18 BTT EAGER - Engineering complex traits using targeted, multiplexed genetic and epigenetic mutagenesis

Lead Research Organisation: Earlham Institute
Department Name: Research Faculty

Abstract

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. Genetic variations are for crop improvement by selecting plants with specific variants associated with desirable traits for inclusion in breeding programs. To date, most focus has been on creating and exploiting genetic variations 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 mutations that reprogram responses to environmental nitrogen availability. These will contribute new tools and approaches for the application of genome engineering to crop improvement and will also provide new knowledge about how variation in non-coding regulatory regions can be exploited to breed or engineer complex traits in crops.

Technical Summary

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. Systems 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 combinatorially. 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. Our work will also test if genetic factors recently identified in Arabidopsis also influence nitrogen use efficiency in tomato.

Planned Impact

The aim of this project is to develop genome engineering technologies for inducing multiplexed mutations in both coding and non-coding genic regions and epimutations in non-coding regions. Their functional outcome will be demonstrated by manipulating the expression of genes that coordinate response to environmental Nitrogen (N) status. Our work will also test if genetic factors recently identified in Arabidopsis also influence nitrogen use efficiency in tomato. This project is intended to develop new tools and approaches for engineering crops that are resilient to stress. While most genome engineering applied to plants has aimed to mutate coding sequences, we also aim to increase genetic variation in non-coding sequences as well as to introduce changes to the epigenetic status of genes. We will ensure that and novel tools, methods and experimental approaches are communicated and disseminated. We will also assess our engineered plants for increased growth and, if observed, progress further experiments to confirm our findings. During the project, we will engage and communicate with the public as well as with agrobiotech and breeding industries.

Publications

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