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Plant J. 2017 Aug;91(3):361-370. doi: 10.1111/tpj.13582. Epub 2017 Jun 21.

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

Author information

1
USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA.
2
Genomic Analysis Laboratory, The Salk Institute for Biological Studies and the Howard Hughes Medical Institute, 10010 North Torrey Pines Rd., La Jolla, CA, 92037, USA.
3
DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA.
4
Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB, R6M 1Y5, Canada.
5
Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA.

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/.

KEYWORDS:

Brachypodium distachyon ; T-DNA; functional genomics; insertional mutagenesis; model grass; mutant sequencing

PMID:
28432803
DOI:
10.1111/tpj.13582
[Indexed for MEDLINE]
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