Understanding the rules of life

Bioscience for sustainable agriculture and food

Category: Standard Studentships

Examining the impact of transposable elements in rice domestication from a population genetics perspective

Project No.2203

Primary Supervisor

Dr Alexandros Bousios – University of Sussex


Dr Yann Bourgeois – University of Portsmouth

Prof Adam Eyre-Walker – University of Sussex


Understanding the impact of genetic variation on fitness is of major importance in crops.

Plants are often challenged by biotic and abiotic selective pressures during their spread across geographic areas, making them excellent models to investigate adaptation to environmental changes. On the other hand, bottlenecks during domestication may reduce the efficiency of natural selection against deleterious mutations. Such an accumulation may lead to a strong genetic load that results in lower fitness.

Transposable elements (TEs) are mobile DNA fragments that amplify within genomes, sometimes inserting within or near genes. Despite their likely importance in adaptation and genetic load, their impact on the host’s fitness remains poorly understood. We propose to study the fitness effects (positive, neutral and negative) of TEs in two independent events of rice domestication in Asia (Oryza sativa) and Africa (Oryza glaberrima). Because of their tremendous economic value, these crops benefit from a well-characterized demographic history, hundreds of re-sequenced genomes, and are amenable to functional studies. We will adopt a population genetics perspective to understand how TEs interact with their hosts. We will obtain information about TE polymorphisms for all genomes, and estimate their frequencies in different populations of wild and domesticated rice. We will use extensive annotation (recombination rates, DNA conformation, epigenetic) to identify determinants of TE distribution and frequency along the genome. We will use information about patterns of diversity at single-nucleotide polymorphisms to examine the relative importance of processes such as demography, purifying and background selection on TE accumulation. We will also identify candidate TEs for adaptation by contrasting signatures of selection between haplotypes carrying or not a TE. Finally, we will compare the dynamics of multiple TE families between the two rice species to identify rules underlying TE distribution along the genome and across species, and draw parallels between the two domestication events.