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Genetics, Vol. 168, 1737-1749, November 2004, Copyright © 2004
doi:10.1534/genetics.104.028993
Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs
Recovering QTL Identical-by-Descent Status Information From Marker Data
Sébastien Crepieux*,1,
Claude Lebreton
,
Bertrand Servin
and
Gilles Charmet*
* UMR 1095 INRA-UBP, 63039 Clermont-Ferrand Cedex 2, France
Limagrain Verneuil Holding, site d'ULICE, F-63204 Riom Cedex, France
INRA UMR de Génétique Végétale, INRA/UPS/INAPG, 91 190 Gif sur Yvette, France
1 Corresponding author: Limagrain Verneuil Holding, site d'ULICE, av. G. Gershwin, BP173, F-63204 Riom Cedex, France.
E-mail: sebastien.crepieux{at}limagrain.com
Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated.
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