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Genetica

, 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
Article

Abstract

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.

Keywords

Coffea canephora SSR markers Genetic diversity Core collection Association study 

Notes

Acknowledgments

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)

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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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