A comparative genetic and QTL mapping was performed between Quercus robur L. and Castanea sativa Mill., two major forest tree species belonging to the Fagaceae family. Oak EST-derived markers (STSs) were used to align the 12 linkage groups of the two species. Fifty-one and 45 STSs were mapped in oak and chestnut, respectively. These STSs, added to SSR markers previously mapped in both species, provided a total number of 55 orthologous molecular markers for comparative mapping within the Fagaceae family. Homeologous genomic regions identified between oak and chestnut allowed us to compare QTL positions for three important adaptive traits. Colocation of the QTL controlling the timing of bud burst was significant between the two species. However, conservation of QTL for height growth was not supported by statistical tests. No QTL for carbon isotope discrimination was conserved between the two species. Putative candidate genes for bud burst can be identified on the basis of colocations between EST-derived markers and QTL.T HE genetic basis and evolution of adaptive traits that evolve in response to selection are still largely unknown. Because of the prominent neo-Darwinian view that pointed out the major role of mutations with small effects (infinitesimal model) (Fisher 1930), the study of the genetic basis of adaptation has received little attention until recently (Orr and Coyne 1992). At the same time, Barton and Turelli (1989) reviewed theories and experimental results on evolutionary quantitative genetics. Most of the quantitative traits can evolve in response to selection because the additive variance represents a significant part of their phenotypic variance. Nevertheless, the number of loci involved, the magnitude of their effects, the type of gene action (additivity, dominance, epistasis, and pleiotropy), and the existence of genotypeby-environment interaction effect remain unknown for many traits of adaptive significance. In particular, the number of their underlying loci and the magnitude of the allelic effects are key factors of the evolution of adaptive traits. Orr and Coyne (1992) showed that Fisher's model was incomplete and that mutations with large effects were sometimes involved in adaptation. Indeed, on the basis of Orr's (1998) recent theoretical work, adaptation seems to involve many loci of small and moderate effect but also a few loci of large effect, giving rise to an L-shaped distribution of factors fixed during adaptive evolution. Moreover, from an evolutionary point of view, in a complex organism, adaptation would occur mainly with mutations of intermediate effects that permit it to achieve an appropriate tradeoff between an acceptable probability of fixation and an acceptable probability to be favorable (Orr 2000).Quantitative trait locus (QTL) studies were expected to provide new insights into fundamental questions regarding the genetic basis of quantitative traits and adaptation (Mitchell-Olds 1995). Despite some biases in QTL analysis, such as the underestimation of the number ...