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Genetics, Vol. 165, 2107-2116, December 2003, Copyright © 2003

Toward a Marker-Dense Meiotic Map of the Potato Genome: Lessons From Linkage Group I

Edwige Isidorea, Hans van Osb, Sandra Andrzejewskic, Jaap Bakkerd, Imanol Barrenae, Glenn J. Bryana, Bernard Caromelc, Herman van Eckb, Bilal Ghareebc, Walter de Jonga, Paul van Koertd, Véronique Lefebvrec, Dan Milbournea, Enrique Rittere, Jeroen Rouppe van der Voortd, Françoise Rousselle-Bourgeoisc, Joke van Vlietb,d, and Robbie Waugha
a Genome Dynamics Programme, Scottish Crop Research Institute, Dundee DD2 5DA, United Kingdom,
b Laboratory of Plant Breeding, Wageningen University, 6700 AJ Wageningen, The Netherlands,
c Station de Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique, 84143 Monfavet Cedex, France,
d Laboratory of Nematology, Wageningen University, 6709 PD Wageningen, The Netherlands
e NEIKER, E-01080 Vitoria, Spain

Corresponding author: Robbie Waugh, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom., rwaugh{at}scri.sari.ac.uk (E-mail)

Communicating editor: T. BROWN

Segregation data were obtained for 1260 potato linkage group I-specific AFLP loci from a heterozygous diploid potato population. Analytical tools that identified potential typing errors and/or inconsistencies in the data and that assembled cosegregating markers into bins were applied. Bins contain multiple-marker data sets with an identical segregation pattern, which is defined as the bin signature. The bin signatures were used to construct a skeleton bin map that was based solely on observed recombination events. Markers that did not match any of the bin signatures exactly (and that were excluded from the calculation of the skeleton bin map) were placed on the map by maximum likelihood. The resulting maternal and paternal maps consisted of 95 and 101 bins, respectively. Markers derived from EcoRI/MseI, PstI/MseI, and SacI/MseI primer combinations showed different genetic distributions. Approximately three-fourths of the markers placed into a bin were considered to fit well on the basis of an estimated residual "error rate" of 0–3%. However, twice as many PstI-based markers fit badly, suggesting that parental PstI-site methylation patterns had changed in the population. Recombination frequencies were highly variable across the map. Inert, presumably centromeric, regions caused extensive marker clustering while recombination hotspots (or regions identical by descent) resulted in empty bins, despite the level of marker saturation.




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