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

Abstract

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (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 positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. 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.

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

“…The fact that genes involved in immunity escaped this trend suggests an important role of biotic constraints in maintaining diversity even in bottlenecked populations. This confirms the resilience of this type of adaptive variation to demographic perturbations (Bourgeois, Stritt, et al, ; Oliver & Piertney, ).…”

“…We followed a procedure similar in spirit to a previous study (Bourgeois, Stritt, et al, ). We trained the algorithm using a set of 3,000 coalescent simulations using the discoal simulator (Schrider & Kern, ), modelling changes in population sizes inferred from a previous SMC++ analysis (Figure b; Bourgeois, Ruggiero, et al, ; Terhorst, Kamm, & Song, ; Method ).…”

Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon

“…Conducting the marker development for discrimination between Bd21 and Bd21-3 on a larger scale with higher throughput resources, could show more promoter regions with indels that can explain transcriptomic differences between these two accessions, and contribute clues regarding observed phenotypic differences (e.g., transformation efficiency) [37,43]. This approach has merit as genome-wide scans have shown that single nucleotide polymorphisms can give clues about the environmental adaptation of genes [61,62]. Our approach could also help with comparative transcriptomics between Bd21 and Bd21-3 by ensuring that the starting plant materials used for the analyses are accurate, and that the data reported in the scientific literature are precise.…”

Using Brachypodium distachyon natural populations to uncover genomic regions under selection

“…B. distachyon is a model species for monocotyledons and a close relative of major cereal crops (Brkljacic et al ., ), so arguably it can be useful to understand adaptations in both cultivated and wild grass species. B. distachyon has an excellent reference genome (The International Brachypodium Consortium, ), and importantly, for the work described in the highlighted paper (Bourgeois et al ., ), there are whole genome sequences available (Gordon et al ., ) for 44 natural accessions from the Mediterranean region, with 6 million single nucleotide polymorphisms (SNPs). In the highlighted paper, Bourgeois et al .…”

“…In the highlighted paper, Bourgeois et al . () set out to use these Brachypodium datasets to identify genomic regions under positive selection. Soft and hard sweeps are two different ways by which positive selection acts (Mitchell‐Olds et al ., ).…”