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Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

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Abstract

In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotransposons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous.

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Acknowledgements

This project was supported by the EU grant no. BIO4-CT972125 “ANACONGEN.” The authors wish to thank Nicoletta Felice for technical support.

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Authors and Affiliations

  1. Dipartimento di Scienze Agrarie ed Ambientali, Università di Udine, Via delle Scienze 208, 33100, Udine, Italy

    Ivan Scotti, Andrea Burelli, Federica Cattonaro & Michele Morgante

  2. INRA-UMR ECOFOG, Campus Agronomique, BP 709, 97387, Kourou Cedex, French Guyana

    Ivan Scotti

  3. INRA-UMR BIOGECO, 69 route d'Arcachon, 33612, Cestas, France

    David Chagné, Celine Lalanne, Delphine Madur & Christophe Plomion

  4. Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    John Fuller, Peter E. Hedley & Wayne Powell

  5. Skogforsk, Uppsala Science Park, Uppsala, 75183, Sweden

    Gunnar Jansson

  6. Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Department of Environmental Horticulture, University of California, Davis, CA, 95616, USA

    David Neale & Michela Troggio

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  1. Ivan Scotti
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Correspondence to Ivan Scotti.

Electronic supplementary materials

11295_2005_12_MOESM1_ESM.pdf

EST markers (a) reference for each marker (b) Primer sequences for five new markers. Five additional markers will be described in a subsequent paper (PDF 42 kb)

11295_2005_12_MOESM2_ESM.pdf

“Inclusive” linkage map (see text for details). Linkage groups are named after the groups in the “framework“ map. Some of the framework groups (a and b; g and h) are connected by accessory markers in the inclusive map. Two extra groups (n and o) appear here relative to the framework map (PDF 101 kb)

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Scotti, I., Burelli, A., Cattonaro, F. et al. Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst). Tree Genetics & Genomes 1, 93–102 (2005). https://doi.org/10.1007/s11295-005-0012-2

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  • DOI: https://doi.org/10.1007/s11295-005-0012-2

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