Epigenetic control of seed dormancy using capsella bursa-pastoris as a model species

Resumen

The function of seed dormancy is to spread germination across time in synchrony with seasonal cycles to avoid unfavourable environmental conditions. Phase transitions during seeds’ life require genome reprogramming at a large scale, which is often associated with major changes in chromatin structure. Recent advances have highlighted the role of chromatin remodelling in dormancy regulation. Despite the high importance of dormancy for plants competitiveness and life cycle timining, there is an enourmous lack of knowledge about its regulation at the molecular level. Natural variation in the responses of the epigenetic regulation processess to the environment could be informative regarding adapatation to climate. A greater understanding of seed dormancy is essential in a future where the impact of climate change on natural plant communities is uncertain. Capsella bursa-pastoris has a very small phylogenetic distance with Arabidopsis thaliana, but the latter appears to be uncompetitive and is actually relatively rare in the wild. We think that C. bursa-pastoris is an excellent choice as a model species for seed dormancy research. The principal aim of this doctoral thesis was to determine the possible implication of epigenetic processes in the regulation of secondary seed dormancy induction and maintenance and in the depth differences between natural genotypes of C. bursa-pastoris. Our research was approached using a broad set of techniques, including quantification of global DNA methylation, immunolocalizations and RNA-Seq. Substantial variation in the potential of induction of secondary seed dormancy was found between the whole range of seed accessions studied, with genotype being the most important factor. Two accessions were selected for their extreme responses to the conditions tested, -367, (deep-dormant), and -799 (non-deep dormant), for an RNA-Seq analysis. The general patterns of H4Ac and 5-mC in the immunolocalizations showed wide varation within and between different tissues of the seeds and between different dormancy states. There was a lower number of H4Ac marked nuclei in deeper dormancy conditions. For primary dormant seeds, there was a higher number of 5-mC marked nuclei and higher DNA methylation levels in deeper dormant states. When secondary seed dormancy was induced, the highest DNA methylation level was reached after 3 d of imbibition in darkness, showing decreasing levels towards a deeper dormancy. The same pattern was observed in the immunolocalizations. The RNA-Seq results showed an active involvement of epigenetic regulation in the establishment of different secondary seed dormancy depths. The up-regulated SNL1, and several other up-regulated histone deacetylases, could be affecting the expression of genes related to the synthesis or signalling of ABA and of genes related to ethylene, but also they could be implicated in the down-regulation of genes implicated in the synthesis, signalling and transport of auxin. The cross-talk between phytohormones plays an important role in the regulation of the germination capability and in the differences in secondary dormancy depth between accessions. The hyper-acetylation caused by valproic acid provoked alterations in the expression of genes implicated in the biosynthesis and signalling pathways of different phytohormones. Seeds imbibed in this histone deacetylase inhibitor had the biosynthesis of auxin repressed. Our data clearly highlight the role of histone deacetylation in the establishment of secondary seed dormancy depth differences. These results could be indicating a common pathway in the regulation of secondary seed dormancy induction and in the delay of germination through histone deacetylase complexes, with SNL proteins as central components.