Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase.

BACKGROUND: Epigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1. PURPOSE: Here, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system. RESULTS: Methylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification. CONCLUSION: Collectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.

Exploring interspecific hybridization dynamics in artificial forests of Pinus brutia and P. halepensis: Implications for sustainable afforestation.

Interspecific hybridization increases genetic diversity, which is essential for coping with changing environments. Hybrid zones, occurring naturally in overlapping habitats of closely related species, can be artificially established during afforestation. The resulting interspecific hybridization may promote sustainability in artificial forests, particularly in regions facing degradation due to climate change. Currently, there is limited evidence of hybridization during regeneration of artificial forests. Here, we studied the frequency of Pinus brutia Ten. × P. halepensis Mill. hybridization in five planted forests in Israel in three stages of forest regeneration: seeds before dispersal, emerged seedlings and recruited seedlings at the end of the dry season. We found hybrids on P. brutia, but not on P. halepensis trees due to asynchronous cone production phenology. Using 94 single-nucleotide polymorphism (SNP) markers, we found hybrids at all stages, most of which were hybrids of advanced generations. The hybrid proportions increased from 4.7 ± 2.1 to 8.2 ± 1.4 and 21.6 ± 6.4 per cent, from seeds to emerged seedlings and to recruited seedlings stages, respectively. The increased hybrid ratio implies an advantage of hybrids over P. brutia during forest regeneration. To test this hypothesis, we measured seedling growth rate and morphological traits under controlled conditions and found that the hybrid seedlings exhibited selected traits of the two parental species, which likely contributed to the fitness and survival of the hybrids during the dry season. This study highlights the potential contribution of hybrids to sustainable-planted forests and contributes to the understanding of genetic changes that occur during the regeneration of artificial forests.