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Protocols

T3 specifications

Information


Unique identifier OMICS_32163
Name T3
Alternative name The Triticeae Toolbox
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Jean-Luc Jannink

Additional information


https://github.com/TriticeaeToolbox/T3

Publication for The Triticeae Toolbox

T3 citations

 (6)
library_books

Inferring defense related gene families in Arabidopsis and wheat

2017
BMC Genomics
PMCID: 5738178
PMID: 29258426
DOI: 10.1186/s12864-017-4381-3

[…] The data sets consisting of mapped SNPs for rust resistance at seedling or adult stage were taken from the “GWAS Results” in the Triticeae Toolbox (T3) database (https://triticeaetoolbox.org/wheat/qtl/qtl_report.php) []. By selecting ‘Biotic stress’ in the “Category” column and by clicking appropriate rust traits at adult o […]

library_books

Genome Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum

2017
PMCID: 5633397
PMID: 28855281
DOI: 10.1534/g3.117.300222

[…] al of 54,118 SNP markers. Marker names were assigned based on their chromosome location and base pair position (bp) on the barley reference genome (). Genotypic data for the WBDC will be deposited in The Triticeae Toolbox (T3) (https://triticeaetoolbox.org/). […]

library_books

Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)

2017
BMC Plant Biol
PMCID: 5477749
PMID: 28633642
DOI: 10.1186/s12870-017-1056-9

[…] Two data sets, each with 2500 quantitative trait loci (QTLs) for leaf rust resistance at seedling or adult stage, were extracted from the “GWAS Results” in the Triticeae Toolbox (T3) database (https://triticeaetoolbox.org/wheat/qtl/qtl_report.php) []. By selecting ‘Biotic stress’ in the “Category” column and by clicking appropriate leaf rust traits at ad […]

call_split

Genomic and pedigree based prediction for leaf, stem, and stripe rust resistance in wheat

2017
PMCID: 5487692
PMID: 28393303
DOI: 10.1007/s00122-017-2897-1
call_split See protocol

[…] e BVs of the individuals. To obtain the chromosomal locations of the significant markers, the basic local alignment search tool (BLAST) (https://triticeaetoolbox.org/wheat/viroblast/viroblast.php) in the Triticeae Toolbox website was used. A nucleotide BLAST (BLAST-n) was performed against the wheat markers in Triticeae Toolbox (T3) database (updated on April 2015), wheat contigs (1A to 7D) from t […]

call_split

Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races

2015
BMC Plant Biol
PMCID: 4606553
PMID: 26467989
DOI: 10.1186/s12870-015-0628-9
call_split See protocol

[…] ]. Allele calls were performed using the computer program GenomeStudio v2011.1 (Illumina Inc.). As genotyping of these lines was carried out as a part of the TCAP, the genotype data was obtained from The Triticeae Toolbox. During data download, SNP markers with minor allele frequency less than 0.05 and no calls for more than 10 % of the lines were removed from the dataset. Lines that were genotype […]

library_books

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

2015
PLoS One
PMCID: 4514886
PMID: 26208213
DOI: 10.1371/journal.pone.0133767

[…] 34 accessions genotyped, 68 were excluded from the analysis because they had more than 10% missing genotypic data. Therefore, the GWAS is based on 1,466 barley accessions. SNP data was retrieved from The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/; verified 13 October 2014) (Blake et al. 2012).Linkage map positions from the barley consensus map [] were used to identify the position of SNP […]

Citations

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T3 institution(s)
USDA-ARS Western Regional Research Center, Albany, CA, USA; USDA-ARS Robert Holley Center, Ithaca, NY, USA
T3 funding source(s)
Supported by the Agriculture and Food Research Initiative Competitive Grant No. 2011-68002-30029 from the USDA National Institute of Food and Agriculture.

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