This analysis can be used to identify quantitative trait locus (QTL) by displaying associations between markers and traits for trials within the T3 database.
Analysis Methods: The analysis includes genotype and phenotype trials where there were more than 50 germplasm lines in common.
1. Trial Analysis - GWAS with no fixed effects.
2. Breeding Program Analysis - 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-value = qnorm( 1.0 - ( pvalue / 2.0 ))

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Trait:

aboveground biomassanthocyanin reflectance index 1anthocyanin reflectance index 2bacterial leaf streakbasal aborted spikelets per headbiomass at maturityBYDV incidence 0-9canopy normalized difference vegetation indexcanopy normalized pheophytinization indexcanopy normalized water index 1canopy normalized water index 2canopy photochemical reflectance indexcanopy senescence score T3canopy senescence score T4canopy senescence score T5canopy senescence score T7canopy water indexcarotenoid reflectance index 2Cdchlorophyll ratioCocommon buntdays to flag leaf senescencedays to headingdays to heading (fall planting)enhanced vegetation indexfertile spikelets per headflag leaf glaucousnessflag leaf lengthflag leaf stay-green periodflag leaf widthflowering dateflowering date (fall planting)forage yieldfreeze injurygrain fill durationgrain hardnessgrain numbergrain numbergrain weightgrain yieldgrain yield grain yield harvest indexH. avenae damageheading dateheading timehead waxhessian fly damageKleaf rust reaction typeleaf rust reaction type seedling (Field Mix)leaf rust reaction type seedling (Race 1)leaf rust responseleaf rust severityLilodging degreelodging incidencelodging incidence Z50lodging incidence Z55maturity date (canopy)maturity date (physiological)maturity date (spikes)maturity timemeris terrestrial chlorophyll index 2meris terrestrial chlorophyll index 2 MgNinormalized difference pigment indexnormalized difference pigment index Normalized Difference Vegetation IndexNormalized water index 3optimized soil adjusted vegetation indexPpeduncle lengthpigment simple ratio chlorophyll aplant heightplant heightplot shatteringpowdery mildew reaction typePratylenchus neglectus damagePratylenchus thornei damageratio analysis of reflectance spectra for chlorophyll bSSDS sedimentationseeds per headsingle kernel weightspike colorspike lengthspikelets per headspike shatteringspike weightstem diameterstem rust coefficient of infectionstem rust incidencestem rust infection responsestem rust infection response T1stem rust infection type seedling BCCBCstem rust infection type seedling TRTTFstem rust infection type seedling TTKSKstem rust infection type seedling TTTTFstem rust severitystem solidnessstripe rust reaction typestripe rust reaction type seedlingstripe rust reaction type T1stripe rust reaction type T2stripe rust reaction type T3stripe rust reaction type T4stripe rust severitystripe rust severity T1stripe rust severity T2stripe rust severity T3test weightthousand kernel weightthousand kernel weightthousand kernel weight (main tillers)waxinesswaxiness (spikes)whole grain proteinWSBMV reaction typeyellow rustZn

Analysis Method:

trial breeding program