Analysis of a Complex Polyploid Plant Genome using Molecular Markers: Strong Evidence for Segmental Allooctoploidy in Garden Dahlias

Abstract

In some plant genera that contain species with complex genomes, the level and type of ploidy are still unknown due to a lack of characterized reference species and contradictory results from genetic and cytogenetic studies. Herein, we present the analysis of the genome of garden dahlias using molecular markers; this species is one for which the genome ploidy has remained controversial. We generated simple‐sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data from two segregating populations of garden dahlias. The combined analysis of SSR marker segregation, the ratio of single‐dose to multidose markers, the ratio of markers linked in coupling and repulsion, and map construction revealed a predominantly autooctoploid genome with a low degree of preferential pairing. This finding indicates that dahlias are segmental allooctoploids that originated from autotetraploid ancestral genomes. Our results demonstrate that marker analysis is a suitable method for ploidy analysis in nonmodel crops. Novel marker techniques, such as restriction site associated DNA, will make this analysis even more effective before whole genome sequencing can be realized for these crops.