Meeting Notes for:
Third meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Date: 28/01/2010
Attendees (everyone): Andrew Thompson, John Hammond, Miriam Gifford, James
Lynn, Carol Ryder, Helen Bowen, Martin Sergeant
Notes (Actions in bold)
Action points from last time (reviewed by Miriam):
-
COMPLETE - MG to chase Finance team for a ledger code and request new
shared area from IT once the code is released
-
IN PROGRESS - AT to sort out contract for isotope analysis.
-
COMPLETE (continuing) - HH, CR and HB to continue with the 118 work as
planned.
-
COMPLETE (but no data found) - MS/HB to check which ecotypes require
vernalisation so to allow proper preparation time/resources.
-
COMPLETE (see notes below) JL to compare association mapping approaches
when data becomes available. It was suggested that no AM be done until the
new methods are available (to save from carrying out the analysis twice).
-
COMPLETE - MG to schedule the next meeting for after HH’s work is
complete (mid-Dec).
Miriam (project leader role work):
MG updated everyone on project management (getting a project/cost code and a
shared area). We now have a code (MG0505), a shared area and an archive area.
Also set up are two webpages for the project, one with a project summary and one
as a web-whiteboard for project members only.
Shared area:
afp://Panthro/Shared Area/Projects/MG/MG0505
External project site:
http://www2.warwick.ac.uk/fac/sci/whri/research/resource_efficiency/
1
Internal members site:
http://www2.warwick.ac.uk/fac/sci/whri/research/resource_efficiency/internal
Action points for the shared area:
-
Also MG to set up an archive area to go with the shared area
Then……..
- MG to move application files to the new shared area, also to separate these
out into old and most recent versions so it’s easy to find the final copies
- CR to check and move relevant files from the AT directory to the new area
- AT to move over relevant Bridging Project documents to this area
Action points for the project folder:
-
MG to update project folder with locations of data:
o Helen: lab book W0251
o Carol: lab book W0094
o Martin: lab book …..
o James: all on his computer/shared area
- MS to send MG the number of his lab book
- HB, CR and MS to take new books for this specific project once their current
books are complete (for QA purposes)
Action points for the webpages:
- MG to put the Gantt chart on the website
Helen:
Backcross 1-F2 seed and backcross 2-F1 seed generation for phosphorus QTL (134).
Helen and Carol checked these using PCR markers. All confirmed. Now collecting
seed and cleaning this seed. John and Andrew discussed the strategy for this cross.
Once this is complete there will be some decisions to be made.
HB to continue as planned.
Carol:
Phenotyping on 118 has been completed (work with Howard). The data was
presented to the group and it was found to not to be fully conclusive at this stage.
There was discussion of sequencing Brassica A12 vs. 118 to look for more marker
snps in regions of marker paucity.
The cost of this sequencing seems reasonable, the difficulty is analysing the
data. MG is working on Illumina data analysis and will keep the group updated as
2
this happens. One plan would be to sequence transcripts from these lines in the
conditions that they are grown in for experiments to allow expression levels to be
examined as well as sequence differences (but then we would need replicates for
this) – wait for the moment.
CR to gain more sequence data to better understand the genotype of the
various lines used for phenotyping (using more snps as they can be found).
John:
(1) Helen covered work on 134.
(2) John to talk with Martin about starting the P x N crosstalk Arabidopsis
experiments. Miriam has relevant N concentrations and John has the relevant P
concentrations.
JH and MS to decide on the Arabidopsis work, MS to set this work up.
Martin:
Busy with collating and obtaining, and sowing out the available Arabidopsis
ecotypes. There are various problems with this, at the forefront being the lack of
confirmation at the stock centre or at HRI about the origin and genotype of these
ecotypes.
MS to continue with this and start work on the N x P work as detailed above
Andrew:
(1) Spoke to Robin Allaby about the method that he uses for association mapping.
Robin has a project student working on this and we will keep in touch so that we can
coordinate and compare our different approaches.
(2) Discussed glasshouse usage and assignment for project codes.
All of group: on the 1st of April move all plants and work into E2.
Miriam (science work):
Working on analysis of her root x nitrogen data from previous work at NYU. This
data consists of root architecture measurements of 96 ecotypes on low N or high N.
James has run association mapping on this data and now Miriam has to look at the
results of this analysis.
MG to continue with this work.
3
James:
(1) Has been comparing old and new methods of association mapping. Problem
with the new method has been the time it has taken to analyse but James has come
up with some solutions to this.
(2) Milestone at end of January: come up with a new list (more balanced) of
Arabidopsis ecotypes. Progress on this is that the list has not been determined but a
method for determining these has almost been worked out.
JL to continue as planned and identify the ecotypes asap.
4