UMR 6553 ECOBIO Avenue du Général Leclerc
Campus de Beaulieu
Evolution of recombination landscapes during Angiosperms domestication
Supervisor(s): Sylvain Glémin & Thomas Brazier
Lab: UMR 6553 ECOBIO – EGA team
Université de Rennes 1 - UMR 6553 ECOBIO
Recombination is a major process for species and genome evolution, affecting both phenotypic and genetic diversity. Understanding how recombination is distributed within a genome is important because of its role in the creation of novel haplotypes, hence improving adaptive capacities of plants to face novel environments and increasing selection efficiency. In Angiosperms, recombination landscapes (i.e. the distribution of recombination along the genome) seem largely linked to chromosomes architecture and functional structure of the genome (e.g. genome size, gene density). Besides, domestication resulting to the formation of new lineages is often associated to genome rearrangements at large scale, especially polyploidization between multiple wild diploid progenitors. In addition, theoretical works predict selection for higher recombination rates in domesticated plants, because of a strong directional selection and rapid evolutionary changes. Consequently, the evolution of recombination landscapes linked to domestication seems very interesting to understand the maintenance of genetic diversity and the response to selection of domesticated species. Yet, empirical evidences of genetic processes behind domestication are still under development, and little is known about changes in recombination in Angiosperms crops. Although a meta-analysis spotted higher averaged recombination rates in domesticated species compared to their wild relatives by counting chiasmas frequencies, there is no comparative studies to assess differences in recombination landscapes. A recent study showed differences of fine-scale recombination rates in barley, but the global recombination landscape remained highly conserved. So far, it was one of the very few studies to investigate the fine-scale recombination rate in a wild/domesticated plant system, and comparative analyses of multiple species should help to describe the pattern involved in plant domestication.
This internship is focused on comparative genomics and genome evolution. Objectives will be to characterize and compare recombination landscapes in a large sample of wild/domesticated systems (e.g. rice, wheat, soybean, maize, cotton) and to unravel the possible impacts of domestication processes on the evolution of recombination, both in terms of magnitude and distribution across chromosomes. The student will start with an existing genomic database of polymorphism data (SNPs dataset) and reference genomes from which she/he will apply population genomic tools to estimate recombination map from linkage disequilibrium patterns (e.g. LDhat software). It will also be appreciated to extend the database to new species. Furthermore, the student will need skills in bioinformatic to manipulate heterogeneous data gathered from open publications and to perform the pipeline used to estimate recombination rates.
Dreissig, S., Mascher, M., Heckmann, S., 2019. Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley. Molecular Biology and Evolution 36, 2029–2039. https://doi.org/10.1093/molbev/msz141
Ross‐Ibarra, J., 2004. The Evolution of Recombination under Domestication: A Test of Two Hypotheses. The American Naturalist 163, 105–112. https://doi.org/10.1086/380606
Stumpf, M.P.H., McVean, G.A.T., 2003. Estimating recombination rates from population-genetic data. Nat Rev Genet 4, 959–968. https://doi.org/10.1038/nrg1227
Duration: 6 months, at the beginning of 2021