Wheat

Contact Us

  T3/Wheat

Genomic Association and Prediction

Genome Wide Association (consensus genotype)
1. Select a set of lines, trait, and trials (one trait).
2. Select the genetic map which has the best coverage for this set.
3. Return to this page and select model options then GWAS Analysis
Genome Wide Association (single genotype experiment)
1. Select a set of lines by genotype experiment.
2. Select a trait and phenotype trial.
3. Select the genetic map which has the best coverage for this set.
4. Return to this page and select model options then GWAS Analysis
Genomic Prediction
1. Select a set of lines, trait, and trials (one trait).
2. Return to this page and select G-BLUP Analysis for cross-validation of the training set. Then save Training Set.
3. To select a validation set, select a new set of lines using a different trial, then return to this page for analysis.
4. To select a prediction set, select a new set of lines without phenotype measurements, then return to this page for analysis.

Additional notes on GWAS and G-BLUP methods

Select a set of traits and phenotype trials

This table lists the total markers in each map. If a marker is not in the the selected map set then it will be assigned to chromosome 0.

selectmarkers
(total)
map namecomment (mouse over item for complete text)
877Aegilops tauschii, 2009
From Luo et al, (2009) PNAS 106(37):15780-15785
19720SynOp GBS BinMap, 2012
Bin map of Synthetic W9784 x Opata M85 constructed using 19,720 GBS SNP markers. Common markers bet
1485SynOp GBS AntMap, 2012
Genetic linkage map of Synthetic W9784 x Opata M85 constructed de novo using the Antmap algorithm ma
1625KleinProteo x KleinChaja, 2012
Contacts: Jorge Dubcovsky, Luxmi Tomar.Contributors: Luxmi Tomar, Laura Pfluger, Shiaoman Chao, Deve
3503wsnp 2013 Consensus
Consensus wsnp map from C.R. Cavanaugh et. al. (2013) PNAS 110:8057-8062
3883290K Array Consensus
From: Wang et. al. (2014) Characterization of polyploid wheat genomic diversity using a high-density
145004Chromosome Survey Sequence, 2014
A physical map from the Chromosome Survey Sequence (CSS) assembled by the International Wheat Genome
125340CSS POPSEQ 2014
A genetic map created by locating the markers on the 1,397,432 contigs of the IWGSC2, Nov 2014. Cont
3393777CSS GBS 2014
A physical map of GBS markers starting with the prefix WCSS1. The Chromosome Survey Sequence (CSS) a
140682TGACv1
A physical map from from the Chromosome Survey Sequence (CSS) and CS42 libraries assembled by the Ea

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.