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

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

Risultato della ricerca: Article

13 Citazioni (Scopus)

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 suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within B. distachyon populations. 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.
Lingua originaleEnglish
pagine (da-a)1-20
Numero di pagine20
RivistaTHE PLANT GENOME
Volume9
Stato di pubblicazionePublished - 2016

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Brachypodium
Brachypodium distachyon
Poaceae
population structure
grasses
flowering
Population
Genome-Wide Association Study
provenance
Hordeum
single nucleotide polymorphism
Triticum
Single Nucleotide Polymorphism
Armenia
photoperiodism
Albania
Genome
loci
genome
vernalization

All Science Journal Classification (ASJC) codes

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

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Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. / Troia, Angelo; Tyler, Ludmila; Lee, Scott J.; Deiulio, Gregory A.; Sysopha, Jessica; Reagon, Michael; Benavente, Elena; Caicedo, Ana L.; Baldini, Riccardo M.; Hazen, Samuel P.; Young, Nelson D.

In: THE PLANT GENOME, Vol. 9, 2016, pag. 1-20.

Risultato della ricerca: Article

Troia, A, Tyler, L, Lee, SJ, Deiulio, GA, Sysopha, J, Reagon, M, Benavente, E, Caicedo, AL, Baldini, RM, Hazen, SP & Young, ND 2016, 'Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas', THE PLANT GENOME, vol. 9, pagg. 1-20.
Troia, Angelo ; Tyler, Ludmila ; Lee, Scott J. ; Deiulio, Gregory A. ; Sysopha, Jessica ; Reagon, Michael ; Benavente, Elena ; Caicedo, Ana L. ; Baldini, Riccardo M. ; Hazen, Samuel P. ; Young, Nelson D. / Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. In: THE PLANT GENOME. 2016 ; Vol. 9. pagg. 1-20.
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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 suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within B. distachyon populations. 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.",
author = "Angelo Troia and Ludmila Tyler and Lee, {Scott J.} and Deiulio, {Gregory A.} and Jessica Sysopha and Michael Reagon and Elena Benavente and Caicedo, {Ana L.} and Baldini, {Riccardo M.} and Hazen, {Samuel P.} and Young, {Nelson D.}",
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T1 - Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

AU - Troia, Angelo

AU - Tyler, Ludmila

AU - Lee, Scott J.

AU - Deiulio, Gregory A.

AU - Sysopha, Jessica

AU - Reagon, Michael

AU - Benavente, Elena

AU - Caicedo, Ana L.

AU - Baldini, Riccardo M.

AU - Hazen, Samuel P.

AU - Young, Nelson D.

PY - 2016

Y1 - 2016

N2 - 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. 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.

AB - 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. 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.

UR - http://hdl.handle.net/10447/209837

UR - https://dl.sciencesocieties.org/publications/tpg/pdfs/9/2/plantgenome2015.08.0074

M3 - Article

VL - 9

SP - 1

EP - 20

JO - Plant Genome

JF - Plant Genome

SN - 1940-3372

ER -