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


Bourgeois, Yann; Stritt, Christoph; Walser, Jean-Claude; Gordon, Sean P; Vogel, John P; Roulin, Anne C (2018). Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. The Plant Journal, 96(2):438-451.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:580 Plants (Botany)
Uncontrolled Keywords:Plant Science, Genetics, Cell Biology
Language:English
Date:1 October 2018
Deposited On:10 Jan 2019 12:10
Last Modified:25 Sep 2019 00:03
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0960-7412
OA Status:Closed
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1111/tpj.14042
Project Information:
  • : FunderSNSF
  • : Grant IDPZ00P3_154724
  • : Project TitlePopulation genomics and local adaptation: genome wide analysis of transposable elements and natural population evolutionary trajectories.

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