Alterations of DNA methylation and gene expression during hybridization and polyploidization in Fragaria spp.

- We investigated the alterations of DNA methylation and gene expression during hybridization and polyploidization in genus Fragaria.
- Changes in DNA methylation were mainly the result of hybridization rather than genome doubling.
- Both hybridization and genome doubling influenced gene expression to a certain degree.
- Allopolyploidization influenced gene sequences that are involved in various biological pathways.

Allopolyploidization occurs frequently in plant evolution and has created many crops with high yield. The consequences of allopolyploidization events are not always the same between different plant systems. In this study, we investigated the epigenetic and transcriptomic changes caused by interspecific hybridization and genome doubling in the strawberry. Changes were found both in DNA methylation and gene expression during allopolyploidization. Changes in DNA methylation were mainly attributable to hybridization which caused the methylation states of 31.92% of all the loci studied to change and were maintained by genome doubling. Hybridization and genome doubling all together influenced 13.05% of gene expression. Most of the changes in interspecific hybridization and genome doubling events were reproducible, but a small number of them were stochastic between different pentaploid and decaploid lines. Sequence analysis of the fragments that underwent changes in DNA methylation or gene expression indicated that these changes were associated with various biological pathways. Our results suggest that alterations in DNA methylation caused by hybridization and polyploidization may induce changes in gene expression and lead to new agronomic traits in polyploids.