Meeting Notes for:
Meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Discussing progress with reference to the annual report.
Date: 16/09/2011
Attendees: Andrew Thompson, Miriam Gifford, James Lynn (Applied Statistical
Solutions), Sajjad Awan
Updates & action points (**)
Fine mapping of SL118 (Objective 1)
Sajjad repeated some of Carol’s marker work, all fine. Conclusion so far is that
Introgression 7 or 1 or both is/are responsible for the modified WUE. There are
now some new markers that can be used to refine the mapping on chr 7.
Current gravimetric water use experiment: used A12, SL118 lines. Designed to
tell if chr 7 or 1 or both is/are required for water use efficiency; effect is higher
conductance but lower water use.
Very preliminary porometer results suggest that SL118 (1+6+7) gave higher
conductance than lines with just 1+7, suggesting that 6 may have a role. **
SAJJAD: continue porometer readings and complete gravimetric
experiment to determine the relative contributions of the three
introgressions.
Crossing being used to fix introgression on 1 and then map the introgression on
7. We have a number of lines with 1 fixed and with different bits of 7. These
were selfed and they are now segregating lines.
**SAJJAD: Need WUE data for these lines. To get the data within the next few
months (rather than having to spend another generation of time), straight after
getting the WUE results from the lines we need to set out the seed from these
lines – then genotype them and identify the homozygotes; keep enough material
to test them directly for WUE (rather than having to bulk them up first). Sow out
about 70 of these seeds. Alternatively, check Carol’s data since some lines might
already have been genotyped in the F3.
**SAJJAD: remember to archive dry material for future mineral analysis.
Fine mapping of SL134 (Objective 1)
** JOHN – progress?
Brassica field trial (Objective 3)
1
Sajjad completed two field trials. May-July (trial 1), 780 plots, 150 plots no good.
All data, specific leaf area SLA, dry leaf weight, fresh plant weight, fresh leaf
weight, whole plant dry weight, chlorophyll content, for all lines (but needs
QCing). Dry material ground up (for mineral analysis at Wellesbourne and
stable isotope at ANU).
- once quality checked the data will be sent to James
Trial 2: differences to the first field trial: same plots but there was putative club
root (check with John Clarkson to get confirmation). No P treatment (high P area
in the soil but there was no difference when it was tested between the trials) and
only 6 replicates rather than 8 (due to seed germination, ran out of decent seed).
Question: did the first P treatment really work: to answer can compare plant size
between P+ and P- plots: should be a difference. Can also look at treatment
effects on leaf P.
Both trials were irrigated, so no irrigation response data. However there were
weather differences across the two trials (check with the weather station (50 yds
away) and plot the temperature and rainfall next to information about
irrigation).
**SAJJAD: discuss these experimental issues in the 2nd year annual report.
GWAM on Brassica diversity lines:
1000s of KASPar markers are being run right now (Guy Barker+Graham Teakle)
on diversity set and mapping populations. These should allow some GWAM in
our diversity set/trait data set (although our diversity set is slightly different to
the diversity set that is being genotypes with KASPar markers….)
**Miriam/Andrew to attend VeGIN meetings to keep updated.
It is urgent to identify Arabidopsis candidates and develop Brassica markers
from them for targeted AM in Brassica.
Arabidopsis experiment (Objective 2)
Data from PUE, WUE, and roots, 2 experiments each. The GWAM used data from
the 1st exp, the 2nd exp, and the combined exp (3 GWAM)
In theory the combined exp hits should have more support (e.g. if the individual
experiments are both almost but not quite significant) but the combined might
give you false support if the two experiments are very different.
Methodology: James has used his method so far, will try EMMA too. Volkan is
using this so might want some support. Either way we end up with 20Kb
windows of genes (not just a single gene position) to deal with linkage
disequilibrium
**JAMES: try EMMA, compare to existing method
**JAMES: write up the methods.
2
**JAMES: use random data to generate a confidence pvalue cutoff.
**JAMES: repeat GWAM once we have the 13C and 16O data.
We plan to select 2 genes for each (include in the annual report but say they are
provisional choices).
**JOHN/ANDREW/MIRIAM/SAJJAD: look at relevant lists of candidates, perhaps
comparing to ‘known’ genes or QTL data in order to identify promising loci.
**JOHN/ANDREW/MIRIAM/SAJJAD: define what the selection process should be
**SAJJAD: take candidate Arabidopsis genes, identify the (multiple) hit Brassica
genes, then design markers.
Arabidopsis marker genes; order T-DNA knockouts for all.
General: need to contribute to Vegin meetings (dissemination etc)
3