Haouane H, Moukhli A, Costes E, Van Damme P, Khadari B (2013) Construction of core collections suitable for association mapping to optimize use of mediterranean olive (Olea europaea L.) genetic resources. PLoS ONE 8(5):e61265PubMedCentralPubMedCrossRefGoogle Scholar
  17. Escribano P, Viruel MA, Hormaza JI (2008) Comparison of different methods to sequence repeat markers. A case study in cherimoya (Annona cherimola, Annonaceae), an underutilised subtropical fruit tree species. Ann Appl Biol 153:25–32CrossRefGoogle Scholar
  18. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolut Bioinform Online 1:47–50Google Scholar
  19. Franco J, Crossa J, Warburton ML, Taba S (2006) Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Sci 46:854–864CrossRefGoogle Scholar
  20. Frankel OH, Brown AHD (1984) Plant genetic resources today: a critical appraisal. Crop genetic resources. In: Holden JHW, Williams JT (eds) Conservation and evaluation. Georges Allen and Unwin Ltd, London, pp 249–257Google Scholar
  21. Gomez C, Dussert S, Hamon P, Hamon S, Kochko A, Poncet V (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9:167PubMedCentralPubMedCrossRefGoogle Scholar
  22. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J Hered 92:93–94PubMedCrossRefGoogle Scholar
  23. Hamon S, Noirot M, Anthony F (1995) Developing a coffee core collection using the principal components score strategy with quantitative data. In: Brown AHD, van Hintum TJL, Morales EAV (eds) Hodgkin T. IPGRI Wiley-Sayce publication, Core collections of Plant Genetic resources, pp 117–126Google Scholar
  24. Haouane H, El Bakkali A, Moukhli A, Tollon C, Santoni S, Oukabli A, El Modafar C, Khadari B (2011) Genetic structure and core collection of the world olive germplasm bank of Marrakech: towards the optimized management and use of Mediterranean olive genetic resources. Genetica 139:1083–1094PubMedCentralPubMedCrossRefGoogle Scholar
  25. ICO (2013) International Coffee Organization.ICO Annual Review 2012/13.
  26. Laucou V, Lacombe T, Dechesne F, Siret R, Bruno JP, Dessup M, Dessup T, Ortigosa P, Parra P, Roux C, Santoni S, Varès D, Péros JP, Boursiquot JM, This P (2011) High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theor Appl Genet 122:1233–1245PubMedCrossRefGoogle Scholar
  27. Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, Boursiquot JM, This P (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biol 8:31PubMedCentralPubMedCrossRefGoogle Scholar
  28. Leroy T, Montagnon C, Charrier A, Eskes AB (1993) Reciprocal recurrent selection applied to Coffeacanephora Pierre. I. Characterization and evaluation of breeding populations and value of intergroup hybrids. Euphytica 67:113–125CrossRefGoogle Scholar
  29. Leroy T, Montagnon C, Cilas C, Yapo AB, Charmetant P, Eskes AB (1997) Reciprocal recurrent selection applied to Coffea canephora Pierre. III.Genetic gains and results of first intergroup crosses. Euphytica 95:347–354CrossRefGoogle Scholar
  30. Leroy T, Marraccini P, Dufour M, Montagnon C, Lashermes P, Sabau X, Ferreira LP, Jourdan I, Pot D, Andrade AC, Glaszmann JC, Vieira LGE, Piffanelli P (2005) Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor Appl Genet 111:1032–1041PubMedCrossRefGoogle Scholar
  31. Leroy T, De Bellis F, Legnate H, Kanamura E, Gonzales G, Pereira LFP, Andrade AC, Charmetant P, Montagnon C, Cubry P, Marraccini P, Pot D, de Kochko A (2011) Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora. Tree Genet Genomes 7:781–798. doi: 10.1007/s11295-011-0374-6 CrossRefGoogle Scholar
  32. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi: 10.1093/bioinformatics/bti282 PubMedCrossRefGoogle Scholar
  33. Montagnon C (2000) Optimisation des gains génétiques dans le schéma de sélection récurrente réciproque de Coffea canephora Pierre. ENSA Montpellier, France, PhD thesisGoogle Scholar
