Meeting Notes for:
Fourth meeting for Defra project WU0128 - Crop Improvement for Resource-Use
Efficiency
Date: 24/06/2010
Attendees: Andrew Thompson, John Hammond, Miriam Gifford, James Lynn, Helen
Bowen, Martin Sergeant (Carol Ryder absent)
Notes (Actions in bold)
Action points from last time (reviewed by Miriam):
-
ANDREW to sort out contract for isotope analysis
ANDREW – discussing GWAM methods with Robin, coordinate
-
MIRIAM – N-ecotypes Arabidopsis analysis
-
HELEN – continue with 134 crosses/genotyping, strategy for cross with
Andrew/John
-
CAROL – repeating phenotyping of 5 homozygous SL118 lines?
CAROL - more sequence data to better understand the genotype of the
various lines used for phenotyping (using more snps as they can be found)
-
MARTIN/MIRIAM/JOHN - JH and MG to decide on the Arabidopsis work, MS
to set this work up
- MARTIN – complete ecotype bulking, confirm genotypes of ecotypes (?)
- JAMES – complete choice of ecotypes (MILESTONE JAN)
JAMES – complete GWAM method comparison
-
ALL: on the 1st of April move all plants and work into E2 (?)
- we’re also in E8 and D12
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Updates:
Miriam (project leader role work):
- Use of glass is fine, may just shift plants around.
- Need to check the spend so far.
- Plan on moving into CE (book this) - - - need to know which ecotypes to test
(almost there) and the bulked seed (got).
Miriam (science work):
- EMMA, phenotyping tDNA homozygous lines.
- Miriam’s student Jo Hulsmans is testing Root Trace at Nottingham in Malcolm
Bennet’s lab
Helen:
- Put out Bx1 F2 10 seeds of each for crosses to A12. But only one had an
introgression so went back to Bx1 F1 and put 10 more seeds out. For these three
were A12 at LG1 and het at LG3 (good); two resulting from male parent and one
from a female parent. Next they will be crossed to A12.
- 118 has already been through one backcross, took F1, backcrossed it to A12 and
then selfed.
- Should have (Bx2 F1 and Bx1 F2) the seed ready by the end of September. Then
the plan is to grow them all out, genotype then and identify homozygotes and then
phenotype them.
- want a line that is homozygous for the chr 1 introgression, het for the chr7
introgression and wild-type for the chr 6 introgression
Andrew describing Carol’s work:
- BX1 F3, started with 3 introgressions. Expected the introgression to be on chr 7,
but also chose a range of lines, some with introgression on chr1 in case that had a
contributory effect. Phenotypics results were that you needed the two
introgressions.
John:
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- Tried Robin’s association mapping method. Had some overlaps with James’
method; but Robin’s methods doesn’t have a FDR. Also you need to have prior
knowledge of which direction the trait selection is moving in (difficult to know,
often going in both directions). We will keep talking to Robin as he develops this
method; there is a student that is currently doing this as far as we understand.
Martin:
ARABIDOPSIS ROOT SCREEN - Completed the N/P phenotype screen with Col0 and
Kas (data on the shared area). May need to use a ‘0’ for P level.
- Martin is measuring root parameters for the experiment so far; rep 1 done and
reps 2 & 3 to measure. Have fresh weight for each seedling in all replicate already.
- Next step is to use 96 ecotypes for phenotyping for all the root traits (dependent
on
ECOTYPE BULKING - Grew up the Borevitz 365. Have 260 lines, about 750ul of
seed for each. Just need to clean the seed (it is currently in bags).
SL118 - Need more snps for genotyping.
Using next-gen sequencing results. SMPs and paralogs can be distinguished by using
the ESTs. SMPs were scored and then the top five SMPs were chosen for sequencing.
Now just waiting for the results next week.
Andrew:
- Isotope work agreed (no formal contract).
- Andrew gave an update on the status of the Brassica snps project (from Graham
Teakle and Guy Barker).
James:
- Need a biological perspective for selection of the set of lines to analyse. Want to
end up with 96 lines.
- Want pairs of sets of traits & possibly snps of interest. e.g. primary and lateral root
length that we expect to be correlated.
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- Identify lists of ecotypes that differ for these values for a range of different
ecotypes. Choose ecotypes that have diversity across a range of ecotypes; select the
ones that are in the 260 ecotypes.
- A minimum of 10 common lines.
- John, Andrew and Miriam to meet to finalise lists of traits (decide a time in the next
few weeks). James then will have a week to analyse and come up with a list of 96
ecotypes. Then compare this to see which of them have already been bulked (out of
260). Miriam/Andrew/John to decide if we want to wait for the absent lines to be
bulked. Should then be in a position to decide which ecotypes to analyse.
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