Meeting for Defra project WU0128 - Crop Improvement for Resource-Use Efficiency

Meeting Notes for:
Meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Date: 12/10/2011
Objective: Discuss plans for the final year
Attendees: Andrew Thompson, Miriam Gifford, James Lynn (Applied Statistical
Solutions), Sajjad Awan, John Hammon (Nottingham)
Updates & action points (**)
2nd year annual report
MG working on putting final draft together, has most contributions needed.
** SA to come up with a gantt chart for the work he has to do and a timeline (we
need to review this to check that everything is finished on the right timescale)
** MG and AT to look over budget to check remaining costs etc
Fine mapping of SL118 (Objective 1)
- Sajjad latest experiment: need introgression 7, and possibly 1: still unclear.
- Send off material from this experiment, find old material – try to analyse this.
- Plans for more experiments to conclude this: gravimetric water use
experiments (C isotope)
- New field trial? April 1st.
*** AT and SA to work to check the information about how the plants were
generated so that SA can select appropriate seed lines: choose which
recombinants to use that are fixed for 7 and that have parts of 1, and choose the
markers that will be important for screening. Try to make use of the new
Brassica sequence data to use this and Arabidopsis data together to try and
predict the introgression of importance
** AT and SA to construct a Pedigree diagram to aid tracking the samples for this
** JL to analyse all data together to test significance
Fine mapping of SL134 (Objective 1)
- John Update: Bx lines F1 ---- selfed over the summer in Nottingham glasshouse;
half flowered in the bags, rest sent out new shoots, rebagged, cut back. In
a heated glasshouse. Likely seed at Christmas.
** SA: SL134 lines will need genotyping (grow on high P) in Spring, 4 or 5 plants;
30-100 seeds. Get leaf data; then select plants for growth on low P and
high P and do mineral analysis (P), shoot dry weight, keep a subsample
for P. Could do dry weight of a leaf and P content.
Arabidopsis experiments (Objective 2)
- James is comparing different algorithms for GWAS. EMMA assumes there is a
single environmental term and a genetic term. Treatments are fixed effects, but
cabinets are random effects (boxes within cabinets etc).
** MG Need to set up a meeting for us to decide upon the selection process and
select which Arabidopsis alleles to map to Brassica with orthology (for Obj 3)
** MG to email James to ask him when the AM is ready; need to prioritise the
traits for analysis.
** JL: try EMMA, compare to existing method
** JL: repeat GWAM once we have the 13-C and 16-O data (Nov/Dec?)
Once we have the list of genes…
** SA: take candidate Arabidopsis genes, identify the (multiple) hit Brassica
genes, then design markers.
** MG: order Arabidopsis T-DNA knockouts for all.
Brassica field trial (Objective 3)
- Complicating factor: our DFSS are not the same, so partially overlapping (can
use some markers from Vegin) and K-biosciences can do this
- Sajjad’s latest data analysis: need to account for plot effects; need some data
** JL and SA: to work together on data analysis
** SA: need to carry out some marker development