skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

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:
Sponsoring Org.:
USDOE
OSTI Identifier:
1468356
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
[Journal Name: The Plant Journal Journal Volume: 96 Journal Issue: 2]; Journal ID: ISSN 0960-7412
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
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 Kingdom: 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 Kingdom. 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 Kingdom. doi:10.1111/tpj.14042.
@article{osti_1468356,
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 = {},
doi = {10.1111/tpj.14042},
journal = {The Plant Journal},
number = [2],
volume = [96],
place = {United Kingdom},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/tpj.14042

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

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


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


Evolution and Conservation of Plant NLR Functions
journal, January 2013


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


Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range
journal, July 2015

  • Lopez-Alvarez, D.; Manzaneda, A. J.; Rey, P. J.
  • American Journal of Botany, Vol. 102, Issue 7
  • DOI: 10.3732/ajb.1500128

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools
journal, July 2015


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

  • Al-Shahrour, Fátima; Minguez, Pablo; Marqués-Bonet, Tomás
  • PLoS Computational Biology, Vol. 6, Issue 10
  • DOI: 10.1371/journal.pcbi.1000953

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


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


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

  • Karasov, Talia L.; Horton, Matthew W.; Bergelson, Joy
  • Current Opinion in Plant Biology, Vol. 18
  • DOI: 10.1016/j.pbi.2013.12.003

Ecological genomics of local adaptation
journal, October 2013

  • Savolainen, Outi; Lascoux, Martin; Merilä, Juha
  • Nature Reviews Genetics, Vol. 14, Issue 11
  • DOI: 10.1038/nrg3522

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

  • Colton-Gagnon, Katia; Ali-Benali, Mohamed Ali; Mayer, Boris F.
  • Annals of Botany, Vol. 113, Issue 4
  • DOI: 10.1093/aob/mct283

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


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


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


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


Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella
journal, January 2012

  • Gos, Gesseca; Slotte, Tanja; Wright, Stephen I.
  • BMC Evolutionary Biology, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2148-12-152

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


Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits
journal, February 2007


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

  • Liu, Wei; Frick, Michele; Huel, Réné
  • Molecular Plant, Vol. 7, Issue 12
  • DOI: 10.1093/mp/ssu112

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

  • Morris, G. P.; Ramu, P.; Deshpande, S. P.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
  • DOI: 10.1073/pnas.1215985110

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


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


Evolution of Grasses and Grassland Ecosystems
journal, May 2011


The genomic basis of adaptation in plants
journal, April 2017


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

  • Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca
  • Molecular Ecology, Vol. 25, Issue 1
  • DOI: 10.1111/mec.13485

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

  • Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-02292-8

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


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

  • Bourgeois, Yann; Roulin, Anne C.; Müller, Kristina
  • Evolution, Vol. 71, Issue 4
  • DOI: 10.1111/evo.13209

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

  • Park, Chang-Jin; Caddell, Daniel F.; Ronald, Pamela C.
  • Frontiers in Plant Science, Vol. 3
  • DOI: 10.3389/fpls.2012.00177

The variant call format and VCFtools
journal, June 2011


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

  • van Ooijen, Gerben; Mayr, Gabriele; Kasiem, Mobien M. A.
  • Journal of Experimental Botany, Vol. 59, Issue 6
  • DOI: 10.1093/jxb/ern045

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


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

  • Chavan, Suchitra; Gray, Judy; Smith, Shavannor M.
  • Theoretical and Applied Genetics, Vol. 128, Issue 5
  • DOI: 10.1007/s00122-015-2484-2

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


Genetic and forma specialis diversity in Blumeria graminis of cereals and its implications for host-pathogen co-evolution
journal, May 2003


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

  • Key, Felix M.; Teixeira, João C.; de Filippo, Cesare
  • Current Opinion in Genetics & Development, Vol. 29
  • DOI: 10.1016/j.gde.2014.08.001

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


Cadmium and lead contamination in vegetables collected from industrial, traffic and rural areas in Bursa Province, Turkey
journal, May 2008


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

  • Bettgenhaeuser, Jan; Gilbert, Brian; Ayliffe, Michael
  • Frontiers in Plant Science, Vol. 5
  • DOI: 10.3389/fpls.2014.00664

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

  • Barbieri, Mirko; Marcel, Thierry C.; Niks, Rients E.
  • Genome, Vol. 55, Issue 2
  • DOI: 10.1139/g2012-001

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


Molecular Signatures of Natural Selection
journal, December 2005


Discoal: flexible coalescent simulations with selection
journal, August 2016


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


Evolutionary and ecological functional genomics
journal, August 2003

  • Feder, Martin E.; Mitchell-Olds, Thomas
  • Nature Reviews Genetics, Vol. 4, Issue 8
  • DOI: 10.1038/nrg1128

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure
journal, March 2012


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


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

  • Zhong, Yan; Li, Yingjun; Huang, Kaihui
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep16638

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


Evolution and Distribution of Grasses
journal, January 1981

  • Clayton, W. D.
  • Annals of the Missouri Botanical Garden, Vol. 68, Issue 1
  • DOI: 10.2307/2398808

