• Research

Engineering complex traits

Creating genetic and epigenetic variation in non-coding regulatory sequences of plant genes.

Project summary.

Start date: April 2019

End date: July 2021

Duration: 27 months

Funding: £202,347

Grant code: BB/S020853/1

Complex plant traits that respond to changes in the environment are regulated by large suites of genes. For example, the depletion of Nitrogen in the soil alters the levels and patterns of expression of large numbers of genes, affecting features such as root development, growth rate and flowering time.

This has a considerable impact on the way that plants grow and develop and can lead to reductions in crop yields. To date, most focus has been on creating and exploiting genetic variation in the coding regions of genes.

In this project we will focus on developing tools to create genetic and epigenetic variation in the non-coding regulatory sequences. Our aims are to introduce novel variation and predictably reprogram plant responses to the availability of nitrogen.


Genetic variations within coding sequences have been heavily exploited for crop improvement. However, quantitative, complex traits that respond to changes in the environment are the result of genetic and epigenetic variation in the non-coding regulatory sequences of multiple genes.

Analyses of transcriptional networks have enabled the identification of suites of genes that coordinate network responses, shaping complex phenotypes. For example, a plant's environmental nitrogen status is coordinated by multiple factors interacting in combination. Such advances have coincided with the development of molecular tools for targeted genome engineering.

Here, we propose to apply our expertise in genome engineering, systems and synthetic biology to engineer a complex trait. We will develop genome engineering technologies for inducing multiplexed mutations in coding and non-coding genic regions as well as epimutations in non-coding regions.

We will apply these tools to create mutations in the genes that coordinate large-scale transcriptional responses to environmental nitrogen availability.


Siobhan Brady

UC Davis


David Segal

UC Davis

Impact statement.

This project is intended to develop new tools and approaches for engineering crops that are resilient to stress.