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 Chagne, John Fuller, Peter E. Hedley, Gunnar Jansson, Celine Lalanne, Delphine Madur, David Neale, Christophe Plomion, Wayne Powell, Michela Troggio, Michele Morgante

Research output: Contribution to journalArticlepeer-review

12 Citations (SciVal)

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.
Original languageEnglish
Pages (from-to)93-102
Number of pages10
JournalTree Genetics and Genomes
Volume1
Issue number3
Early online date01 Oct 2005
DOIs
Publication statusPublished - 01 Nov 2005

Keywords

  • Picea abies
  • Conifers
  • Linkage map
  • Genome structure
  • Molecular markers
  • Autocorrelation

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