Gordon, Sean P.Priest, HenryMarais, David L. DesSchackwitz, WendyFigueroa, MelaniaMartin, JoelVogel, John P.Tuna, Metin2022-05-112022-05-1120140960-74121365-313Xhttps://doi.org/10.1111/tpj.12569https://hdl.handle.net/20.500.11776/10149Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.en10.1111/tpj.12569info:eu-repo/semantics/openAccessBrachypodium distachyonnatural diversitygenome sequencingtranscriptomedroughtArabidopsis-ThalianaModel SystemDroughtStressExpressionOverexpressionPatternsRevealsRiceMapArticle793361374Q1WOS:0003401635000012-s2.0-8490511143024888695Q1