Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

Grasses are essential plants for ecosystem functioning. Thus, quantifying the selection pressures that act on natural variation in grass species is essential regarding biodiversity maintenance. In this study, we investigated the selection pressures that act on natural populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. To do so, we took advantage of whole-genome sequencing data produced for two natural populations of B. distachyon and used complementary genome-wide scans of selection (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species and affects different genomic regions across the two populations. Gene Ontology annotation of candidate genes reveals that pathogens may constitute important factors of selection in Brachypodium distachyon. We eventually cross-validated our results with QTL data available for leaf-rust resistance in this species and demonstrated that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Our study revealed widespread signatures of natural selection on genes involved in adaptation in B. distachyon and suggests that pathogens may constitute an important driving force of genetic diversity and evolution in this system. Thanks to a near-base perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.