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

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Abstract

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.

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Abbreviations

AFLP:

amplified fragment length polymorphism

CATIE:

Tropical Agricultural Research and Higher Education Center

CIRAD:

Centre de Cooperation Internaionale en Recherche Agronomique pour le Développement

LG:

linkage group

LOD:

log likelihood score

QTL:

quantitative trait locus (loci)

RAPD:

random amplified polymorphic DNA

RFLP:

restriction fragment length polymorphism(s)

RGH:

resistance gene homologue

SCL:

strongest crosslink

SHRS:

Subtropical Horticulture Research Station

SSR:

simple sequence repeat

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Acknowledgements

We would like to acknowledge Dr. Claire Lanaud of CIRAD, Montpellier, France, as well as other researchers at or related to CIRAD, for the development of the population and molecular marker data mentioned above from their research. We would also like to acknowledge Dr. Wilbert Phillips of CATIE, Turrialba, Costa Rica, and other researchers involved in the production of the population mentioned above from their location. We also acknowledge Dr. Uilson Lopes of CEPLAC, Itabuna, Bahía, Brazil, for the F2 cacao population used for mapping, as mentioned in the text. In addition, we acknowledge the helpful suggestions concerning mapping technique of Dr. Johan van Ooijen of Kyazma, Wageningen, The Netherlands.

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Authors and Affiliations

  1. Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA

    J. Steven Brown, Robert T. Sautter, Cecile T. Olano, James W. Borrone, David N. Kuhn & Raymond J. Schnell

  2. Subtropical Horticulture Research Station, M & M Mars, International, Inc., c/o USDA-ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA

    J. C. Motamayor

Authors
  1. J. Steven Brown
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  2. Robert T. Sautter
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  3. Cecile T. Olano
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  4. James W. Borrone
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  5. David N. Kuhn
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  6. J. C. Motamayor
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  7. Raymond J. Schnell
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Correspondence to J. Steven Brown.

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Brown, J.S., Sautter, R.T., Olano, C.T. et al. A Composite Linkage Map from Three Crosses Between Commercial Clones of Cacao, Theobroma cacao L.. Tropical Plant Biol. 1, 120–130 (2008). https://doi.org/10.1007/s12042-008-9011-4

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  • DOI: https://doi.org/10.1007/s12042-008-9011-4

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