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

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

Journal Article · 29 April 2016 · The Plant Genome

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

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

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.

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

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

Grant/Contract Number:: SC0006621

OSTI ID:: 1312966

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

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

Country of Publication:: United States

Language:: English

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Cited by: 22 works

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