Associations between markers and complex quantitative traits were investigated in a collection of 146 modern two-row spring barley cultivars, representing the current commercial germ plasm in Europe. Using 236 AFLP markers, associations between markers were found for markers as far apart as 10 cM. Subsequently, for the 146 cultivars the complex traits mean yield, adaptability (Finlay-Wilkinson slope), and stability (deviations from regression) were estimated from the analysis of variety trial data. Regression of those traits on individual marker data disclosed marker-trait associations for mean yield and yield stability. Support for identified associations was obtained from association profiles, i.e., from plots of P-values against chromosome positions. In addition, many of the associated markers were located in regions where earlier QTL were found for yield and yield components. To study the oligogenic genetic base of the traits in more detail, multiple linear regression of the traits on markers was carried out, using stepwise selection. By this procedure, 18-20 markers that accounted for 40-58% of the variation were selected. Our results indicate that association mapping approaches can be a viable alternative to classical QTL approaches based on crosses between inbred lines, especially for complex traits with costly measurements.T HE genetic dissection of complex traits still prepleiotropic effects on a number of performance traits in barley, but Cattivelli et al. (2002) concluded that sents a challenge. The oligo/polygenic character little is known about the regulatory mechanisms controlof complex traits, combined with interactions between ling stress responses, mainly because all stress responses loci, makes the task a priori difficult and intricate. In involve many genes. addition, environmental factors trigger and modify geneThe polygenic basis of complex traits has conseactions and thereby further complicate the analysis.quences for the application of quantitative trait locus Yield is the classical example of a complex trait. Yield (QTL) mapping methodology, as many markers that fluctuations in relation to environmental factors are are associated with the trait need to be identified. Typioften described in terms of adaptability and stability.cally, for QTL mapping, a cross between two inbred The latter can be considered to constitute complex traits lines is made and the cosegregation of alleles of mapped on their own. Parameters quantifying adaptability and marker loci and phenotypic traits allows the identificastability require observations across a range of environtion of linked markers. For complex traits with GE interments for their estimation. The parameters are typically action, this approach implies large-scale testing of spedefined in terms of linear and quadratic functions of cial mapping populations across a range of environments. the genotype by environment (GE) interaction (Lin et

A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus (BYD)), and morphological traits (rachilla hair length, lodicule size) with AFLP markers and SSR markers were found. Known major genes and QTLs were confirmed, but also new putative QTLs were found. The LD mapping clearly indicated the common occurrence of Rph3, a gene for hypersensitivity resistance against Puccinia hordei, and also confirmed the QTL Rphq2 for prolonging latency period of P. hordei in seedlings. We also found strong indication for a hitherto not reported gene for resistance or tolerance to BYD on chromosome 2, linked to SSR marker HVM054. Our conclusion is that LD mapping is a valuable additional tool in the search for applicable marker associations with major genes and QTLs.