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Thanks to advances in next generation sequencing it is now straightforward to develop tens or even hundreds of thousands of SNP markers. Advances in genotyping technology have made it feasible to genotype progenies of crosses, panels of genotypes, or even a complete breeding program, by using arrays with tens of thousands of SNPs, or by random or targeted sequencing technologies. Recently software has been developed for dosage scoring and linkage mapping in polyploid crops. This means that advanced genetic analyses can now also be performed in many polyploid ornamentals. A DNA marker, such as a single nucleotide polymorphism (SNP), linked to a trait enables following a gene or allele during crosses and in a breeding program. Association of a SNP marker to a trait or a component of a trait may be done through QTL analysis in segregating populations, by genome-wide association analysis (GWAS) in a set of accessions, or through an analysis across a pedigree. In these analyses, a dense linkage map is a very important tool, to delineate and possibly narrow down the QTL interval and to filter away false positive SNPs. New developments in linkage mapping include paying attention to even marker coverage, and new ways to use markers to infer haplotypes. The latter is especially important in polyploids, in populations with multiple parents, or in wide panels used for association studies. In such cases multiple functional alleles may segregate simultaneously, that cannot all be tagged uniquely by single biallelic SNP markers.

Many ornamental crops are polyploid or even exist at different ploidy levels. Polyploid QTL analysis tools have been developed in recent years, yet they are limited in the population types they accept. Biparental populations are nowadays being regarded as a limited tool for QTL discovery, as only a limited number of QTLs occurs in an experimental cross and their effects might not be stable across genetic backgrounds. Genome-Wide Association Studies include more genetic diversity but suffer from (hidden) genetic structure and low frequency of QTL alleles. Both factors influence QTL detection and effect estimation, decreasing the sensitivity of QTL analysis. Alternatively, multiparental populations (MPP) can be used, potentially combining multiple QTLs and QTL alleles with known population structure and balanced allele frequencies. Breeding populations of interconnected crosses also constitute a form of MPP and QTLs identified in them might be more applicable to commercial cultivars. To perform QTL analysis in polyploids, mixed models or Bayesian approaches that consider pedigree information are recommended. During the analysis, QTL effects are ideally estimated using Identity by Descent (IBD) alleles (genomic regions that originate from the same ancestor) which can be obtained through haplotype estimation. Although MPPs could thus be a powerful set-up to estimate polyploid haplotypes, a software gap was identified as no current polyploid haplotyping tools are able to utilize MPP pedigree information to obtain haplotypes across an MPP. In order to utilize MPPs to their full extent and expand polyploid QTL analyses to encompass typical breeding populations, new haplotyping tools must be developed.

Thanks to recent advances in high-throughput genotyping tools and software for genetic analyses, it is now possible to perform QTL mapping and genome-wide association analysis in tetraploid roses and to establish the effect of favorable SNP marker haplotype(s) (“plus-alleles”). The challenge is how to use these tools and technologies for rose breeding in a cost-effective way. At least four points need to be addressed: (1) which steps of the breeding process may benefit from marker information; (2) what is the value of the identified plus-alleles for the trait; (3) where in the breeding germplasm do these plus-alleles occur, and (4) how can plants carrying these plus-alleles be selected efficiently. Here we discuss for which purposes markers may be applied.

Understanding the genetic basis of plant development in potato requires a proper characterization of plant morphology over time. Parameters related to different aging stages can be used to describe the developmental processes. It is attractive to map these traits simultaneously in a QTL analysis; because the power to detect a QTL will often be improved and it will be easier to identify pleiotropic QTLs. We included complex, agronomic traits together with plant development parameters in a multi-trait QTL analysis. First, the results of our analysis led to coherent insight into the genetic architecture of complex traits in potato. Secondly, QTL for parameters related to plant development were identified. Thirdly, pleiotropic regions for various types of traits were identified. Emergence, number of main stems, number of tubers and yield were explained by 9, 5, 4 and 6 QTL, respectively. These traits were measured once during the growing season. The genetic control of flowering, senescence and plant height, which were measured at regular time intervals, was explained by 9, 10 and 12 QTL, respectively. Genetic relationships between aboveground and belowground traits in potato were observed in 14 pleiotropic QTL. Some of our results suggest the presence of QTL-by-Environment interactions. Therefore, additional studies comparing development under different photoperiods are required to investigate the plasticity of the crop.

