PhD position in the IJPB team "Epigenetics, Reproduction and Transposable Elements" EPIREP

Project
In flowering plants, crosses between different species or parents with differing ploidy often fail to develop viable seeds because of unbalanced expression of imprinted genes in the endosperm. This phenomenon is known as the "triploid block" response, and has been regarded as a major path towards reproductive isolation and speciation, especially in plants where polyploidization events are recurrent throughout evolution. Previous studies in Arabidopsis thaliana have shown that paternal DNA methylation and small RNAs trigger triploid seed lethality by targeting transposable elements (TEs) flanking imprinted genes. Notably, this includes the conserved microRNA 845 family and the RNA-directed DNA methylation (RdDM) pathway that were found depleted in strains that lost the triploid block response. Therefore, in this project we will leverage natural variation in A. thaliana to i) investigate the impact of miR845 and RdDM depletion in the epigenetic control of TE activity during polyploidization and interploidy hybridizations, and attempt to ii) map the epigenetic basis of triploid seed viability. The student will participate actively in all experiments, including plant transformation, polyploidization and interploidy hybridizations, Fluorescence-Activated Cell Sorting, DNA methylation analysis by bisulfite and Nanopore sequencing, transcriptome and small RNA profiling by RNA sequencing, and CRISPR-based technologies for (epi)genome editing.

Required qualifications
> Master degree in biology or related fields
> Motivation for scientific research
> Strong ability to work in collaboration
> Proficiency in English Additional qualifications
not essential
> Experience in plant biology
> Experience in molecular biology
> Basic bioinformatic skills

Environment
the student will join the EPIREP team at the Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), situated at the INRAE center of Versailles. The IJPB belongs to the circle of 14 entities of the  Université Paris-Saclay and is a founding member of its Graduate School of Research dedicated to Plant Sciences (SPS-GSR).

References
> K Pachamuthu, M Simon and F Borges. Targeted suppression of siRNA biogenesis in Arabidopsis pollen promotes triploid seed viability. Nature Communications (2024). https://doi.org/10.1038/s41467-024-48950-6
>  K Pachamuthu and F Borges. Epigenetic control of transposons during plant reproduction: From meiosis to hybrid seeds. Current Opinion in Plant Biology (2023). https://dx.doi.org/10.1016/j.pbi.2023.102419