Global diversity of the brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate

Authors: WILSON, PIP - Australian National University; STREICH, JARED - Australian National University; MURRAY, KEVIN - Australian National University; EICHTEN, STEVE - Australian National University; CHENG, RIYAN - Australian National University; AITKIN, NICCY - Australian National University; Spokas, Kurt; WARTHMANN, NOLRMANN - Australian National University; BOREVITZ, JUSTIN - Australian National University

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2018
Publication Date: 1/1/2019
Citation: Wilson, P., Streich, J., Murray, K., Eichten, S., Cheng, R., Aitkin, N., Spokas, K.A., Warthmann, N., Gordon, S., Vogel, J., Borevitz, J. 2019. Global diversity of the brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate. Genetics. 211(1):317-331. https://doi.org/10.1534/genetics.118.301589.
DOI: https://doi.org/10.1534/genetics.118.301589

Interpretive Summary: We utilize known systems as reference models in order to improve our scientific understanding. This is particularly useful for plant genetic studies. One area of critical importance is the interaction of environmental factors (e.g. temperature and light quality) with the genetic expressions that results in the plant. In this study, we utilized a vast collection (over 1800 individual members) of the plant genius Brachypodium (grass) to 1) improve the genetic data available for this plant genius and 2) determine the impact of temperature and light quality on the plant's genetic sequences. We observed 8 sets of quantitative trait loci (QTL) that were related to flowering time; 22 QTLs for early vigor; and 47 QTLs that were associated with energy transformation. This study highlights the potential use of genetics with model species to assess the impact of environmental factors on the growth of plants. This could be an important first step in the selection of plant species that would be optimum for cover crop use to prevent erosion or selection of a species that could out compete invasive weeds. These results are significant to farmers and policy makers and will assist scientists and engineers in understanding the genetic traits to achieve a desired plant growth attribute.

Technical Abstract: 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 translational 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 sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines were 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 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of the Brachypodium species complex and allow powerful complex trait dissection within this new grass model species.