The study of quantitative trait's expression over time helps to understand developmental processes which occur in the course of the growing season. Temperature and other environmental factors play an important role. The dynamics of haulm senescence was observed in a diploid potato mapping population in two consecutive years (2004 and 2005) under field conditions in Finland. The available time series data were used in a smoothed generalized linear model to characterize curves describing the senescence development in terms of its onset, mean and maximum progression rate and inflection point. These characteristics together with the individual time points were used in a Quantitative trait loci (QTL) analysis. Although QTLs occurring early in the senescence process coincided with QTLs for onset of senescence, the analysis of the time points made it difficult to study senescence as a continuous trait. Characteristics estimated from the senescence curve allowed us to study it as a developmental process and provide a meaningful biological interpretation to the results. Stable QTLs in the two experimental years were identified for progression rate and year-specific QTLs were detected for onset of senescence and inflection point. Specific interactions between loci controlling senescence development were also found. Epistatic interaction between QTLs on chromosomes 4, 5 and 7 were detected in 2004 and pleiotopic effects of QTLs on chromosomes 3 and 4 were observed in 2005.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and m

The genotype by environment interaction study of broccoli, amongst others demonstrates that traits of a cultivar are sometimes ranked differently when grown in an organic production system compared to a conventional system. This has strong implications for breeding strategies. The breeders interviewed acknowledged that more attention on abiotic and biotic stress resistance in a broccoli breeding programme is needed which is in accordance with the farmers' varietal requirements. The first findings of the field trials show that cultivar performance is influenced by season and region, and differences in treatment (organic versus conventional management). The field trials showed that there are cultivars with broad adaptation such as "Green Goliath". These cultivars performed across locations, seasons and treatments within the sub-top group, however, organic farmers would benefit more from cultivars specifically adapted to their region and season. The trial results showed a wide range of glucosinolate levels. Glucoraphanin was very genotype dependent, while glucobrassicin and neoglucobrassicin were more influenced by abiotic and biotic environmental factors. Therefore, there are opportunities for nutritional performance enhancement under organic conditions which would provide an added value to the product quality with respect to human and plant health. Further elaboration of the dataset will contribute to the design of regional breeding strategies for improved broccoli cultivars for the organic market.

Genetic analysis in strictly outcrossing species is far more complicated than in species that can be selfed. When, in addition to that, a species has a long generation cycle, and when progenies from crosses require much space, as is the case for apple trees, then acquiring genetic knowledge about the species is a matter of high costs and much patience. However, for a breeder such knowledge is highly valuable, since it enables him or her better to combine desired characters into new cultivars.DNA techniques developed in the eighties and nineties have made it possible to visualize variation on the DNA level, e.g. between the two parents of a cross. These differences, usually visualized as differences in banding patterns on a photographic film, are called molecular markers. Molecular markers correspond to physical locations on chromosomes, the marker loci. By studying a progeny of a cross for the absence and presence of combinations of markers, the order of the marker loci on the chromosomes can be estimated and presented in a molecular linkage map. Furthermore, molecular markers also allow the estimation of the location of genes for important traits. Many traits are determined by more than a single gene and in addition to that, suffer from strong influence of environmental factors such as the weather and the soil. The contributions of each of the separate genes, the quantitative trait loci or 'QTLs' are not individually observable, but have to be estimated using statistical techniques called QTL analysis or QTL mapping.In this doctoral thesis, properties of genetic analysis with molecular markers in outbreeding species are studied. A molecular linkage map of apple is presented and map positions of some important genes, such as resistance to apple scab, and fruit acidity, were estimated. Furthermore, quantitative traits in apple were studied and QTLs for fruit quality traits were mapped. Also, frequentist and Bayesian methods for QTL analysis of multiple QTLs were comp