The genotype determines not only the appearance, development, and adaptive strategies of the given individual. It also carries far-reaching information on past changes and adaptations of the phenotype. Researchers from Heidelberg University and the Max Planck Institute for Plant Breeding Research in Cologne have investigated this evolutionary change process using model organisms from the Brassicaceae plant family, focusing on leaf shape. With the aid of modern sequencing technologies and a new research approach - an interspecific genome comparison - they were able to identify genes in the genotype of related species which have a direct influence on a special type of genotype modification and hence evolutionary rates.
The complete genome, in all its complexity, regulates all processes of the life of an organism and is therefore a major determinant of its form and function. At the same time, genomes change throughout evolution in response to pressures to adapt, thus giving rise to new traits and abilities. "This process of change can be analysed retrospectively because it has left different signatures in the genomes of related organisms", says study leader Dr Korbinian Schneeberger from the Max Planck Institute for Plant Breeding Research in Cologne.
To reveal these genetic signatures of evolution, the researchers in Heidelberg and Cologne developed a new approach to the research: Their association study takes the expression of the different phenotypes, genetic variation as well as their genetic relatedness into account, and hence their evolutionary history. "By applying this method, we now have the opportunity to look at the variations of the phenotype we are interested in and use our knowledge about evolution in order to analyse the genetic bases of very different phenotypes. It was really exciting to see that it is mainly the number of gene copies that emerge and are lost over the course of evolution. That number plays a major role in the new concept", states Dr Christiane Kiefer. Together with Dr Eva-Maria Willing, Dr Kiefer is the primary author of the study. She moved from Cologne two years ago to join the Centre for Organismal Studies (COS) of Heidelberg University.
The researchers were able to confirm the functionality of their new approach by finding a known key regulator that is responsible for the complexity of leaf shape in plants. They also detected an unusual connection between an unexpectedly high mutation of the sequence motif ’CG’ to ’TG’ and the absence of the gene chromomethylase 3 (CMT3). The absence of this gene leads to missing modifications of the genome - complex, genome-wide methylation patterns-, an important element in the mechanism for adaptation to the environment but also in evolutionary processes such as gene silencing of previously duplicated genes.
"The Brassicaceae with their 4000 species are among the most important plant model systems. In addition to thale cress, the family includes Brassica crops, such as cabbage", states Marcus Koch, whose "Biodiversity and Plant Systematics" research group is considered a worldwide network and competence centre for Brassicaceae. "The evolutionary biological potential of this group of plants, for which we generated unique resources at COS over the past 15 years, is particularly impressive and makes it attractive for studying numerous far-reaching biological issues."
In the framework of an ERC Starting Grant from the European Research Council awarded to Dr Schneeberger the research setting will be continued in a long-term collaboration. The data are available in a public access database. The results of this research were published in the journal "Nature Plants".
C. Kiefer, E.-M. Willing, W.B. Jiao, H. Sun, M. Piednoel, U. Hümann, B. Hartwig, M. A. Koch & K. Schneeberger: Inter-species association mapping links reduced CG-TG substitution rates to the loss of gene body methylation. Nature Plants 2019.