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Phylogenetic association mapping and its application to secondary metabolite variation in Brassicaceae species

Project description

Inter-species association mapping in genomics studies

The classical genetics approach does not allow the study of between-species variation as crosses between distinct species do not occur, and their genomes are usually highly rearranged. The goal of the EU-funded INTERACT project is to develop genomics-based methods for inter-species (phylogenetic) association mapping to discover signals in highly rearranged genomes of different species. The approach will be validated via its application to the variations in secondary metabolites within the Brassicaceae plant family. Secondary metabolites are highly variable and have broad application in cancer prevention, pest control and food design. The work and results of this project will significantly advance genetics research.

Objective

During the past years, great progress has been made in connecting phenotypes to genotypes based on within-species variation. However, the more dramatic variation that can be found between species has not been explored for phenotype/genotype associations so-far. Using classical genetics to mine between-species variation is mostly impossible, because crosses between distinct species hardly work and their genomes are usually highly rearranged.
The goal of this project is to develop unprecedented genomics-based methods for inter-species (phylogenetic) association mapping, which can find signals even in highly re-arranged genomes of different species. To ensure that these methods are also useful in practice, we will apply them to the variation in secondary metabolites within the Brassicaceae plant family. Secondary metabolites are highly variable, genetically controlled, easy to measure and have broad application in cancer prevention, pest control and food design. Given the great potential of phylogenetic association mapping in general and secondary metabolites in particular, our work promises to be ground-breaking and have profound impact on many different fields of genetic research.

Specifically, our work plan includes the following points:
I) We will develop strategies for phylogenetic association mapping and implement them in publicly-available software.
II) We will establish a panel of inbred lines from ~200 Brassicaceae species and generate whole-genome assemblies for each of them.
III) We will exemplify the usefulness of phylogenetic association mapping by correlating the diversity of secondary metabolites to the differences in the respective genomes and validate the results by transforming or mutating candidate genes in appropriate species.

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Coordinator

LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Net EU contribution
€ 1 306 714,00
Address
Geschwister scholl platz 1
80539 Muenchen
Germany

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Region
Bayern Oberbayern München, Kreisfreie Stadt
Activity type
Higher or Secondary Education Establishments
Links
Other funding
€ 0,00

Beneficiaries (2)