Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

Tyler, Ludmila; Lee, Scott J.; Young, Nelson D.; DeIulio, Gregory A.; Benavente, Elena; Reagon, Michael; Sysopha, Jessica; Baldini, Riccardo M.; Troia, Angelo; Hazen, Samuel P.; Caicedo, Ana L.

doi:10.3835/plantgenome2015.08.0074

Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

Journal Article · Fri Apr 29 00:00:00 EDT 2016 · The Plant Genome

DOI:https://doi.org/10.3835/plantgenome2015.08.0074· OSTI ID:1312966

Tyler, Ludmila ^[1]; Lee, Scott J. ^[2]; Young, Nelson D. ^[2]; DeIulio, Gregory A. ^[2]; Benavente, Elena ^[3]; Reagon, Michael ^[4]; Sysopha, Jessica ^[2]; Baldini, Riccardo M. ^[5]; Troia, Angelo ^[6]; Hazen, Samuel P. ^[2]; Caicedo, Ana L. ^[2]

Univ. of Massachusetts, Amherst, MA (United States); University of Massachusetts
Univ. of Massachusetts, Amherst, MA (United States)
ETSIA, Technical Univ. of Madrid, Madrid (Spain)
The Ohio State Univ.-Lima, Lima, OH (United States)
Univ. of Florence, Florence (Italy)
Univ. di Palermo, Palermo (Italy)

The small, annual grass Brachypodium distachyon (L.) Beauv., a close relative of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in B. distachyon by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 B. distachyon, seven B. hybridum, and three B. stacei accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Over 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the B. hybridum genome, which appears as a mosaic of B. distachyon-like and B. stacei-like sequences. Analysis of more than 50,000 SNPs for the B. distachyon accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between B. distachyon populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within B. distachyon populations. As a result, our characterization elucidates genes underlying population differences, expands the germplasm resources available for Brachypodium, and illustrates the feasibility and limitations of GWAS in this model grass.

View Accepted Manuscript (DOE)

Research Organization:: Univ.of California, San Diego, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0006621

OSTI ID:: 1312966

Journal Information:: The Plant Genome, Journal Name: The Plant Genome Journal Issue: 2 Vol. 9; ISSN 1940-3372

Publisher:: Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon Vogel, John P.; Tuna, Metin; Budak, Hikmet BMC Plant Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471‐2229‐9‐88	journal	January 2009
Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis Gomez, Leonardo D.; Bristow, Jennifer K.; Statham, Emily R. Biotechnology for Biofuels, Vol. 1, Issue 1 https://doi.org/10.1186/1754-6834-1-15	journal	January 2008
Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis Gomez, Leonardo D.; Bristow, Jennifer K.; Statham, Emily R. Biotechnology for Biofuels, Vol. 1, Issue 1 https://doi.org/10.1186/1754‐6834‐1‐15	journal	January 2008
Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality Lee, Scott J.; Warnick, Thomas A.; Pattathil, Sivakumar Biotechnology for Biofuels, Vol. 5, Issue 1 https://doi.org/10.1186/1754‐6834‐5‐5	journal	January 2012
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Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb‐2014‐15‐3‐r41	journal	January 2014
Brachypodium Bragg, Jennifer; Tyler, Ludmila; Vogel, John Handbook of Bioenergy Crop Plants https://doi.org/10.1201/b11711-27	book	March 2012
Population Structure and Eigenanalysis Patterson, Nick; Price, Alkes L.; Reich, David PLoS Genetics, Vol. 2, Issue 12 https://doi.org/10.1371/journal.pgen.0020190	journal	January 2006
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Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses Higgins, Janet A.; Bailey, Paul C.; Laurie, David A. PLoS ONE, Vol. 5, Issue 4 https://doi.org/10.1371/journal.pone.0010065	journal	April 2010
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi PLoS ONE, Vol. 6, Issue 5, Article No. e19379 https://doi.org/10.1371/journal.pone.0019379	journal	May 2011
Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon Cui, Yu; Lee, Mi Yeon; Huo, Naxin PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0038333	journal	June 2012
A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae) López-Alvarez, Diana; López-Herranz, Maria Luisa; Betekhtin, Alexander PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0051058	journal	December 2012
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Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping‐by‐sequencing data and niche modelling Villa‐Machío, Irene; Fernández de Castro, Alejandro G.; Fuertes‐Aguilar, Javier Journal of Biogeography, Vol. 47, Issue 4 https://doi.org/10.1111/jbi.13808	journal	April 2020
Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes Sancho, Rubén; Cantalapiedra, Carlos P.; López-Alvarez, Diana New Phytologist, Vol. 218, Issue 4 https://doi.org/10.1111/nph.14926	journal	December 2017
Evolutionary processes from the perspective of flowering time diversity Gaudinier, Allison; Blackman, Benjamin K. New Phytologist, Vol. 225, Issue 5 https://doi.org/10.1111/nph.16205	journal	October 2019
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 The Plant Journal, Vol. 96, Issue 2 https://doi.org/10.1111/tpj.14042	journal	September 2018
Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon Marques, Isabel; Shiposha, Valeriia; López-Alvarez, Diana BMC Evolutionary Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12862-017-0996-x	journal	June 2017
Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate Wilson, Pip B.; Streich, Jared C.; Murray, Kevin D. Genetics, Vol. 211, Issue 1 https://doi.org/10.1534/genetics.118.301589	journal	November 2018
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland Agronomy, Vol. 9, Issue 12 https://doi.org/10.3390/agronomy9120881	journal	December 2019
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland ETH Zurich https://doi.org/10.3929/ethz-b-000386451	text	January 2019
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P. Nature Publishing Group https://doi.org/10.5167/uzh-148888	text	January 2017

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