Elucidating mechanisms underlying trait instability in maize

ongoing

Crop trait instability, particularly under climate change, poses a significant challenge to global food security. Epigenetic mechanisms are increasingly recognized as key contributors to this instability. Paramutation, an epigenetic phenomenon where one silenced inducing allele heritably silences its homologous active sensitive counterpart, leads to unstable traits across generations. Despite its implications for breeding, the mechanisms underlying paramutation remain largely elusive. Recent findings from the host lab suggest that specific DNA methylation and histone modification patterns play central roles in this process. Building on these insights, this project investigates how these epigenetic modifications influence paramutation, using the maize booster1 (b1) gene as a model. The project is structured into two main objectives: First, I will investigate the hypothesis that inactive DNA flanking the sensitive b1 allele facilitates its silencing by the inducing b1 allele. If true, when exposed to the inducing allele, DNA methylation will spread from the inactive flanking DNA into the active b1 sequences, triggering their silencing. To test this, I will generate detailed DNA methylation profiles during key developmental stages using the novel Cas9-targeted long-read sequencing (nCATS) method. Second, I will explore the relationship between DNA methylation and repressive histone modifications, focusing on the order in which these epigenetic marks are established during paramutation. I will also employ the novel dCas12a-SunTag-TET1-system to specifically demethylate the flanking inactive regions of the active b1 allele, and assess its impact on paramutation. These approaches will advance our understanding of paramutation and provide clues on how to stabilise desirable crop traits. This project is a critical step toward my goal of becoming an independent researcher, by deepening my expertise in epigenetics, advanced lab techniques and crucial transferable skills.