Genetic mapping in a full-sib family of apple

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 compared, using data of an apple cross.