Meeting Notes for:
Sixth meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Date: 22/11/2010
Attendees: Andrew Thompson, Miriam Gifford, Carol Ryder, Martin Sergeant
Updates:
Carol: QTL for WUE: SL118
Working on getting new markers in gap region on C7:
(1) Working with new VeGIN sequence data (10 new markers in the gap region on
C7, most are SNPs and one is a SCAR marker)
Golden gate assay – 50-60bp region with a SNP in the middle
- series of adapters, central region of homology; get a series of primers and then
extends into polymorphism on the chip. Have to do the analysis on an
Illumina chip.
Instead since we are going for a small number of assays so Carol is working on a way
to SSCP (like a small scale polyacrylamide gel) to sequence - or pyrosequencing?
What about the mass-spec? Amplify a fragment then extend from there with a given
mass (Nottingham/Newcastle).
- could try the traditional method to use the assay
(2) Testing markers that Martin has defined from the next-gen sequencing
- one confirmed and three more still to test – choosing markers but not sure
where they are (need scaffold data, Isobel Park and Andy Sharp – Brassica oleracea
data in Canada – Andrew to push on this)
- need to confirm the location of the markers – Martin will try to use his
alignment tool on the 10 sequences to try and confirm these as well as the new
markers.
Purpose of these new markers:
Want to identify the polymorphisms in the 1+7 line and then introgress back to the
chromosome 1 line. Have 150 individuals – should be enough to map the whole
population, get down to about a cM of map distance.
Growing plants for next generation:
Fixed for 1 and heterozygous for parts of 7. Sown 5 different lines to screen, 3 are as
described, others should be hets for all of 7. - - - need to screen these with the new
markers and test the original line with the effect.
Want to take this one more generation along to fix them.
Now screening these plants with the new markers. Adding markers but there is still
some uncertainly.
Could exclude some markers by comparing 101 to 118.
Carol: Saxcil experiment
Cleaning and preparing seed for the P/N cabinet experiment; just need 1 ½ days
more for seed cleaning.
Almost ready to start the cabinet experiment. Ecotypes bulked. Cabinets booked.
Soil type is being organised, adjusting the density etc.
Field trial: Might have to reduce the number of lines due to seed volume OR reduce
the number of individuals per line.
Martin: Investigating root traits for resource use efficiency
The full scale experiment involves growing all 96 ‘Nordborg’
Data analysis by end of week, choose the conditions required for the N and P levels.
Decide on ‘Nordborg 96’ vs. new selection of Arabidopsis ecotypes
Then move on to the full experiment: grow ecotypes on 3 combinations of N (KNO3)
and P (H2KO4P) with 30mM sucrose for 12 days. At day 12 measure plant fresh mass
and measure root size/architecture.