LWV22014 Tapping into the genome diversity of Chrysanthemum (BO-68-001-052)

As the hexaploid cultivated crop is outcrossing showing a very high genetic diversity, crossing populations can potentially harbor 12 different alleles at any given locus of importance, making conventional breeding very demanding. Furthermore, variation may occur among homoeologous chromosomes. A pangenome study in potato (Hoopes et al., 2022) showed that considerable variation may be present even among haplotypes of a cultivar suggesting not all critical genes may be present on all homologs.

Diploid (and tetraploid) wild species may serve as an opportunity to study the effects of genes and alleles of genes for important traits more easily. Results may subsequently direct trait discovery and marker assisted selection in the hexaploid crop or be used in breeding germplasm directly. Knowledge on structural variation and presence/absence of genes within these wild species would be very helpful in dealing with this complexity and our understanding of interactions of genetic variation and the origin of hexaploid chrysanthemum.

Within this project we want to establish a framework for this both in terms of assessing and cataloging sequence variation among species as well as start exploring a pangenome in a diploid-hexaploid setting. We aim to sequence different accessions from several wild species and compare those amongst each other and with sequences of hexaploid cultivars to study several aspects of genetic diversity. The study will contribute to the understanding of the effects of the polyploidization process. It will improve insight in the genetic diversity of chrysanthemum as a crop and aspects of the pan-genome of chrysanthemum, lineage radiation and synteny within chrysanthemum specifically (diploid and hexaploid plants) and among the Asteraceae in general. By doing so we will also lay the basis for gene function analysis in one or more of the diploid species for the purpose of directing breeding efforts in the cultivated hexaploid Chrysanthemum crop.