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  T3/Wheat

GWAS Results

This analysis can be used to identify quantitative trait locus (QTL) by displaying associations between markers and traits for trials within the T3 database. If traits and trials are selected then only results for the selected trials are shown otherwise results are shown for all trials. ZBrowse instructions. Expression data is provided by "WheatExp: An Expression Database for Polyploid Wheat" and "Wheat Expression Browser: expVIP".

Analysis Methods: The analysis includes genotype and phenotype trials where there were more than 50 germplasm lines in common.
1. phenotype trial - GWAS with no fixed effects.
2. phenotype experiment - GWAS on a set of related phenotype trials (different location and same year or same location different year). Principle Components that accounted for more than 5% of the relationship matrix variance were included as fixed effects in the analysis. Each phenotype trial (if more than one) was included as a fixed effect.
GWAS: The analysis use rrBLUP GWAS package (Endleman, Jeffery, "Ridge Regression and Other Kernels for Genomic Selection with R package rrBLUP", The Plant Genome Vol 4 no. 3). The settings are: MAF > 0.05, P3D = TRUE (equivalent to EMMAX). The q-value is an estimate of significance given p-values from multiple comparisons using a false discovery rate of 0.05. To view the p-value and q-value for each trial, select the trial count link.
External Links: The "Pathway" column contains links to Plant Reactome from http://plantreactome.gramene.org/download/gene_ids_by_pathway_and_species.tab.

Phenotype Trials: 1177
Genotype platforms: Infinium 9K, Infinium 90K, GBS restriction site

Genome AssemblyDescription
IWGSC1+popseqIWGSC.31, Triticum aestivum CS42 whole genome assembly. The CSS assemblies have been further refined into chromosomal pseudomolecules using POPSEQ data.
Wheat_PangenomeWhole-genome sequence reads from 18 wheat cultivars were mapped to the new Chinese Spring assembly
Wheat_TGACv1IWGSC.37, Triticum aestivum CS42 whole genome assembly. Assembled using modified DISCOVAR + SOAP and scaffolds classified into arm bins using CSS reads
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In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement.

I agree to the Data Usage Policy as specified in Toronto Statement.