RESEARCH

Genetics of core vernalization network in Arabidopsis halleri gemmifera

Vernalization provides a powerful system for uncovering epigenetic principles and is often cited as key evidence for chromatin-based memory. However, this understanding largely stems from laboratory studies on winter annuals, which represent an evolutionarily derived life history strategy that has been examined largely in  laboratory and not  under natural conditions. While perennial plants exhibit the ancestral form of vernalization, they are typically not amenable to genetic analysis. To bridge these gaps, our lab is developing the perennial Arabidopsis halleri gemmifera as a model system for genetics as well as ecological studies. This includes: optimizing Agrobaterium mediatiaded trasnformation for CRISP/Cas9 and RNAi delivery, "near-nature" assays to study ancestral vernalization in a relevant context, breaking the self incompatability etc. 

ww.frontiersin.org/articles/10.3389/fpls.2021.640442/full 

Seasonal Responses in Wasabi (Eutrema japonicum), a Perennial Crucifer 

In addition to Arabidopsis thaliana and Arabidopsis halleri subsp gemmifera model systems, we are studying seasonal responses in wasabi (Eutrema japonicum), a perennial relative of Arabidopsis. This species is distinctive for its preference for cold, clean water streams, such as those in the mountains of Shizuoka and Ito, yet its vernalization process and seasonal adaptations remain largely uncharacterized. Since 2016, we have established a study focusing on a natural wasabi population from the Ikawa forest in Shizuoka. This research seeks to finnally understand how the length of response to past temperatures (memory duration) is determined and to identify the thermo-sensory elements involved in its seasonal cycle. Initial findings have characterized common features within the core vernalization pathway genes of this wasabi population compared to Arabidopsis halleri gemmifera (Endo et al., manuscript in preparation). Furthermore, functional analysis of non-coding RNAs derived from the FLC locus is currently underway (Buzas, manuscript in preparation).

The DNA, RNA, and Chromatin Architecture of Vernalization Memory 

The persistence of vernalization memory relies on specific configurations of DNA, RNA, and chromatin. Studies focused on the FLC locus demonstrated that its chromatin is dynamically organized into functional domains (updated from two to three). These domains underpin the differing memory durations observed, such as stable memory in Arabidopsis thaliana (annual) versus transient memory in Arabidopsis halleri gemmifera (perennial). This Polycomb/Trithorax-dependent memory incorporates input from a variety of cis-acting DNA elements (PREs/TREs) within the FLC region, alongside the transcription of several non-coding RNAs. We aim to functionally dissect these FLC chromatin domains, map their interactions, and compare these aspects between annual and perennial crucifers to understand the basis for their different memory lengths

academic.oup.com/pcp/article/53/5/785/1942850 

academic.oup.com/pcp/article-abstract/58/8/1302/3923480?redirectedFrom=fulltext