The aim of this project is to develop a suite of tools for molecular breeding of crop plants for sustainable and competitive agriculture. The tools help the breeder in predicting phenotypic response of genotypes for complex traits under a range of environmental conditions. Pepper will be used as a model crop. The idea is to use a crop growth model as a tool to predict the phenotypic response of a genotype under different environmental conditions and to use genetic markers in the QTL regions to estimate the genotype specific model parameters. We will adapt an existing growth model to cope with genotype specific information. Specific QTL-analysis methods will be developed as a tool to find the corresponding QTL for the crop growth parameters. QTL can be used directly in marker assisted breeding, but it would be more interesting to find the genes in the QTL region, which account for the genotypic differences of the model parameters. These genes will help to unravel the genetic basis of complex traits such as yield. In this project two approaches will be used to find these genes: candidate gene finding, using known genes from other species, and differential gene expression. Molecular breeding will not completely replace large scale phenotyping. Hence, automated and fast high-throughput tools to reduce the amount of manual labour necessary in phenotyping experiments are called for. In this project an image analysis tool and a fluorescence tool will be developed to measure large numbers of phenotypic traits automatically. In the last year of the project a validation experiment will be conducted to show the potential use of the total concept developed in this study and the potential impact of every single tool or technique. Dissemination of results to plant breeding industry will be done in close cooperation with an industrial advisory board and will involve specialized workshops and a molecular breeding course as well as lectures, papers and website.