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Author home page(s):
Hans van van Os
Sandra Andrzejewski
Erin Bakker
Imanol Barrena
Glenn Bryan
Bernard Caromel
Bilal Ghareeb
Edwige Isidore
Walter de Jong
Véronique Lefebvre
Dan Milbourne
Enrique Ritter
Francoise Rousselle-Bourgeois
Joke van Vliet
Robbie Waugh
Richard GF Visser
Jaap Bakker
Herman J. van Eck
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doi:10.1534/genetics.106.055871
A more recent version of this article appeared on June 1, 2006.
REGULAR RESEARCH PAPERS |
Construction of a 10,000 marker ultra-dense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genome-wide physical map
Hans van van Os 1, Sandra Andrzejewski 2, Erin Bakker 1, Imanol Barrena 3, Glenn Bryan 4, Bernard Caromel 2, Bilal Ghareeb 2, Edwige Isidore 4, Walter de Jong 4, Paul van Koert 1, Véronique Lefebvre 2, Dan Milbourne 4, Enrique Ritter 5, Jeroen N.A.M. Rouppe van der Voort 1, Francoise Rousselle-Bourgeois 2, Joke van Vliet 1, Robbie Waugh 4, Richard GF Visser 1, Jaap Bakker 1 and Herman J. van Eck 1*
1 Wageningen University
2 INRA
3 NEIKER
4 SCRI
5 Neiker
* To whom correspondence should be addressed. E-mail: herman.vaneck{at}wur.nl.
Submitted on January 16, 2006
Revised on March 8, 2006
Accepted on 30 March 2006
An ultra-dense genetic linkage map with more than 10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge this is the densest meiotic recombination map ever constructed. A fast marker ordering algorithm was used, based on the minimisation of the total number of recombination events within a given marker order, in combination with genotyping error-detection software. This resulted in "skeleton bin maps"which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in cM but in "BINS". A bin is a position on the genetic map with a unique segregation pattern and separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers probably due to cold spots for recombination. Conversely, recombination hotspots resulted in large intervals up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92 %) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples on contig construction and map based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approx. one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net)
Key Words: Solanum tuberosum, chiasma interference, map based cloning, marker saturation, recombination
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