Tropical Plant Biology

, 1:120

A Composite Linkage Map from Three Crosses Between Commercial Clones of Cacao, Theobroma cacao L.

  • J. Steven Brown
  • Robert T. Sautter
  • Cecile T. Olano
  • James W. Borrone
  • David N. Kuhn
  • J. C. Motamayor
  • Raymond J. Schnell


In this paper, we report the construction of the first composite map of cacao from linkage data of one F2 and two F1 mapping populations with a high number of codominant markers in common. The combination of linkage information from all three maps results in the currently most precise estimates of marker locations and distances between markers, especially in densely marked areas. JoinMap®V4 software was used for all marker quality assessment and mapping. Individual (sub-composite) maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes. Homogeneity of marker placement was very high among sub-composite maps, the composite map, and the designated “reference” map. Care was exercised in the re-creation of sub-composite maps and the composite map to include only markers with acceptable mapping quality parameters. The composite map places more markers with higher precision than any individual map. This research clearly demonstrates for the first time a very high level of marker homogeneity among commercial cacao clones compared to other species. The observed homogeneity between different maps, including the composite one, is probably due to a narrow genetic base of commercial cacao clones. Markers linked to identified quantitative trait loci (QTLs) are more likely to retain linkage in other commercial clones, rendering the QTLs in cacao potentially more stable than in other species.


Cacao Cacao linkage maps Codominant markers Composite linkage maps Marker quality 



amplified fragment length polymorphism


Tropical Agricultural Research and Higher Education Center


Centre de Cooperation Internaionale en Recherche Agronomique pour le Développement


linkage group


log likelihood score


quantitative trait locus (loci)


random amplified polymorphic DNA


restriction fragment length polymorphism(s)


resistance gene homologue


strongest crosslink


Subtropical Horticulture Research Station


simple sequence repeat


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • J. Steven Brown
    • 1
  • Robert T. Sautter
    • 1
  • Cecile T. Olano
    • 1
  • James W. Borrone
    • 1
  • David N. Kuhn
    • 1
  • J. C. Motamayor
    • 2
  • Raymond J. Schnell
    • 1
  1. 1.Subtropical Horticulture Research StationUSDA-ARSMiamiUSA
  2. 2.Subtropical Horticulture Research StationM & M Mars, International, Inc., c/o USDA-ARSMiamiUSA

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