Evolution of Gene Regulation through sRNA-mediated Neofunctionalisation

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Through a combination of genomic, genetic, transcriptomic, phylogenetic, population and transgenic approaches, we will test the hypothesis that small RNA-mediated neofunctionalisation (S-NF) provides a natural mechanism for refining gene expression patterns during evolution. Through bioinformatics analysis of genomes of Antirrhinum species with diverse morphologies, we will identify candidate S-NF inverted duplications and analyse their function through genetic and expression analysis of segregating populations, and clarify their relationship to microRNAs. Through phylogenetic analysis we will determine when and how a particular case of S-NF, the SULF locus which restricts yellow flower colour in Antirrhinum, arose in relation to the duplication and diversification of its homologues, and whether it was a one-off event, specific to the Antirrhinum lineage or whether similar events have occurred in other clades. By analysing genetic and molecular interactions between SULF and promoter changes in its target, Am4'CGT (Antirrhinum majus chalcone 4'-O-glucosyltransferase) we will determine how S-NF combines with regulatory neofunctionalisation (R-NF) to control gene expression. The role of these interactions in a natural context will be evaluated by measuring selective sweeps in natural populations and cline steepness at a hybrid zone. Mechanisms of interaction and potential for engineering gene expression control will be evaluated by recreating the SULF system transgenically in Torenia. We will also analyse the role of S-NF and R-NF in the evolution of flower colour changes in other species (Linaria) to determine whether evolution follows the same or different routes. Taken together these approaches should provide deeper insights into how S-NF evolves and contributes to variation within and between species, providing potential for refining gene expression through evolution and breeding.

This project will benefit non-academic beneficiaries, in the following ways:

1. Breeders will benefit from knowledge of how S-NF may contribute to genetic variation. Neofunctionalisation provides a major source of genetic variation exploited by breeders, and understanding the origins and properties of all its forms is critical for the long-term goal of predictive breeding. For example, candidate S-NF loci are involved in oil content of sunflower and olives, and microRNA loci (which likely evolve from S-NF loci) influence barley cleistogamy and wheat spike formation. By applying the knowledge, methods and pipelines developed in this project to crop genomes, it should be possible to identify S-NF candidates and evaluate the roles they play in control of expression patterns. This knowledge may then inform breeding programmes which target particular traits. The expected time frame for this beneficial impact will be 10 years after the start of the project.

2. Biotech industries will benefit from our work through improved ability to control gene expression patterns. A typical initial goal of genetic modification is to introduce a new gene activity. In the longer term, gene activities need to be refined and restricted to particular tissues or regions. One approach is to engineer promoters to target gene expression. However, promoters may still be leaky and by exploiting the principles of S-NF it may be possible to enhance specificity by expressing inverted duplications in complementary domains. This may be a natural mechanism that has been employed during the evolution of flower colour. By showing how this system operates in both natural and engineered systems, the project will underpin such approaches. Genetic modification is still some way from gaining public acceptance, but having the tools for controlling expression patterns more precisely will be invaluable should attitudes change. The time frame for this type of impact is expected to be 10-20 years.

3. The general public and school children will benefit directly from this project through the proposed hands-on events and through dissemination of latest research findings in an accessible way via media routes like youtube videos and press articles. Through these events they will learn how genetic variation underlies evolution and breeding; how genetic engineers may employ methods that have already been explored naturally through the course of evolution; and how genes and environment interact to modify organisms. The public will also benefit in the longer term because of the contribution that this project will make to maintaining and developing forward-looking scientific research that provides the foundations of a modern healthy and growing economy. These activities will have immediate impact on audiences (throughout the 3 years of the project) as well as longer term impact on career choices and society (10-20 years).

4. BBSRC will benefit because the project is directly relevant to the research priorities in food security, synthetic biology, new strategic approaches to industrial biotechnology, data-driven biology and interdisciplinary research. The project also meets the BBSRC objective of building partnerships, through the involvement of an interdisciplinary team that involves a BBSRC institute, university and researchers in Japan, Israel and Spain. The time frame for this type of impact is 3-20 years.