Valerian (Valeriana officinalis L. s.l.) is an important medicinal plant, which is used for insomnia and restlessness. Preparations for treating of such indications are produced from the dried rootstock (roots and rhizome). The raw material comes invariably from field cultivation. Due to the very fine, carpet-like root structure, a high proportion of soil is attached to the root system after the harvest, which requires an extensive post-harvest treatment. Losses of root-yield and important secondary compounds are the consequences. Therefore, a breeding project was set up to develop varieties with coarser root structure and acceptable secondary compound contents by selection- and cross-breeding.The aim of this thesis was to investigate two fundamental aspects in order to support valerian breeding:•Root structure analyses and the localization of secondary compounds within the root system•Mating behavior under conditions of open pollination in the fieldKnowledge about the relationship between root structure and secondary compounds contents is of central importance for the breeding project. For instance, a decrease of secondary compound contents with increasing root thickness would be disadvantageous for the primary breeding goal.Two techniques were developed and applied to localize secondary compounds in different parts of the root system of four cloned valerian genotypes. An analytical determination of the valerenic acids and the essential oil contents was performed by HPLC and water-distillation, respectively. The horizontal distribution of the essential oil droplets within root cross-sections was determined by a fluorescence-microscopic image-analysis. Based on the analytical investigations on the sesquiterpene acids (sum of valerenic acid and acetoxyvalerenic acid) and essential oil contents, the adventitious roots showed 25 to 30 % higher contents than the lateral roots, and these in turn had a 25 to 30 % higher contents compared to the rhizomes. Differences between four root diameter fractions were not detectable for any secondary compound. The image analysis showed that 43 % of the detected oil droplets were located in the root cortex (parenchyma) close to the root surface (epidermis). The remaining 57 % were detected in the subjacent root cortex (inner parenchyma). The central cylinder was free of essential oil droplets. Differences in oil droplet distribution and density between the genotypes, the root thickness and the harvesting depth are detectable. In summary, the results indicate that a coarser root structure did not lead to a decrease of important secondary compounds. The second aim of this thesis dealt with the determination of the outcrossing rate under conditions of open pollination. Cross-pollination is described as the naturally pollination system of valerian, however self-pollination cannot be excluded. Within the offspring from open pollinated and random mated (panmixia) valerian plants, the proportion of descendants, who were generated by cross-pollination, was determined by marker based analyses (AFLP). The cross-pollination was accepted, if the reference marker of the crossing partner was detected. The determined proportion of cross-pollination ranged from 76.5 to 97.7 %. Thus, the predominant tendency of the valerian breeding material to outbreeding was confirmed.