Population Structure in the Model GrassBrachypodium distachyonIs 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. Core Ideas• Genotyping diverse Brachypodium accessions expands research tools for grasses.• The B. hybridum genome is a mosaic of B. distachyonand B. stacei-like sequences.• Three distinct, genetically defined populations of B. distachyon were identified.• Flowering time, more than geography, distinguishes B. distachyon populations.• Results support the feasibility of genome-wide association studies in a model grass.

Natural Variation in Brachypodium Links Vernalization and Flowering Time Loci as Major Flowering Determinants

“…The authors did not rule out the effects of population structure and proposed that elucidating the role of VRN2 in B. distachyon will require more in-depth genetic studies. A recent comprehensive analysis of population structure in B. distachyon collections revealed that flowering time, and not geographic origin, is indeed the major distinguishing factor between genotypically distinct clusters (Tyler et al, 2016). Our results confirm VRN2 as an important flowering regulator in the ABR6 3 Bd21 mapping population and highlight structural and expression variation between parental accessions.…”

“…Two additional QTLs on chromosomes Bd2 (qFLT3) and Bd3 (qFLT7) were detected in two environments, whereas four minoreffect QTLs (qFLT2, qFLT4, qFLT5, and qFLT8) were found in individual environments only. Two recent genomewide association studies used the natural variation found within B. distachyon germplasm to identify SNPs associated with flowering time (Tyler et al, 2016;Wilson Figure 6. Phenotype-by-genotype plot for the two major loci controlling flowering time in the ABR6 3 Bd21 mapping population.…”

“…To date, most studies on the regulation of flowering time of B. distachyon have used reverse genetic approaches to implicate the role of previously characterized genes from other species (Higgins et al, 2010;Lv et al, 2014;Ream et al, 2014;Woods et al, 2016b), while only a few studies have used the natural variation present among B. distachyon accessions to identify flowering loci (Tyler et al, 2016;Wilson et al, 2016). Currently lacking is the characterization of loci that control variation in flowering time in a biparental B. distachyon mapping population.…”

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

“…Recently, two flowering-time GWAS in B. distachyon identified nine and five associated peaks, none of which overlap with the QTLs identified in this study (Tyler et al, 2016;Wilson et al, 2015). Thus, the QTL identified in our RIL population may represent rare alleles that do not surface in GWAS, or the GWAS that was conducted contains too few accessions or compounding population structures (issues that are common when conducting GWAS in in-breeding species; Weigel and Nordborg 2015).…”

Winter Memory throughout the Plant Kingdom: Different Paths to Flowering

“…Furthermore, studies in the small temperate grass model Brachypodium distachyon, which is an early diverging pooid sister to the crown pooid clade, have contributed to understanding the evolution of vernalization systems in pooids (Woods and Amasino, 2015). Like wheat and barley, B. distachyon is a long-day plant that exhibits an extensive natural variation of flowering behavior across accessions with respect to photoperiod and vernalization responses (Ream et al, 2014;Tyler et al, 2016) and has a "memory" of winter (Woods et al, 2014a). Additionally, B. distachyon contains orthologs of all of the VRN genes discovered in wheat and barley, and these genes also likely contribute to natural variation in flowering responses among different accessions of B. distachyon (Higgins et al, 2010;Woods et al, 2016Woods et al, , 2017Bettgenhaeuser et al, 2017).…”