Examining Flowering Time in the Grasses: Population Structure and Genome-Wide Association Mapping in Brachypodium distachyon

The small, annual grass Brachypodium distachyon, a close relative of wheat and barley, is emerging as 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 prevented in Brachypodium by the lack of sufficient numbers of well-characterized accessions.  We have performed genotyping-by-sequencing of 84 B. distachyon, eight B. hybridum, and three B. stacei accessions with diverse geographic origins, including Albania, Armenia, Georgia, Sicily, 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 has revealed three distinct, genetically defined populations.  Surprisingly, these genomic profiles are more readily explained by differences in flowering time than by geographic origin.  Preliminary GWAS has implicated several known photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation as well as loci with no obvious candidate genes.  Our characterization expands the germplasm resources available for Brachypodium and demonstrates the feasibility of GWAS in this model grass.