Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

• Published in: Genetics (Austin) Vol. 211; no. 1; pp. 317 - 331
• Main Authors: Wilson, Pip B, Streich, Jared C, Murray, Kevin D, Eichten, Steve R, Cheng, Riyan, Aitken, Nicola C, Spokas, Kurt, Warthmann, Norman, Gordon, Sean P, Vogel, John P, Borevitz, Justin O
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01.01.2019
• Subjects: Agricultural production; Agronomy; Barley; BASIC BIOLOGICAL SCIENCES; Biodiversity; Bioinformatics; Biomass; Brachypodium; Climate change; Climatic conditions; Computer simulation; Consortia; Efficiency; Energy; Energy crops; Flowering; Gene sequencing; Genetic diversity; Genetics; Genome-wide association studies; Genomes; Genomics; Genotypes; Grain; Grasses; Inbreeding; Investigations; Life history; Natural populations; Phenotyping; Population genetics; Principal components analysis; Quantitative trait loci; Respiration; Species; Species diversity; Vigor; Wheat; Australia; plant physiology; population genetics; Brachypodium distachyon; agronomic traits; genotyping; climate simulation; ecogenomics; genome-wide association studies; climate change
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1534/genetics.118.301589

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.