  34. Montagnon C, Leroy T, Yapo A (1992) Diversité génotypique et phénotypique de quelques groupes de caféiers (Coffea canephora Pierre) en collection. Conséquences sur leur utilisation en sélection. Café Cacao Thé 36:187–198Google Scholar
  35. Montagnon C, Leroy T, Eskes AB (1998) Amélioration variétale de Coffea canephora. II. Les programmes de sélection et leurs résultats. Plantations, recherche, développement 5(2): 18–31Google Scholar
  36. Montagnon C, Cubry P, Leroy T (2012) Amélioration génétique du caféier Coffea canephora Pierre :connaissances acquises, stratégies et perspectives. Cahiers de l’Agriculture 21:143–153. doi: 10.1684/agr.2012.0556 Google Scholar
  37. Musoli P, Cubry P, Aluka P, Billot C, Dufour M, De Bellis F, Pot D, Bieysse D, Charrier A, Leroy T (2009) Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 52:634–646. doi: 10.1139/G09-037 PubMedCrossRefGoogle Scholar
  38. Odong TJ, Jansen J, van Eeuwijk FA, van Hintum TJL (2013) Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation. Theor Appl Genet 126:289–305PubMedCentralPubMedCrossRefGoogle Scholar
  39. Peakall R, Smouse P (2006) GENALEX6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  40. Perrier X, Jacquemoud-Collet JP (2006) DARwin software.
  41. Pessoa-Filho M, Rangel PHN, Ferreira ME (2010) Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach. BMC Plant Biol 10:127PubMedCentralPubMedCrossRefGoogle Scholar
  42. Poncet V, Dufour M, Hamon P, Hamon S, de Kochko A, Leroy T (2007) Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species. Genome 50:1156–1161PubMedCrossRefGoogle Scholar
  43. Rafalski JA (2009) Association genetics in crop improvement. Curr Opin Plant Biol 13:174–180CrossRefGoogle Scholar
  44. Ronfort J, Bataillon T, Santoni S, Delalande M, David JL, Prosperi JM (2006) Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biol 6:28PubMedCentralPubMedCrossRefGoogle Scholar
  45. Rovelli P, Mettulio R, Anthony F, Anzueto F, Lashermes P (2000) Microsatellites in Coffea arabica L. In: Sera T, Soccol CR, Pandey A, Roussos S (eds) Coffee biotechnology and quality, Kluwer Academic Publishers, The Netherlands, pp 123–133Google Scholar
  46. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  47. Schoen DJ, Brown AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc Natl Acad Sci USA 90:10623–10627PubMedCentralPubMedCrossRefGoogle Scholar
  48. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462PubMedCentralPubMedGoogle Scholar
  49. Thomas AS (1947) The cultivation and selection of Robusta coffee in Uganda. Emp J Exp Agric 15:66–81Google Scholar
  50. Upadhyaya HD, Bramiel PJ, Sube S (2001) Development of a chickpea core subset using geographic distribution and qualitative traits. Crop Sci 41:206–210CrossRefGoogle Scholar
  51. Van Hintum TJL, Brown AHD, Spillane C, Hodgkin T (2000) Core collections of plant genetic resources. IPGRI Technical Bulletin 3, International Plant Genetic Resource Institute, RomeGoogle Scholar
  52. Volk GM, Richards CM, Reilley AD, Henk AD, Forsline PL, Aldwinckle HS (2005) Ex situ conservation of vegetatively propagated species: development of a seed-based core collection for Malus sieversii. J Am Soc Hort Sci 130:203–210Google Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Thierry Leroy
    • 1
    Email author
  • Fabien De Bellis
    • 1
  • Hyacinthe Legnate
    • 2
  • Pascal Musoli
    • 3
  • Adrien Kalonji
    • 4
  • Rey Gastón Loor Solórzano
    • 5
  • Philippe Cubry
    • 1
    • 6
  1. 1.CIRAD-UMR AGAPMontpellierFrance
  2. 2.CNRADivoCôte d’Ivoire
  3. 3.CORECMukonoUganda
  4. 4.University of KinshasaKinshasaRDC
  5. 5.INIAPEstación Experimental PichilingueLos RiosEcuador
  6. 6.INRA, UR 629 Ecologie des Forêts MéditerranéennesURFM, Domaine Saint Paul, Site AgroparcAvignon Cedex 9France

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