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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. https://doi.org/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. https://doi.org/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},
url = {https://www.osti.gov/biblio/1529121}, journal = {The Plant Journal},
issn = {0960-7412},
number = 2,
volume = 96,
place = {United States},
year = {2018},
month = {9}
}

Works referenced in this record:

Fast model-based estimation of ancestry in unrelated individuals
journal, July 2009


Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes
journal, October 2010


Determination of lead, cadmium and copper in roadside soil and plants in Elazig, Turkey
journal, March 2007


QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.
journal, February 2012


Nonhost resistance to rust pathogens – a continuation of continua
journal, December 2014


Vegetation of Eurasia from the last glacial maximum to present: Key biogeographic patterns
journal, February 2017


Detecting local adaptation in widespread grassland species ? the importance of scale and local plant community
journal, November 2006


Parasitism drives host genome evolution: Insights from the Pasteuria ramosa - Daphnia magna system : BRIEF COMMUNICATION
journal, March 2017


Plant-Parasite Coevolution: Bridging the Gap between Genetics and Ecology
journal, September 2011


Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
journal, November 2007


Rapid Decline of a Grassland System and Its Ecological and Conservation Implications
journal, January 2010


Balancing Selection and Its Effects on Sequences in Nearby Genome Regions
journal, January 2006


Diversity and evolution of Rp1 rust resistance genes in four maize lines
journal, March 2015


Evolution and Distribution of Grasses
journal, January 1981


Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005


Regulation of pattern recognition receptor signalling in plants
journal, August 2016


Genomic signatures of selection at linked sites: unifying the disparity among species
journal, March 2013


The variant call format and VCFtools
journal, June 2011


Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
journal, January 2014


On the importance of balancing selection in plants
journal, August 2013


Comparative analysis of the cold acclimation and freezing tolerance capacities of seven diploid Brachypodium distachyon accessions
journal, December 2013


Recognition events and host–pathogen co-evolution in gene-for-gene resistance to flax rust
journal, January 2009


The two-speed genomes of filamentous pathogens: waltz with plants
journal, December 2015


Using GOstats to test gene lists for GO term association
journal, November 2006


Evolutionary and ecological functional genomics
journal, August 2003


Detecting balancing selection in genomes: limits and prospects
journal, June 2015


The genomic basis of adaptation in plants
journal, April 2017


Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
journal, November 2011


Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
journal, July 2014


Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
journal, December 2017


Human influence lowers plant genetic diversity in communities with extinction debt
journal, November 2009


Who believes in whole-genome scans for selection?
journal, August 2009


Post-glacial re-colonization of European biota
journal, September 1999


The genetic legacy of the Quaternary ice ages
journal, June 2000


Diversity of Puccinia striiformis on Cereals and Grasses
journal, September 2011


Enhancing the crops to feed the poor
journal, August 2002


Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon
journal, May 2011


Evolution and Conservation of Plant NLR Functions
journal, January 2013


Genomic variability as a driver of plant–pathogen coevolution?
journal, April 2014


Discoal: flexible coalescent simulations with selection
journal, August 2016


diploS/HIC: An Updated Approach to Classifying Selective Sweeps
journal, April 2018


Size-related deterioration of semi-natural grassland fragments in Sweden
journal, January 2002


Molecular genetics and evolution of disease resistance in cereals
journal, July 2016


Circos: An information aesthetic for comparative genomics
journal, June 2009


The Stripe Rust Resistance Gene Yr10 Encodes an Evolutionary-Conserved and Unique CC–NBS–LRR Sequence in Wheat
journal, December 2014


Natural variation of drought response in Brachypodium distachyon
journal, October 2010


The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes
journal, September 2014


Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae)
journal, December 2011


Clusters of Resistance Genes in Plants Evolve by Divergent Selection and a Birth-and-Death Process
journal, November 1998


Which evolutionary processes influence natural genetic variation for phenotypic traits?
journal, November 2007


Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana
journal, September 2002


Population genomic and genome-wide association studies of agroclimatic traits in sorghum
journal, December 2012


Molecular Signatures of Natural Selection
journal, December 2005


Brachypodium distachyon: making hay with a wild grass
journal, April 2008


Serine/Threonine Protein Phosphatases type 2A and their roles in stress signaling
journal, November 2009


Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling
journal, January 2012


A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans
journal, July 2012


PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
journal, April 2014


The Scale of Population Structure in Arabidopsis thaliana
journal, February 2010


BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010


Genome-Wide Inference of Ancestral Recombination Graphs
journal, May 2014


A Photoreceptor Contributes to the Natural Variation of Diapause Induction in Daphnia magna
journal, September 2016


Ecological genomics of local adaptation
journal, October 2013


Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
journal, December 2015


S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning
journal, March 2016


The impact of linked selection on plant genomic variation
journal, April 2014


SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes
journal, June 2013


Evolution of Grasses and Grassland Ecosystems
journal, May 2011


Origin and Domestication of the Fungal Wheat Pathogen Mycosphaerella graminicola via Sympatric Speciation
journal, November 2006


The Brachypodium distachyon BdWRKY36 gene confers tolerance to drought stress in transgenic tobacco plants
journal, September 2014


Glacial refugia of temperate trees in Europe: insights from species distribution modelling
journal, November 2008


A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
journal, June 2007


Sambamba: fast processing of NGS alignment formats
journal, February 2015


Advantageous diversity maintained by balancing selection in humans
journal, December 2014


Robust and scalable inference of population history from hundreds of unphased whole genomes
journal, December 2016


Structure–function analysis of the NB-ARC domain of plant disease resistance proteins
journal, April 2008


Identifying targets and agents of selection: innovative methods to evaluate the processes that contribute to local adaptation
journal, June 2017


Managing water resources for crop production
journal, July 1997


Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives
journal, November 2017


Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)
journal, November 2015