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

  • Krattinger, Simon G.; Keller, Beat
  • New Phytologist, Vol. 212, Issue 2
  • DOI: 10.1111/nph.14097

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

  • Fijarczyk, Anna; Babik, Wiesław
  • Molecular Ecology, Vol. 24, Issue 14
  • DOI: 10.1111/mec.13226

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

  • Pfeifer, Bastian; Wittelsbürger, Ulrich; Ramos-Onsins, Sebastian E.
  • Molecular Biology and Evolution, Vol. 31, Issue 7
  • DOI: 10.1093/molbev/msu136

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


Enhancing the crops to feed the poor
journal, August 2002

  • Huang, Jikun; Pray, Carl; Rozelle, Scott
  • Nature, Vol. 418, Issue 6898
  • DOI: 10.1038/nature01015

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

  • Michelmore, Richard W.; Meyers, Blake C.
  • Genome Research, Vol. 8, Issue 11
  • DOI: 10.1101/gr.8.11.1113

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

  • Kern, Andrew D.; Schrider, Daniel R.
  • G3: Genes|Genomes|Genetics, Vol. 8, Issue 6
  • DOI: 10.1534/g3.118.200262

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


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

  • Stukenbrock, E. H.; Banke, S.; Javan-Nikkhah, M.
  • Molecular Biology and Evolution, Vol. 24, Issue 2
  • DOI: 10.1093/molbev/msl169

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


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


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


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

  • Roulin, Anne C.; Bourgeois, Yann; Stiefel, Urs
  • Molecular Biology and Evolution, Vol. 33, Issue 12
  • DOI: 10.1093/molbev/msw200

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


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

  • Dong, Suomeng; Raffaele, Sylvain; Kamoun, Sophien
  • Current Opinion in Genetics & Development, Vol. 35
  • DOI: 10.1016/j.gde.2015.09.001

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

  • Dodds, Peter; Thrall, Peter
  • Functional Plant Biology, Vol. 36, Issue 5
  • DOI: 10.1071/FP08320

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

  • Wadgymar, Susana M.; Lowry, David B.; Gould, Billie A.
  • Methods in Ecology and Evolution, Vol. 8, Issue 6
  • DOI: 10.1111/2041-210X.12777

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

  • Huo, Naxin; Garvin, David F.; You, Frank M.
  • Theoretical and Applied Genetics, Vol. 123, Issue 3
  • DOI: 10.1007/s00122-011-1598-4

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


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

  • Pavlidis, Pavlos; Jensen, Jeffrey D.; Stephan, Wolfgang
  • Molecular Biology and Evolution, Vol. 29, Issue 10
  • DOI: 10.1093/molbev/mss136

Testing for local adaptation in Avena barbata : a classic example of ecotypic divergence
journal, September 2009


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


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

  • Terhorst, Jonathan; Kamm, John A.; Song, Yun S.
  • Nature Genetics, Vol. 49, Issue 2
  • DOI: 10.1038/ng.3748

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


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

  • País, Silvia Marina; Téllez-Iñón, María Teresa; Capiati, Daniela Andrea
  • Plant Signaling & Behavior, Vol. 4, Issue 11
  • DOI: 10.4161/psb.4.11.9783

Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas
journal, January 2016


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

  • Browning, Sharon R.; Browning, Brian L.
  • The American Journal of Human Genetics, Vol. 81, Issue 5
  • DOI: 10.1086/521987

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


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

  • Bakirdere, Sezgin; Yaman, Mehmet
  • Environmental Monitoring and Assessment, Vol. 136, Issue 1-3
  • DOI: 10.1007/s10661-007-9695-1

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


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


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

  • Mitchell-Olds, Thomas; Willis, John H.; Goldstein, David B.
  • Nature Reviews Genetics, Vol. 8, Issue 11
  • DOI: 10.1038/nrg2207

Managing water resources for crop production
journal, July 1997

  • Wallace, J. S.; Batchelor, C. H.
  • Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 352, Issue 1356
  • DOI: 10.1098/rstb.1997.0073

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

  • Cutter, Asher D.; Payseur, Bret A.
  • Nature Reviews Genetics, Vol. 14, Issue 4
  • DOI: 10.1038/nrg3425

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

  • Couto, Daniel; Zipfel, Cyril
  • Nature Reviews Immunology, Vol. 16, Issue 9
  • DOI: 10.1038/nri.2016.77

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

  • Delph, Lynda F.; Kelly, John K.
  • New Phytologist, Vol. 201, Issue 1
  • DOI: 10.1111/nph.12441

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

  • Pavlidis, Pavlos; Živković, Daniel; Stamatakis, Alexandros
  • Molecular Biology and Evolution, Vol. 30, Issue 9
  • DOI: 10.1093/molbev/mst112

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

  • Gordon, Sean P.; Priest, Henry; Des Marais, David L.
  • The Plant Journal, Vol. 79, Issue 3
  • DOI: 10.1111/tpj.12569