Meeting Notes for:
Fifth meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Date: 05/08/2010
Attendees: Andrew Thompson, John Hammond, Miriam Gifford, James Lynn (part),
Martin Sergeant (part), Carol Ryder (part)
Updates:
Carol’s work:
Also been finishing off the Arabidopsis work.
Have several bags of seed of lines (BX1 F3) that are segregating for the introgression
on chromosome 7. But we don’t know which line to choose since we don’t know
how the region is behaving. So we need more markers to identify this.
-
identifying new markers: there are about 8 markers already and then need
up to about 20 additional markers
Martin has a list of possible markers and will compare these to Brassica
sequence information from line 102 and other sequence information that
becomes or is available
now need to decide which lines to take forward
How are we going to measure the snps with enough throughput. Mass spec? Wave
machine? Sequencing.?
Work out a plan for what will be carried out with SL118 here when John leaves.
Plan is to sow them out and continue all of the work in the grant: genotyping and
phenotyping work here.
Martin:
Designing a program to identify SMPs.
Database from A12 EST library - should get no SMPs if you map this data against the
Illumina data.
For most, SL1218 and A12 were the same and then GD33 was different.
Get about 70 SMPs between A12 and SL118; so far tried 5 of these in the lab and
they are different between the A12 and SL118 samples – so successful method.
1
James:
Determining the new set of ecotypes:
- a snp divides the accessions into two groups - - then compare the average values in
the two accessions
- list of accessions had 26 snps broken up down well
- the problem is that then similar genotypes (e.g. from the same region)
- we also only have 11 of the new 89 lines bulked up
- ACTION send James the IDs of the lines we have and get a new list of ecotypes
2