Meeting Notes for:
Meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Date: 24/11/2011
Objective: Discuss plans for dealing with the GWAS hits
Attendees: Andrew Thompson, Miriam Gifford, James Lynn (Applied Statistical
Solutions), Sajjad Awan, John Hammond (Nottingham)
Updates & action points (**)
New data: James’ files
Joint: 176 genotypes
Nordborg: 96
Current: other 96 (more balanced selection)
James: found some but very low correlation between EMMA and WIGWAM
method.
Combine methods: very good on both?
EMMA pvalues: not comparable to James’ method.
Plan:
Take 10kb either side
*** Cluster of snps are good = but this equals one hit each
Take the top 5 (?) hits for each trait (or combinations of traits)
James’ snps – how high you have to be before it isn’t linked to anything else; in
the output spreadsheets (dif)?
Get the genes; use VirtualPlant to get gene description
MG – upload the R script, TAIR version (? TAIR), all of the files
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