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Title: Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

Abstract

Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.

Authors:
 [1]; ORCiD logo [2];  [3];  [1];  [4];  [5];  [1];  [1];  [6];  [1];  [5];  [6];  [7];  [1]; ORCiD logo [8]
  1. US Dept. of Agriculture (USDA)., Albany, CA (United States). ARS Western Regional Research Center
  2. Salk Inst. for Biological Studies and the Howard Hughes Medical Inst., La Jolla, CA (United States). Genomic Analysis Lab.; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. US Dept. of Agriculture (USDA)., Albany, CA (United States). ARS Western Regional Research Center; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Agriculture and Agri-Food Canada, Morden, MB (Canada). Cereal Research Centre
  6. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  7. Salk Inst. for Biological Studies and the Howard Hughes Medical Inst., La Jolla, CA (United States). Genomic Analysis Lab.
  8. US Dept. of Agriculture (USDA)., Albany, CA (United States). ARS Western Regional Research Center; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1476520
Alternate Identifier(s):
OSTI ID: 1401782; OSTI ID: 1575213
Grant/Contract Number:  
AC02-05CH11231; SC0001526; AI02-07ER64452; SC0012400
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 91; Journal Issue: 3; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; insertional mutagenesis; Brachypodium distachyon; functional genomics; T-DNA; mutant sequencing; model grass

Citation Formats

Hsia, Mon Mandy, O'Malley, Ronan, Cartwright, Amy, Nieu, Rita, Gordon, Sean P., Kelly, Sandra, Williams, Tina G., Wood, Delilah F., Zhao, Yunjun, Bragg, Jennifer, Jordan, Mark, Pauly, Markus, Ecker, Joseph R., Gu, Yong, and Vogel, John P. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. United States: N. p., 2017. Web. doi:10.1111/tpj.13582.
Hsia, Mon Mandy, O'Malley, Ronan, Cartwright, Amy, Nieu, Rita, Gordon, Sean P., Kelly, Sandra, Williams, Tina G., Wood, Delilah F., Zhao, Yunjun, Bragg, Jennifer, Jordan, Mark, Pauly, Markus, Ecker, Joseph R., Gu, Yong, & Vogel, John P. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. United States. doi:10.1111/tpj.13582.
Hsia, Mon Mandy, O'Malley, Ronan, Cartwright, Amy, Nieu, Rita, Gordon, Sean P., Kelly, Sandra, Williams, Tina G., Wood, Delilah F., Zhao, Yunjun, Bragg, Jennifer, Jordan, Mark, Pauly, Markus, Ecker, Joseph R., Gu, Yong, and Vogel, John P. Wed . "Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection". United States. doi:10.1111/tpj.13582. https://www.osti.gov/servlets/purl/1476520.
@article{osti_1476520,
title = {Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection},
author = {Hsia, Mon Mandy and O'Malley, Ronan and Cartwright, Amy and Nieu, Rita and Gordon, Sean P. and Kelly, Sandra and Williams, Tina G. and Wood, Delilah F. and Zhao, Yunjun and Bragg, Jennifer and Jordan, Mark and Pauly, Markus and Ecker, Joseph R. and Gu, Yong and Vogel, John P.},
abstractNote = {Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.},
doi = {10.1111/tpj.13582},
journal = {The Plant Journal},
issn = {0960-7412},
number = 3,
volume = 91,
place = {United States},
year = {2017},
month = {6}
}

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    Works referencing / citing this record:

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