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 "EMBL-EBI - Expression Atlas.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.
The Z-score is a average of the p-values, calculated as Z = (1/Trial Count) * Σ abs( qnorm( p-value / 2 ))
To view the p-value and q-value for each trial, select the trial count link.
Phenotype Trials: 3554
Genotype platforms: GoldenGate, Infinium 9K, VeraCode, Infinium 50K
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