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Construction of an integrated consensus map of the apple genome based on four mapping populations

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Abstract

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1 = Discovery × TN10-8, C2 = Fiesta × Discovery, C3 = Discovery × Prima, C4 = Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female–male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ 2 = 16.53, df = 16, p = 0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.

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Acknowledgments

This publication was partly carried out with the financial support from the Commission of the European Communities (European project “HiDRAS”: High-quality Disease Resistant Apples for a Sustainable agriculture; contract no. QLK5-CT-2002-01492), Directorate-General Research—Quality of Life and Management of Living Resources Programme. It does not necessarily reflect the Commission's views and in no way anticipates its future policy in this area. Its content is the sole responsibility of the publishers. The authors want to acknowledge E. Chevreau and M. Gallet (deceased) of INRA, France and S. Manganaris of NAGREF, Greece for providing the isozyme marker data. They also want to acknowledge technical assistance of A. Faure and L. Dondini.

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Authors and Affiliations

  1. UMR1259 Génétique et Horticulture (GenHort), INRA, BP60057, 49071, Beaucouzé, France

    A. N’Diaye & C. E. Durel

  2. Department of Plant Breeding, Wageningen University and Research Centre, Plant Research International, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    W. E. Van de Weg & L. P. Kodde

  3. Ecogenics GmbH, Wagistrasse 23, 8952, Zurich-Schlieren, Switzerland

    B. Koller

  4. Bundesanstalt für Züchtungsforschung an Kulturpflanzen, Institut für Obstzüchtung, Pillnitzer Platz 3a, 01326, Dresden, Germany

    F. Dunemann & M. Thiermann

  5. Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121, Bologna, Italy

    S. Tartarini & F. Gennari

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  1. A. N’Diaye
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  2. W. E. Van de Weg
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  4. B. Koller
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  8. F. Gennari
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  9. C. E. Durel
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N’Diaye, A., Van de Weg, W.E., Kodde, L.P. et al. Construction of an integrated consensus map of the apple genome based on four mapping populations. Tree Genetics & Genomes 4, 727–743 (2008). https://doi.org/10.1007/s11295-008-0146-0

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