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Title: 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 genomewide 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,more » population genomics and evolutionary biology.« less

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [4];  [2]
  1. New York University Abu Dhabi, PO Box 129188 Saadiyat Island, Abu Dhabi United Arab Emirates
  2. Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107 8008 Zürich Switzerland
  3. Genetic Diversity Centre, ETH Zürich, Universitätstrasse 16 Zurich Switzerland
  4. DOE Joint Genome Institute, Walnut Creek CA 94598 USA
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory-National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529121
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 96; Journal Issue: 2; Journal ID: ISSN 0960-7412
Country of Publication:
United States
Language:
English

Citation Formats

Bourgeois, Yann, Stritt, Christoph, Walser, Jean-Claude, Gordon, Sean P., Vogel, John P., and Roulin, Anne C. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. United States: N. p., 2018. Web. doi:10.1111/tpj.14042.
Bourgeois, Yann, Stritt, Christoph, Walser, Jean-Claude, Gordon, Sean P., Vogel, John P., & Roulin, Anne C. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. United States. doi:10.1111/tpj.14042.
Bourgeois, Yann, Stritt, Christoph, Walser, Jean-Claude, Gordon, Sean P., Vogel, John P., and Roulin, Anne C. Sat . "Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon". United States. doi:10.1111/tpj.14042.
@article{osti_1529121,
title = {Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon},
author = {Bourgeois, Yann and Stritt, Christoph and Walser, Jean-Claude and Gordon, Sean P. and Vogel, John P. and Roulin, Anne C.},
abstractNote = {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 genomewide 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.},
doi = {10.1111/tpj.14042},
journal = {The Plant Journal},
issn = {0960-7412},
number = 2,
volume = 96,
place = {United States},
year = {2018},
month = {9}
}