In the Slotte lab we are broadly interested in understanding plant adaptation and the causes of variation in selection within and between plant genomes. A major focus of current research in the group is on the genetic causes and consequences of plant mating system evolution. We are particularly interested in the evolution and breakdown of supergenes and the genomic consequences of altered reproductive strategies. While we historically conducted much of this work in crucifer systems such as Capsella, much of our current work focuses on wild flaxseed species (Linum spp.) which are ideal for this purpose due to the wide variety of mating systems and floral adaptations that they exhibit.

In addition, we also work on methods development for sequencing supergenes and other complex and variable loci. Most recently, we have also started a new project applying and testing the utility of population genetic methods to identify genetic variation in crop wild relatives of potential use for breeding crops more resilient to a changing climate.

Evolution and loss of a plant mating system supergene

Supergenes are genomic regions harboring multiple loci controlling a multi-trait phenotypic polymorphism, and where genetic variation is structured into two or more divergent haplotypes due to suppressed recombination. Supergenes are important for a wide range of balanced polymorphisms in natural populations. An emerging insight from studies of supergenes in disparate systems is that they exhibit great similarities from an evolutionary genetic perspective. However, many fundamental questions remain regarding the tempo and mode of supergene evolution. Linum grandiflorum Linum perenne

In this project, we are investigating the evolutionary processes at one of the first discovered supergenes, the distyly S-locus. The S-locus governs distyly, a balanced floral polymorphism that ensures outcrossing and efficient pollen transfer between compatible plants. We are conducting our studies in Linum, where the dynamic nature of distyly presents an outstanding opportunity to study the evolutionary processes associated with supergene maintenance and loss. Specifically, we have made full use of the latest advances in genome sequencing to establish a genomic framework for the study of distyly in Linum, by sequencing the genomes of distylous and homostylous pairs of taxa widely spread across the Linum phylogeny. We are now using this framework to comprehensively test hypotheses on the evolution and breakdown of the distyly supergene. This project has been funded by a European Research Council Starting Grant, by the Swedish Research Council and by the Carl Tryggers foundation. With a new Swedish Research Council Project Grant, starting in 2024, we will extend this work to study the genetic basis and genomic consequences of the convergent evolution and loss of distyly in Linum.Linum grandiflorum, Linum perenne

Unlocking genetic variation for climate adaptation of crops

There is currently a pressing need to adapt crops to future climates by breeding drought- and heat-resilient varieties. Wild crop relatives harbor untapped genetic variation for breeding but remain underutilized due to the lack of efficient methods to identify beneficial variants in collections. Population genetic methods that identify genetic variants associated with environmental variation could efficiently identify adaptive genetic variation for crop improvement in collections of crop wild relatives.

Here, we will assess the utility of such an approach in a proof-of-concept project focusing on wild relatives of wheat and flax, which are promising sources of genetic variation for climate adaptation. We will focus on genetic variation for drought tolerance, as these crops are grown in regions where drought will be more frequent in the future due to climate change. We will first identify drought tolerance loci and drought adapted accessions using population genetic environmental association analyses, and then validate our findings experimentally. This will result in validated markers of direct utility for developing improved varieties. The results of the project are broadly important for more efficient utilization of crop wild relative collections to unlock wild genetic variation for food security and fibre production in a changing climate.

This project is funded by the Swedish Research Council Formas and is conducted in collaboration with Prof. Pär Ingvarsson (SLU Uppsala), Associate Prof. Therese Bengtsson (SLU Alnarp), Associate Prof. Rocío Perez-Barralez (University of Granada, Spain) and Associate Prof. Adrian Brennan (Durham University, UK).

Evolutionary consequences of plant mating system shifts

The transition from outcrossing to predominant self-fertilization (selfing) is one of the most common mating system shifts in flowering plants. This transition can be favored if the immediate benefits of selfing outweigh the costs of inbreeding depression.

In the long term, however, selfing is thought to constitute a ‘dead end’, and self-compatible lineages experience elevated extinction rates. Selfing is predicted to lead to a reduced potential for adaptation as well as accumulation of deleterious mutations, but the relative importance of these processes for the long-term demise of selfing lineages remains unclear. Moreover, relatively few empirical studies have investigated the effect of partial selfing on adaptation and accumulation of deleterious mutations. Obtaining a better understanding of these questions is vital for our understanding of plant mating system diversity.

In this project, we undertake population genomic analyses of several parallel shifts to selfing, in order to test for an effect of mating system on the efficacy of positive and purifying selection.

To investigate the impact of varying outcrossing rates and postglacial recolonisation, we are currently conducting large-scale population genomic analyses in the  alpine plant Arabis alpina.

Genetic responses to soil warming in Icelandic Arabidopsis lyrata – using a natural experiment to study adaptation

Past Projects