Title:
« Beyond the Field: Genetic Bases of Feralization in Brassica rapa Populations»
Supervision :
Laurène Gay, Sébastien Geneste, Joëlle Ronfort, UMR AGAP institut
This internship is for Master’s 2 students (or those on a gap year) with a background in evolutionary biology/ecology.
The duration can be 5-6 months and can begin at any time
Background:
This internship project forms part of a broader study which aims to understand local adaptation to climate in populations of Brassica rapa, by examining both cultivated local varieties (landraces) and wild populations. The first genetic analyses revealed that some of the populations previously assumed to be wild in continental Europe are in fact feral. Here, we propose focusing on these feral populations to shed light on the genetic mechanisms underlying feralization – a process lying at the intersection of domestication and adaptation and that results in the establishment of new wild-like populations.
Research Question:
Feral populations, formerly domesticated plants that have returned to the wild, are widespread yet poorly studied. Brassica rapa, which includes crops such as turnip, Chinese cabbage, and yellow sarson, offers a compelling case: while truly wild populations have a limited distribution, feral populations have colonized much of the world. Recent evidence suggests that some European populations once considered wild are in fact feral, displaying wild-like phenotypes but genomes closely related to crops.
This project aims to investigate the evolutionary history of feral B. rapa populations, in particular how they adapt to life outside cultivation. We will analyze pool-seq whole-genome data from 117 wild, feral, or domesticated populations sampled in France, Slovenia, Italy, and Algeria, combined with phenotypic data measured in a common garden. The goal is to identify the domesticated ancestors of feral populations and to uncover the genetic bases of feralization. Specifically, we aim to detect the variants that distinguish feral populations from domesticated populations and to assess their links to phenotypic traits and environmental adaptation. In addition, we will evaluate whether feralization involves the accumulation of deleterious alleles (“feralization load”) or a purge. To achieve this, we will track the frequency of putatively deleterious variants across groups and compare it to wild populations, to assess the impact of domestication and feralization bottlenecks. By combining genomic and phenotypic data, this study will shed lights on the genetic mechanisms underlying feralization.
Internship plan:
The student will work closely with the PhD candidate (who was a Darwin student before) on this project that will form a chapter of the thesis and could be published as a scientific paper. The project aims to determine the origin of feral populations and how they adapted to life outside of cultivation.
The work of the Master’s student will focus on analysing readily available genomic data: 55 landraces (turnip and broccoletto), 45 wild populations and 17 feral populations. These populations have been sequenced in pools of 30 individuals, with 15 million SNP markers across the entire genome.
Specifically, the missions will entail the following:
– Identifying variants segregating between domesticated and feral populations of Brassica rapa, by identifying private alleles and using the contrast statistics C2 (Olazcuaga et al. 2020);
– Association analyses linking genomic data with phenotypic traits measured in a common garden experiment. Theses analyses will clarify how limited genetic differentiation between domesticated and feral groups can nevertheless result in strong phenotypic differences, and will allow the identification of genes and variants involved in key processes such as the loss of agronomic traits that could be costly in the wild (e.g. seed dormancy or turnip formation) and local adaptation to novel environments. Depending on the candidate genes identified, it may also be relevant to review the literature to assess whether they have previously been linked to agronomic selection, climate adaptation or other processes. Phenotypic data entail traits such as root weight, shape, seeds production, SLA … The student will use the BayPass software (Gautier 2015) to evaluate potential associations between each SNPs and these phenotypic traits.
– If time and progress permit, the project may also extend to the study of genetic load in feral
populations, by comparing deleterious variation across domesticated, feral, and wild populations.
The internship will take place in the ARCAD building in Montpellier, at the UMR AGAP institute. The project is in collaboration with some researchers in the UMR CBGP in Montferrier.
Methods and tools
The student should have a solid background in evolutionary biology, particularly population genetics, and good proficiency in R. Some familiarity with Bash would be an asset but is not required. The work will be carried out in close collaboration with the PhD candidate, with weekly meetings involving the thesis supervisors. This project is expected to result in a scientific publication co-authored by the student.
Keyword :
Population Genomics, Quantitative Genetics, Brassica rapa, Ferality, Domestication
Contact :
sebastien.geneste@inrae.fr
References:
About Brassica rapa : https://doi.org/10.1093/molbev/msab108
BayPass : https://doi.org/10.1534/genetics.115.181453
C2 statistics : https://doi.org/10.1093/molbev/msaa098
Genetic load : https://peercommunityjournal.org/articles/10.24072/pcjournal.539/
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