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Originally published as Genetics Published Articles Ahead of Print on August 5, 2005.

Genetics, Vol. 171, 1341-1352, November 2005, Copyright © 2005
doi:10.1534/genetics.105.045963

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Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population

Johan D. Peleman*,1, Crispin Wye*, Jan Zethof{dagger}, Anker P. Sørensen*, Henk Verbakel*, Jan van Oeveren*, Tom Gerats{ddagger} and Jeroen Rouppe van der Voort*

* Keygene N.V., NL-6708 PW, Wageningen, The Netherlands, {ddagger} Department of Experimental Botany, Plant Genetics, University of Nijmegen, NL-6525 ED Nijmegen, The Netherlands and {dagger} Department of Plant Systems Biology, University of Ghent/VIB, B-9052 Ghent, Belgium

1 Corresponding author: Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands.
E-mail: johan.peleman{at}keygene.com

In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (COMPLEX TRAIT CONSORTIUM 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.




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