The interaction between transposable elements (TEs) and their hosts is one of the most intricate co-evolutionary processes found in nature. Quantifying how TEs impact their host’s fitness has practical relevance in relation to real-world applications, such as understanding the molecular bases of selected phenotypes, or assessing mutational load in crops (so-called “cost of domestication”). The following project will focus on the impact of TEs on the host’s fitness, using the date palm (Phoenix dactylifera) as a model. This crop is of major economic and social importance in the Middle East and Northern Africa, and its consumption keeps rising every year. However, it is also threatened by more frequent droughts and increasing salinity due to climate change. A precise characterization of its genetic diversity is therefore essential to understand the adaptability of this species to growing environmental pressures. The project will use genomic data to examine the role of polymorphic TEs in selection and differentiation of date palm varieties across the species range. It will revolve around two questions: What is the distribution of TEs fitness effects in date palms? Can this distribution be predicted from functional genomic features such as gene regulatory networks? We will develop and apply new methods in population genomics to estimate the fraction of advantageous and harmful polymorphic TEs. We will compare results with de novo functional annotations of chromatin organization and regulatory networks to draw a comprehensive view of TEs’ impact on a keystone perennial species of agronomic interest for both developed and developing countries.