Lafon-Placette, C. | bioRxiv Science

bioRxiv2024

DNA methylation shows footprints of altitude selection in the clonal plant species Fragaria vesca

O_LIClimate change threatens plant species, potentially pushing them beyond their adaptive capacities. DNA methylation and other epigenetic modifications may enable rapid adaptation to environmental changes by generating locally adapted phenotypes. These phenotypic changes can be inherited across generations and may become targets of natural selection. However, direct evidence for selection on epialleles remains scarce. Addressing this gap is crucial, as population survival may heavily rely on DNA methylation, especially in clonal plants with limited genetic diversity. C_LIO_LIWe employed population genomics approaches to investigate altitude-driven selection on epigenetic sites in clonal offspring of natural woodland strawberry (Fragaria vesca) populations. These offspring were grown in a common garden and derived from seven populations spanning an altitudinal range. C_LIO_LIOur genomic, epigenomic, and transcriptomic analyses identified epialleles in clones exhibiting signs of selection related to altitude. These loci overlapped with genes involved in the O-methyltransferase activity, potentially aiding altitude adaptation through enhanced secondary metabolite production. Interestingly, these epialleles were mostly independent of genetic variation, suggesting they may have arisen stochastically or in response to environmental variation. C_LIO_LIThese findings suggest that heritable epigenetic variation could help clonal species quickly adapt to environmental challenges as those related to varying altitudes and/or temperatures. C_LI

evolutionary biology↗

bioRxiv2018

Genetic basis and timing of a major mating system shift in Capsella

Shifts from outcrossing to self-fertilisation have occurred repeatedly in many different lineages of flowering plants, and often involve the breakdown of genetic outcrossing mechanisms. In the Brassicaceae, self-incompatibility (SI) allows plants to ensure outcrossing by recognition and rejection of self-pollen on the stigma. This occurs through the interaction of female and male specificity components, consisting of a pistil based receptor and a pollen-coat protein, both of which are encoded by tightly linked genes at the S-locus. When benefits of selfing are higher than costs of inbreeding, theory predicts that loss-of-function mutations in the male (pollen) SI component should be favoured, especially if they are dominant. However, it remains unclear whether mutations in the male component of SI are predominantly responsible for shifts to self-compatibility, and testing this prediction has been difficult due to the challenges of sequencing the highly polymorphic and repetitive ~100 kbp S-locus. The crucifer genus Capsella offers an excellent opportunity to study multiple transitions from outcrossing to self-fertilization, but so far, little is known about the genetic basis and timing of loss of SI in the self-fertilizing diploid Capsella orientalis. Here, we show that loss of SI in C. orientalis occurred within the past 2.6 Mya and maps as a dominant trait to the S-locus. Using targeted long-read sequencing of multiple complete S-haplotypes, we identify a frameshift deletion in the male specificity gene SCR that is fixed in C. orientalis, and we confirm loss of male SI specificity. We further analyze RNA sequencing data to identify a conserved, S-linked small RNA (sRNA) that is predicted to cause dominance of self-compatibility. Our results suggest that degeneration of pollen SI specificity in dominant S-alleles is important for shifts to self-fertilization in the Brassicaceae.\n\nAuthor SummaryAlready Darwin was fascinated by the widely varying modes of plant reproduction. The shift from outcrossing to self-fertilization is considered one of the most frequent evolutionary transitions in flowering plants, yet we still know little about the genetic basis of these shifts. In the Brassicaceae, outcrossing is enforced by a self-incompatibility (SI) system that enables the recognition and rejection of self pollen. This occurs through the action of two tightly linked genes at the S-locus, that encode a receptor protein located on the stigma (female component) and a pollen ligand protein (male component), respectively. Nevertheless, SI has frequently been lost, and theory predicts that mutations in the male component should have an advantage during the loss of SI, especially if they are dominant. To test this hypothesis, we mapped the loss of SI in a selfing species from the genus Capsella, a model system for evolutionary genomics. We found that loss of SI mapped to the S-locus, which harbored a dominant loss-of-function mutation in the male SI protein, and as expected, we found that male specificity was indeed lost in C. orientalis. Our results suggest that transitions to selfing often involve parallel genetic changes.

evolutionary biology↗