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

Project Information

INTERACT

Grant agreement ID: 802629

DOI

10.3030/802629

Project closed

EC signature date 10 April 2019

Start date 1 September 2019

End date 31 January 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 494 214,00

EU contribution

€ 1 494 214,00

Coordinated by

LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Germany

Periodic Reporting for period 4 - INTERACT (Phylogenetic association mapping and its application to secondary metabolite variation in Brassicaceae species)

Reporting period: 2024-03-01 to 2025-01-31

Summary of the context and overall objectives of the project

Understanding how genetic traits evolve across species remains a major challenge in biology. This project focused on the Brassicaceae family, a group of plants including Arabidopsis thaliana, to study how meiotic recombination—the process that reshuffles DNA during reproduction—varies and evolves.

We established a panel of ~20 Brassicaceae species representing the full diversity of the family and developed seed stocks to support long-term genetic studies. Using modern sequencing technologies, we generated high-quality genome assemblies and gene annotations for selected species.

To link genetic differences with variation in recombination, we developed a novel method called Phylogenetic Association Mapping (PAM). This approach allows researchers to identify trait–gene associations across species while accounting for their evolutionary relationships.

By applying PAM to recombination traits, we identified genetic factors influencing crossover patterns and validated key candidates. The project delivers new tools and data for studying genome evolution across plant lineages.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Over the course of the project, we established a phylogenetically diverse panel of ~20 Brassicaceae species, covering the major lineages of the family. Seed stocks were acquired, propagated, and maintained to support future genetic and phenotypic research.We generated high-quality genome assemblies and gene annotations for selected species using long-read and Hi-C sequencing, combined with transcriptomic data. These assemblies enabled reliable cross-species comparisons of gene content, structure, and recombination features.

We developed of Phylogenetic Association Mapping (PAM), a novel method that allows the identification of genotype–trait associations across species while accounting for their shared evolutionary history. We applied PAM to meiotic recombination, quantifying recombination landscapes across species using cytological and genomic approaches. Our analyses revealed lineage-specific shifts in recombination rates and identified candidate genes responsible for this variation. Experimental validation of selected genes is ongoing.

All genomic resources, analysis tools, and protocols have been made publicly available through open-access repositories and community platforms. Key results have been presented at international conferences, and publications are in preparation or under review. The project's outputs will continue to support downstream applications in plant breeding, evolutionary biology, and genome analysis across eukaryotes.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project made substantial progress beyond the state of the art in comparative plant genomics and trait mapping across species. Prior to this work, genome-wide association studies (GWAS) were largely limited to within-species variation and lacked statistical tools to incorporate phylogenetic information. Our development of Phylogenetic Association Mapping (PAM) overcomes this limitation by enabling trait–gene associations across species while accounting for evolutionary relationships. This is a major conceptual and methodological advance in evolutionary genetics.

The project also generated one of the most comprehensive genomic resources in Brassicaceae, including high-quality genome assemblies and annotations from phylogenetically diverse species. Combined with our new data on meiotic recombination landscapes, this opens the door to understanding how recombination evolves and how it is genetically controlled across deep evolutionary time.

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