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Title: Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

Abstract

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [2];  [1];  [3];  [1];  [4];  [4]; ORCiD logo [1]
  1. Australian National Univ., Canberra, ACT (Australia)
  2. Univ. of California, San Diego, CA (United States); Australian National Univ., Canberra, ACT (Australia)
  3. United States Department of Agriculture (USDA), St. Paul, MN (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Contributing Org.:
Accession Contributors
OSTI Identifier:
1493985
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genetics
Additional Journal Information:
Journal Volume: 211; Journal Issue: 1; Journal ID: ISSN 0016-6731
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Wilson, Pip B., Streich, Jared C., Murray, Kevin D., Eichten, Steve R., Cheng, Riyan, Aitken, Nicola C., Spokas, Kurt, Warthmann, Norman, Gordon, Sean P., Vogel, John P., and Borevitz, Justin O. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. United States: N. p., 2019. Web. doi:10.1534/genetics.118.301589.
Wilson, Pip B., Streich, Jared C., Murray, Kevin D., Eichten, Steve R., Cheng, Riyan, Aitken, Nicola C., Spokas, Kurt, Warthmann, Norman, Gordon, Sean P., Vogel, John P., & Borevitz, Justin O. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. United States. https://doi.org/10.1534/genetics.118.301589
Wilson, Pip B., Streich, Jared C., Murray, Kevin D., Eichten, Steve R., Cheng, Riyan, Aitken, Nicola C., Spokas, Kurt, Warthmann, Norman, Gordon, Sean P., Vogel, John P., and Borevitz, Justin O. Wed . "Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate". United States. https://doi.org/10.1534/genetics.118.301589. https://www.osti.gov/servlets/purl/1493985.
@article{osti_1493985,
title = {Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate},
author = {Wilson, Pip B. and Streich, Jared C. and Murray, Kevin D. and Eichten, Steve R. and Cheng, Riyan and Aitken, Nicola C. and Spokas, Kurt and Warthmann, Norman and Gordon, Sean P. and Vogel, John P. and Borevitz, Justin O.},
abstractNote = {The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.},
doi = {10.1534/genetics.118.301589},
url = {https://www.osti.gov/biblio/1493985}, journal = {Genetics},
issn = {0016-6731},
number = 1,
volume = 211,
place = {United States},
year = {2019},
month = {1}
}

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Works referenced in this record:

Estimating hourly incoming solar radiation from limited meteorological data
journal, February 2006


Genome-wide association study of leaf architecture in the maize nested association mapping population
journal, January 2011


Breeding for high water-use efficiency
journal, September 2004


Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon
journal, January 2009


Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon
journal, June 2017


Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars
journal, September 2011


GENOTYPIC DIFFERENCES IN DARK RESPIRATION OF MATURE LEAVES IN WINTER WHEAT ( Triticum aestivum L.)
journal, July 1988


Rapid recent growth and divergence of rice nuclear genomes
journal, July 2004


Yield Trends Are Insufficient to Double Global Crop Production by 2050
journal, June 2013


Natural Variation in Brachypodium Links Vernalization and Flowering Time Loci as Major Flowering Determinants
journal, September 2016


TraitCapture: genomic and environment modelling of plant phenomic data
journal, April 2014


QTL for Fatty Acid Composition of Maize Kernel Oil in Illinois High Oil × B73 Backcross-Derived Lines
journal, January 2008


Climate Change Impacts on Global Food Security
journal, August 2013


Pyramiding greater early vigour and integrated transpiration efficiency in bread wheat; trade-offs and benefits
journal, November 2015


Genetic dissection of seedling and early vigor in a recombinant inbred line population of rice
journal, February 2007


A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)
journal, December 2012


Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
journal, December 2011


Genomic breeding for food, environment and livelihoods
journal, March 2015


Genome-wide association studies of 14 agronomic traits in rice landraces
journal, October 2010


Genetic improvement of early vigour in wheat
journal, January 1999


libqcpp: A C++14 sequence quality control library
journal, May 2017


QTLRel: an R Package for Genome-wide Association Studies in which Relatedness is a Concern
journal, January 2011


Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments
journal, December 2014


Natural Variations and Genome-Wide Association Studies in Crop Plants
journal, April 2014


Memory of the vernalized state in plants including the model grass Brachypodium distachyon
journal, March 2014


Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
journal, March 2010


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


Of growing importance: combining greater early vigour and transpiration efficiency for wheat in variable rainfed environments
journal, January 2015


Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery
journal, January 2016


Improved linear mixed models for genome-wide association studies
journal, May 2012


Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature
journal, May 2010


Visual Quantification of Wheat Development1
journal, January 1973


Evolution and taxonomic split of the model grass Brachypodium distachyon
journal, January 2012


Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines
journal, October 2009


Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium
journal, May 2016


Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape: GENOMIC DIVERSITY IN SWITCHGRASS
journal, November 2011


Insight into the Karyotype Evolution of Brachypodium Species Using Comparative Chromosome Barcoding
journal, March 2014


STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
journal, October 2011


Pampered inside, pestered outside? Differences and similarities between plants growing in controlled conditions and in the field
journal, October 2016


AdapterRemoval v2: rapid adapter trimming, identification, and read merging
journal, February 2016


Axe: rapid, competitive sequence read demultiplexing using a trie
journal, June 2018


QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.)
journal, March 2017


Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon
journal, December 2013


The more the better? The role of polyploidy in facilitating plant invasions
journal, October 2011


Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing
journal, May 2016


Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon
journal, July 2012


Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon
journal, October 2016


Quantitative trait loci on chromosome 4B for coleoptile length and early vigour in wheat (Triticum aestivum L.)
journal, January 2001


Genome-wide association studies in plants: the missing heritability is in the field
journal, January 2011


Exploiting the Brachypodium Tool Box in cereal and grass research
journal, May 2011


A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011


Laying the Cytotaxonomic Foundations of a New Model Grass, Brachypodium distachyon (L.) Beauv.
journal, January 2004


Brachypodium distachyon and Setaria viridis : Model Genetic Systems for the Grasses
journal, April 2015


genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
journal, March 2006


Brachypodium distachyon . A New Model System for Functional Genomics in Grasses
journal, December 2001


The combination of gas-phase fluorophore technology and automation to enable high-throughput analysis of plant respiration
journal, March 2017


Supplemental Material for Wilson et al., 2018
collection, January 2018


    Works referencing / citing this record:

    Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing
    journal, May 2016


    Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon
    journal, October 2016


    A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
    journal, May 2011


    Quantitative trait loci on chromosome 4B for coleoptile length and early vigour in wheat (Triticum aestivum L.)
    journal, January 2001


    Brachypodium distachyon and Setaria viridis : Model Genetic Systems for the Grasses
    journal, April 2015


    QTLRel: an R Package for Genome-wide Association Studies in which Relatedness is a Concern
    journal, January 2011


    Improved linear mixed models for genome-wide association studies
    journal, May 2012


    Exploiting the Brachypodium Tool Box in cereal and grass research
    journal, May 2011


    Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon
    journal, December 2013


    Climate Change Impacts on Global Food Security
    journal, August 2013


    A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)
    journal, December 2012


    Yield Trends Are Insufficient to Double Global Crop Production by 2050
    journal, June 2013


    Of growing importance: combining greater early vigour and transpiration efficiency for wheat in variable rainfed environments
    journal, January 2015


    genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
    journal, March 2006


    Genome-wide association studies in plants: the missing heritability is in the field
    journal, January 2011


    Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
    journal, December 2011


    Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature
    journal, May 2010


    The combination of gas-phase fluorophore technology and automation to enable high-throughput analysis of plant respiration
    journal, March 2017


    Axe: rapid, competitive sequence read demultiplexing using a trie
    journal, June 2018


    Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines
    journal, October 2009


    Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars
    journal, September 2011


    Insight into the Karyotype Evolution of Brachypodium Species Using Comparative Chromosome Barcoding
    journal, March 2014


    TraitCapture: genomic and environment modelling of plant phenomic data
    journal, April 2014


    Genetic dissection of seedling and early vigor in a recombinant inbred line population of rice
    journal, February 2007


    GENOTYPIC DIFFERENCES IN DARK RESPIRATION OF MATURE LEAVES IN WINTER WHEAT ( Triticum aestivum L.)
    journal, July 1988


    The more the better? The role of polyploidy in facilitating plant invasions
    journal, October 2011


    Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon
    journal, July 2012


    QTL for Fatty Acid Composition of Maize Kernel Oil in Illinois High Oil × B73 Backcross-Derived Lines
    journal, January 2008


    Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon
    journal, January 2009


    QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.)
    journal, March 2017


    Rapid recent growth and divergence of rice nuclear genomes
    journal, July 2004


    Breeding for high water-use efficiency
    journal, September 2004


    Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon
    journal, June 2017


    Natural Variations and Genome-Wide Association Studies in Crop Plants
    journal, April 2014


    Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments
    journal, December 2014


    Pampered inside, pestered outside? Differences and similarities between plants growing in controlled conditions and in the field
    journal, October 2016


    Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium
    journal, May 2016


    Genetic improvement of early vigour in wheat
    journal, January 1999


    Evolution and taxonomic split of the model grass Brachypodium distachyon
    journal, January 2012


    Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    journal, March 2010


    Estimating hourly incoming solar radiation from limited meteorological data
    journal, February 2006


    Genome-wide association study of leaf architecture in the maize nested association mapping population
    journal, January 2011


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


    Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery
    journal, January 2016


    Laying the Cytotaxonomic Foundations of a New Model Grass, Brachypodium distachyon (L.) Beauv.
    journal, January 2004


    AdapterRemoval v2: rapid adapter trimming, identification, and read merging
    journal, February 2016


    Genomic breeding for food, environment and livelihoods
    journal, March 2015


    STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
    journal, October 2011


    libqcpp: A C++14 sequence quality control library
    journal, May 2017


    Genome-wide association studies of 14 agronomic traits in rice landraces
    journal, October 2010


    Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape: GENOMIC DIVERSITY IN SWITCHGRASS
    journal, November 2011


    Pyramiding greater early vigour and integrated transpiration efficiency in bread wheat; trade-offs and benefits
    journal, November 2015


    Visual Quantification of Wheat Development1
    journal, January 1973


    Natural Variation in Brachypodium Links Vernalization and Flowering Time Loci as Major Flowering Determinants
    journal, September 2016


    Memory of the vernalized state in plants including the model grass Brachypodium distachyon
    journal, March 2014


    Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon
    journal, May 2019