skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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]; 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
+ Show Author Affiliations

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-col lection/.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; DE‐SC0001526; DE‐AI02‐07ER64452; DE‐AC02‐05CH11231; DE‐SC0012400; SC0012400
OSTI ID:
1476520
Alternate ID(s):
OSTI ID: 1401782; OSTI ID: 1575213
Journal Information:
The Plant Journal, Vol. 91, Issue 3; ISSN 0960-7412
Publisher:
Society for Experimental BiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 30 works
Citation information provided by
Web of Science

References (40)

A Role for Flavin Monooxygenase-Like Enzymes in Auxin Biosynthesis journal January 2001
Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection journal September 2012
Rice OsGL1-1 Is Involved in Leaf Cuticular Wax and Cuticle Membrane journal November 2011
Novel Markers of Xylogenesis in Zinnia Are Differentially Regulated by Auxin and Cytokinin journal November 2005
Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon journal December 2013
Cellulose Synthases and Synthesis in Arabidopsis journal March 2011
The Barley Genome Sequence Assembly Reveals Three Additional Members of the CslF (1,3;1,4)-β-Glucan Synthase Gene Family journal March 2014
Activation Tagging in Arabidopsis journal April 2000
Collapsed Xylem Phenotype of Arabidopsis Identifies Mutants Deficient in Cellulose Deposition in the Secondary Cell Wall journal May 1997
Brachypodium as a Model for the Grasses: Today and the Future journal July 2011
Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers: Tonoplastic WAT1 and secondary wall formation journal May 2010
An Active Ac/Ds Transposon System for Activation Tagging in Tomato Cultivar M82 Using Clonal Propagation journal April 2013
Developmental biology of the cereal endosperm journal July 1999
Rapid isolation of high molecular weight plant DNA journal January 1980
BdCESA7, BdCESA8, and BdPMT Utility Promoter Constructs for Targeted Expression to Secondary Cell-Wall-Forming Cells of Grasses journal February 2016
A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants journal November 2007
Molecular characterization of the CER1 gene of arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. journal December 1995
Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro journal November 1992
A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections book January 2015
Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery journal January 2012
Measurement of (1 → 3),(1 → 4)-β-D-glucan in barley and oats: A streamlined enzymic procedure journal January 1991
Brachypodium distachyon book September 2014
A comparative view of the evolution of grasses under domestication: Tansley review journal June 2009
Cloning and Characterization of GLOSSY1 , a Maize Gene Involved in Cuticle Membrane and Wax Production journal April 2005
Cellulose Synthase-Like CslF Genes Mediate the Synthesis of Cell Wall (1,3;1,4)- -D-Glucans journal March 2006
A Xyloglucan Backbone 6-O-Acetyltransferase from Brachypodium distachyon Modulates Xyloglucan Xylosylation journal April 2016
Tab2 is a novel conserved RNA binding protein required for translation of the chloroplast psaB mRNA journal December 2003
An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome journal November 2007
ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins journal November 2006
Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis journal July 2006
Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21: T-DNA tagging in Brachypodium journal March 2010
Loss of Cellulose Synthase - Like F6 Function Affects Mixed-Linkage Glucan Deposition, Cell Wall Mechanical Properties, and Defense Responses in Vegetative Tissues of Rice journal March 2012
Trends and Variability in U.S. Corn Yields Over the Twentieth Century journal March 2005
Arabidopsis RAD51C Gene Is Important for Homologous Recombination in Meiosis and Mitosis journal September 2005
Over-expression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall (1,3;1,4)-β-d-glucans and alters their fine structure: Over-expression of CslF genes in barley journal January 2011
BAS1: A gene regulating brassinosteroid levels and light responsiveness in Arabidopsis journal December 1999
High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3 journal November 2007
A missense mutation in the transmembrane domain of CESA4 affects protein abundance in the plasma membrane and results in abnormal cell wall biosynthesis in rice journal August 2009
Unique aspects of the grass cell wall journal June 2008
Genetic resources offer efficient tools for rice functional genomics research: Rice functional genomics research journal November 2015

Cited By (9)

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
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 journal January 2019
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass text January 2019
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

Similar Records

Related Subjects

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