DNA methylation and histone modification patterns around Agrobacterium T-DNA integrations in woodland strawberry Fragaria vesca

Agrobacterium transformation is widely used for plant genome manipulation, which is completed by integration of transfer DNA (T-DNA) into the plant genome. Application of new biotechnology such as genome editing in many horticultural crops is mediated by Agrobacterium transformation. Currently, our knowledge on the chromatin environment around the T-DNA integration sites is limited. In this study, we mapped the genomic locations of T-DNA integrations in woodland strawberry (Fragaria vesca) to the telomere-to-telomere genome, and found that T-DNA integrations recovered under antibiotic selections were biased towards TE-poor euchromatic sequences. We further performed bisulfite sequencing and chromatin immunoprecipitation to analyze DNA methylation and histone modifications of the integration sites. T-DNA integration sites had low levels of DNA methylation, as well as low levels of 24-nt small RNAs which were associated with RNA-dependent DNA methylation. In addition, the sequences flanking T-DNA integration sites had low levels of a silent mark histone 3 lysine 27 trimethylation, and high levels of an active mark histone 3 lysine 9/lysine 14 acetylation. Such structure indicates an open chromatin environment favored by T-DNA integration and/or antibiotic selection in strawberries. This study provides clues for increasing the transformation efficiency for molecular breeding in Rosaceae species in the future.