Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Estimation Of The Effective Number Of QTL Alleles In Pedigreed Plant Populations

Hans Jansen¹ , Roeland Voorrips² , Eric Van de Weg² , Marco Bink¹

¹  Biometris, P.O. 100, 6700 AC Wageningen, The Netherlands

²  Plant Research International, P.O. Box 16, 6700 AA Wageningen, The Netherlands

In plants, QTL analysis has been carried out predominantly in experimental populations (BC, F2, RIL). A novel approach is to use all available breeding material by incorporating information about genetic relationships between individuals (pedigree information). The advantage of this approach is that QTL are identified in the breeding material and can be employed directly in decisions about future crosses.
In this paper we will focus on QTL analysis of pedigreed observations by means of penalised regression on identity by descent (IBD) probabilities. This method provides us with information about the effective number of QTL alleles present in the pedigree. The methods will be demonstrated using pedigrees of apple. Apple (Malus domestica Borkh.) is an outbreeding species (n = 2x = 34) with a long juvenile period. Apple cultivars consist of clones, where multiplication occurs by (bud) grafting. Apple breeding started in the 19th century and many of the old varieties are still present in orchards.