Projects

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Specialised phenolic glycosides in aspen

We are taking a systems genetics approach to identify additional genes in the biosynthesis pathway of specialised phenolic glycosides (SPGs) in Populus trmeula. SPGs are thought to be important for defence against herbivores and can represent substantial proportions of the biomass of leaves. To date only a small number of genes have been placed within the biosynthesis pathway. We are utilising the high diversity in abundance and composition of SPGs in P. tremula within the Swedish Aspen (SwAsp) collection to link genetic variation to patterns of SPGs. This project is using a combination of metabolomics and gene expression in the SwAsp population to perform GWAS in addition to metabolite and gene expression network analyses to form links between SPG abundance, genetic variation and gene expression. We have identified a number of candidate genes using this approach and are validating these using a combination of over-expression and CRISPR-Cas9 known-out in SwAsp genotypes.

We are also interested to identify functional roles of SPGs. While it is often stated that SPGs are important defence compounds, there is not always a clear link to which herbivores (or other) SPGs are defending against. We are therefore using sets of genotypes with contrasting SPG abundances to test for feeding influences on mammalian and insect herbivores.

 

Interaction between trees and fungi in the forest

Sweden lies in the boreal forest zone and a large part of the country is covered by Norway spruce and Scots pine forests. These species have high ecological, cultural and economical importance and there is an ever increasing need to ensure that these forest can remain productive and survive in response to ongoing climate change. The boreal forest is characterised by a short growing season and by soils with low nitrogen (N) availability, which limit tree growth. An important component of N acquisition for both conifer species is their association with ectomycorrhizal fungi (EmF). These EmF form symbiotic interactions with tree roots exchanging nutrients (primarily N and P) and water for carbon (C).

We have been developing and subsequently deploying sequencing based methods to assay this interaction. We are using RNA-Sequencing (RNA-Seq) of tree roots sampled from control (low N) and fertilised (high N) forest plots at multiple timepoints during the growing season to profile gene expression of both the tree roots and the associated EmF hyphae. This combined analysis enables us to identify correlations in expression between the tree and EmF to understand how they interact an influence each other. Furthermore, we can use the sequence data of EmF derived transcripts to derive taxonomic information on which species are present and, to some extent, their relative abundance.

One current limitation of this approach is a lack of available reference genomes for many of the most abundant EmF. We are therefore producing genome assemblies for a number of these species.

 

The giant genomes of conifers

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Comparative genomics of wood development and abiotic stress response

This page is in progress!