Comparative genome mapping of the Rosaceae : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Molecular Genetics and Genomics, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand

Abstract

Comparative genome mapping uses genetic map and DNA sequence alignment to assess genome conservation between two or more organisms. This study makes use of the recent genome sequence availability of four Rosaceae genera, and the development of new, and the expansion of existing, linkage maps to: 1) explore overall genome synteny between apple and strawberry; 2) assess homology between, and the degree of ancestral genome rearrangement among, four genera; and 3) compare genome synteny with respect to the production of anthocyanins between raspberry and strawberry. The inter-tribal comparison of the genomes of apple and diploid strawberry, conducted by adding 56 newly developed orthologous markers to existing linkage maps, identified 21 regions of genomic synteny between the linkage groups of apple and strawberry. In addition, this work identified two each of potential translocations, inversions and insertions, and provided a set of orthologous markers that will be useful for orienting and anchoring other Rosaceae genome sequences. Orthologous- and other DNA sequence-based markers were used in the construction of new linkage maps for Rubus occidentalis 96395S1 and R. idaeus =Latham‘. The sequences from which the Rubus markers were designed were compared with the draft genome sequences of Malus × domestica =Golden Delicious‘, Fragaria vesca =Hawaii 4‘, and Prunus persica =Lovell‘ to identify regions of orthology. This first comparison of Rubus linkage maps with other members of the Rosaceae identified a nearly 1:1 homology between the linkage groups of Rubus and F. vesca, as well as family-wide conservation among some linkage groups. The F1 progeny of Rubus occidentalis 96395S1 × R. idaeus =Latham‘ was used to conduct a quantitative trait locus (QTL) analysis to explore the presence of associations between genotype and the variation in concentrations of anthocyanins in the fruit. Seven associations of traits with markers designed from the sequences of transcription factors and anthocyanin biosynthetic pathway genes were identified, providing opportunities for further fine-scale mapping, as well as cloning and expression analyses. The comparison of QTL maps of Rubus and Fragaria × ananassa suggests that homologous genomic regions may be important in the expression of various fruit quality traits.