Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate
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 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 B. distachyon 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.
- Authors:
-
[1];
[1]
- Australian National Univ., Canberra, ACT (Australia)
- Univ. of California, San Diego, CA (United States); Australian National Univ., Canberra, ACT (Australia)
- United States Department of Agriculture (USDA), St. Paul, MN (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Contributing Org.:
- Accession Contributors
- OSTI Identifier:
- 1493985
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genetics
- Additional Journal Information:
- Journal Volume: 211; Journal Issue: 1; Journal ID: ISSN 0016-6731
- Publisher:
- Genetics Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
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., and Borevitz, Justin O. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. United States: N. p., 2019.
Web. doi:10.1534/genetics.118.301589.
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. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. United States. https://doi.org/10.1534/genetics.118.301589
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., and Borevitz, Justin O. Wed .
"Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate". United States. https://doi.org/10.1534/genetics.118.301589. https://www.osti.gov/servlets/purl/1493985.
@article{osti_1493985,
title = {Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate},
author = {Wilson, Pip B. and Streich, Jared C. and Murray, Kevin D. and Eichten, Steve R. and Cheng, Riyan and Aitken, Nicola C. and Spokas, Kurt and Warthmann, Norman and Gordon, Sean P. and Vogel, John P. and Borevitz, Justin O.},
abstractNote = {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 B. distachyon 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.},
doi = {10.1534/genetics.118.301589},
journal = {Genetics},
number = 1,
volume = 211,
place = {United States},
year = {Wed Jan 09 00:00:00 EST 2019},
month = {Wed Jan 09 00:00:00 EST 2019}
}
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