Cultivated Chrysanthemum, Chrysanthemum x morifolium, is a complex crop plant harbouring six sets of chromosomes (2n=6x=54) and is characterized by a high genetic diversity and a relative large genome size (6-7Gb). The plant can be considered a neo-polyploid (recently derived polyploid), its polyploidisation results from hybridisation events among a number of wild diploid species but the exact cause of event is not known i.e. the diploid ancestors are (partly) known, however their contribution to hexaploid chrysanthemum is unclear. Polyploidisation in leads to significant changes in genome structure which phenomena together have been termed genomic shock.
The resulting polyploid genomes are often not simply the sum of parental genotypes. Similar historic hybridisation and polypoidisation events are seen in many modern polyploidy crop. But very little is known about the genetic effects. There are a multitude of outcomes upon polyploidisation, none of which are ubiquitous or have been studied in depth. Hexaploid chrysanthemum cultivars seem to show both disomic as well as random pairing, there is evidence for a multivalent repressor system and species at different ploidy levels are available. Therefore, chrysanthemum is an extremely interesting system to study the effects of hybridisation and polyploidisation events on the genome structure.
The project as a start aims to retrieve a high quality genome sequence of one of the diploid ancestral chrysanthemum species de novo. The genome sequence of the diploid genome will be complemented by re-sequencing in diploid and tetraploid species, and a number of hexaploid cultivars This will be used to establish the baseline genetic distance between these diploid species which subsequently will be used to estimate species ancestry in the hexaploid cultivars. Sequencing results will be matched with genetic linkage studies in three diploid populations involving both the species chosen for the high quality genome sequencing as well as other species. These results will be compared with a genetic map of hexaploid chrysanthemum, to study genome structure changes. This study is fundamental by nature and will contribute to the understanding of the effects of polyploidisation, to studies on gene collinearity, lineage radiation and diversification within chrysanthemum specifically and among the Asteraceae in general. In addition, it will also deliver essential information on the genome structure of the hexaploid crop plant which can later on be used as a first step to enable the use of Marker Assisted Selection (MAS).
An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis
Theoretical and Applied Genetics 130 (2017)12. - ISSN 0040-5752 - p. 2527 - 2541.
Disentangling hexaploid genetics : towards DNA-informed breeding for postharvest performance in chrysanthemum
University. Promotor(en): Richard Visser, co-promotor(en): Uulke van Meeteren; Paul Arens. - Wageningen : Wageningen University - ISBN 9789463436427 - p.
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study
Briefings in Bioinformatics 19 (2018)3. - ISSN 1467-5463 - p. 387 - 403.
High-density SNP maps for genetics and genomics in tetraploid rose
Partial preferential chromosome pairing is genotype dependent in tetraploid rose
The Plant Journal 90 (2017)2. - ISSN 0960-7412 - p. 330 - 343.