Problem Statement

Modern plant breeding relies heavily on identifying new traits from breeding populations that can be associated with genetic (DNA sequence) markers. However, some traits are driven by changes in sRNAs or epigenetic marks, making them harder to associate with a specific DNA sequence alteration. Thus, maintaining such traits is a significant challenge. Our project aims to use flower pigmentation as a visual marker in combination with genetic screens, advanced omics techniques, visualisation of sRNA movement, and genome editing to understand and exploit mechanisms regulating variation driven by sRNAs and epigenetic marks. This will open new opportunities for introducing novel traits and speeding up crop improvements, ultimately leading to economic impact for breeders and farmers.

Scientific Summary

Multicellular organisms develop from clusters of identical cells with the same genome. These cells can differentiate in gene expression due to internal or external cues, using mechanisms such as epigenetic marks, transcription factors, and small RNAs (sRNAs). While some factors involved in generating these patterns have been identified, we still lack a comprehensive understanding of how these patterns are induced in response to developmental or environmental cues and how distinct gene expression patterns are established and maintained. This knowledge gap hinders our ability to leverage a plant's natural adaptability to environmental cues and develop new traits for breeding programs.

This proposal aims to study flower pigmentation patterns, especially in ornamental plants like petunias, chrysanthemums, and orchids, as a model for understanding the development and maintenance of complex patterns of cell identity. In specific petunia cultivars, patterns of pigmented and unpigmented cells are driven by Post-Transcriptional Gene Silencing (PTGS) of CHALCONE SYNTHASE (CHS), a key enzyme in the synthesis of the anthocyanin pigment, through sRNA-mediated RNA interference (RNAi). Using genetic screens, advanced omics techniques, visualisation of sRNA movement, and genome editing we will explore how stable sRNA populations are formed and maintained to apply this knowledge to improve breeding strategies across both ornamental and non-ornamental crops.