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

Journal Article · · The Plant Journal
DOI:https://doi.org/10.1111/tpj.13582· OSTI ID:1476520
 [1];  [2];  [3];  [1];  [4];  [5];  [1];  [1];  [6];  [1];  [5];  [6];  [7];  [1];  [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
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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/.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1476520
Alternate ID(s):
OSTI ID: 1401782
OSTI ID: 1575213
Journal Information:
The Plant Journal, Journal Name: The Plant Journal Journal Issue: 3 Vol. 91; ISSN 0960-7412
Publisher:
Society for Experimental BiologyCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (9)

Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon journal June 2019
Highly efficient generation of T-DNA insertion lines and isolation of flanking sequence tags (FSTs) of Brachypodium distachyon journal June 2018
Voltage-dependent gating of SV channel TPC1 confers vacuole excitability journal June 2019
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass journal January 2019
Blurring the boundaries between cereal crops and model plants journal November 2019
Non-redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium journal October 2017
Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon journal May 2019
In Vitro Tissue Culture in Brachypodium: Applications and Challenges journal February 2020
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass text January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
Brachypodium distachyon
T-DNA
functional genomics
insertional mutagenesis
model grass
mutant sequencing