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

Abstract

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 suggestmore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [3];  [1];  [4];  [5];  [1];  [1]
  1. Univ. of Massachusetts, Amherst, MA (United States)
  2. ETSIA, Technical Univ. of Madrid, Madrid (Spain)
  3. The Ohio State Univ.-Lima, Lima, OH (United States)
  4. Univ. of Florence, Florence (Italy)
  5. Univ. di Palermo, Palermo (Italy)
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1312966
Grant/Contract Number:  
SC0006621
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The Plant Genome
Additional Journal Information:
Journal Volume: 9; Journal Issue: 2; Journal ID: ISSN 1940-3372
Publisher:
Alliance of Crop, Soil, and Environmental Science Societies
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS

Citation Formats

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., and Caicedo, Ana L. Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. United States: N. p., 2016. Web. doi:10.3835/plantgenome2015.08.0074.
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. Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. United States. https://doi.org/10.3835/plantgenome2015.08.0074
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., and Caicedo, Ana L. Fri . "Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas". United States. https://doi.org/10.3835/plantgenome2015.08.0074. https://www.osti.gov/servlets/purl/1312966.
@article{osti_1312966,
title = {Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas},
author = {Tyler, Ludmila and Lee, Scott J. and Young, Nelson D. and DeIulio, Gregory A. and Benavente, Elena and Reagon, Michael and Sysopha, Jessica and Baldini, Riccardo M. and Troia, Angelo and Hazen, Samuel P. and Caicedo, Ana L.},
abstractNote = {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.},
doi = {10.3835/plantgenome2015.08.0074},
url = {https://www.osti.gov/biblio/1312966}, journal = {The Plant Genome},
issn = {1940-3372},
number = 2,
volume = 9,
place = {United States},
year = {2016},
month = {4}
}

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    Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes
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