Tree Genetics & Genomes

, 1:93 | Cite as

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

  • Ivan Scotti
  • Andrea Burelli
  • Federica Cattonaro
  • David Chagné
  • John Fuller
  • Peter E. Hedley
  • Gunnar Jansson
  • Celine Lalanne
  • Delphine Madur
  • David Neale
  • Christophe Plomion
  • Wayne Powell
  • Michela Troggio
  • Michele Morgante
Original Paper

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.

Keywords

Picea abies Conifers Linkage map Genome structure Molecular markers Autocorrelation 

Notes

Acknowledgements

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

Supplementary material

11295_2005_12_MOESM1_ESM.pdf (41 kb)
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 (99 kb)
“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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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Ivan Scotti
    • 1
    • 2
  • Andrea Burelli
    • 1
  • Federica Cattonaro
    • 1
  • David Chagné
    • 3
  • John Fuller
    • 4
  • Peter E. Hedley
    • 4
  • Gunnar Jansson
    • 5
  • Celine Lalanne
    • 3
  • Delphine Madur
    • 3
  • David Neale
    • 6
  • Christophe Plomion
    • 3
  • Wayne Powell
    • 4
  • Michela Troggio
    • 6
  • Michele Morgante
    • 1
  1. 1.Dipartimento di Scienze Agrarie ed AmbientaliUniversità di UdineUdineItaly
  2. 2.INRA-UMR ECOFOGKourou CedexFrench Guyana
  3. 3.INRA-UMR BIOGECOCestasFrance
  4. 4.Scottish Crop Research InstituteDundeeUK
  5. 5.SkogforskUppsalaSweden
  6. 6.Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Department of Environmental HorticultureUniversity of CaliforniaDavisUSA

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