Transcript Slide 1

Collinearity defined: - mosaic of segmental blocks
Arabidopsis
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Brassica A + C genomes: B. napus
Parkin et al. 2005 (Genetics)
Database developments
• adopt GERMINATE as public-domain
repository
• curate data locally in CropStore
• use agreed nomenclature
• input template spreadsheets
• parse into GERMINATE
• Perl-cgi Web interface
Fady Mohareb: MSc project at RRES with Cranfield
OREGIN data presented from GERMINATE interface
Populations (TN, DY, et al)
BnDFS, BnDFFS
Maps (TN, DY, Parkin et al.)
Marker loci and sequence-tags
Links to A and C genome maps
Brassica linkage maps,
in GERMINATE with CMAP (GMOD) viewer
Loci will link to genomic resources
Rosetta Stone for Brassica linkage group/chromosome assignments
CKDH sensu
Parkin et al.,
Sharpe et al.
NIAB LGs
R1 - R10 = N1
- N10
Kim et al.
Lim et al.
R1
LG10
Chr8
6
LG9
R2
LG3
Chr6
8
LG6
R3
LG1
Chr2
1
LG7
R4
LG4
Chr3
10
LG2
R5
LG7
Chr5
3
LG8
R6
LG5
Chr4
2
LG1
R7
LG6
Chr7
4
?KooR2
LG5
R8
LG9
Chr9
7
?KooR9
LG10
R9
LG2
Chr1
5
KooR1
LG4
R10
LG8
Chr10
9
NIAB
chromosomes
NVITS, Japan
(Suwabe) LGs
Parkin et al., (2005) map based on 1000 RFLP markers
Kim et al., (2005) map based on >500 RFLP markers
CK reference B. rapa map paper almost ready for submission
Chiifu (CNU)
chromosomes
sensu Koo et al
CNU CK LGs
Choi et al.
LG3
Selection of markers for diversity screening
N01
N02
Ol12F11
0.0
1.1
18.0
33.6
BRMS-056
50.0
RA2E04
BRMS-024
73.8
N03
N04
N05
N06
BRMS-215
Na10B10
56.1
BRMS-026
80.0
90.6
Ol10F04
Ol10A05
15.8
BRMS-043
31.9
BRMS-106
69.4
BRMS-042
90.6
Na12A01
BRMS-001
13.3
26.7
BRMS-054
41.5
BRMS-195
Na12A01
90.6
BRMS-034
BRMS-061
13.0
20.8
52.4
BRMS-242
80.2
BRMS-007
93.0
Ra3H01
0.0
Na12B08
1.0
22.0
Na12H07
22.0
48.2
55.0
Ra1F06
BRMS-027
RA2G08
BRMS-018
58.5
Ra2A01
69.9
BRMS-036
92.6
Ra2A05
N09
N10
BRMS-094
0.0
20.5
Ra2E12
31.8
BRMS-088
42.6
BRMS-246
BRMS-006
83.4
0.0
29.5
Ni4D09
54.9
64.4
BRMS-029
Ra2A11
80.2
BRMS-247
96.3
BRMS-060
Na14D07
121.1
Na12D04
134.8
Ol10B01
232.0
N11
N12
N13
0.0
20.5
33.0
REM1b-SSR
48.8
Nga248
108.0
N08
BRMS-008
108.0
66.0
72.9
N07
Ol10F11
Na12C08
Ni4B10
36.0
42.6
N14
Na10G10
Ra2E12
Ol12B03
Ni2C12
54.4
N15
Na14E02
5.0
26.1
Ol10F12
49.3
Ni4F08
38.1
43.9
66.6
75.0
Ol13G05
89.3
Na12C03
105.0
Ol11H09
94.0
98.0
115.2
CALSSR(LSI07)
BN12A
76.1
Na14E08
92.0
102.1
Ol12D02
Na12E05
95.0
N16
N17
Ol10A10
6.1
16.9
Ol10F09
29.7
NGA111
Ni4C11
Na12D10
sORA21
Na12G12
40.5
64.4
93.0
101.0
Ca72
N18
Na12F03
7.8
N19
BN35D
BN35D
80.8
BN72A
Ol11B03
Ni2B01
28.9
Ol12A04
47.6
Ol12G04
45.0
51.9
Na10D07
Ol13C03
62.1
69.1
Ol12D05
MT1-SSR
63.8
BN83B1
89.9
Ol11H06
CHIA-SSR
63.5
0.0
10.1
BRMS-015
Na12A05
Na12F12
232.0
Ol10B01
Reactions performed on subset 1 with 12 markers highlighted in pink
Analysis will be performed using BioGene GeneMarker software to replace ABI
GeneMapper
45.0
46.6
56.9
58.9
Ol11B03
Na10D07
Ra2E07
BRMS-019
Ni4A03
Testing fidelity of GenomiPhiTM amplification
• We are planning to perform our diversity screening on, and to distrtibute genomic DNA
amplified with GenomiPhi.
• Concerns regarding the fidelity of GenomiPhi were raised at the last OREGIN
Stekeholder meeting
• So we need to estimate the likely mutation rate resulting from the GenomiPhi reactions
Two lines showing high allelic diversity with two SSR markers have been identified
No. of alleles detected in a sample of 8 plants per line:
Line name
Source
Na12A07
Na10A08
Marinka
NGB
5
3
Niklas
BAZ
4
3
Experimental design:
• Genomic preps performed from 8 plants each of Marinka and Niklas
• 4 GenomiPhi amplifications performed for each genomic DNA prep
• These will each be assayed with the above two SSRs and compared with duplicate SSR
reactions performed on the original genomic DNA
The control will be 3 genomic preps from Tapidor (DH) each amplified 4 times with GenomiPhi
Acquisition of Tapidor x Victor substitution lines
Graham King has requested permission to adopt this population within
OREGIN:
Peter Werner, CPB Twyfords – yes
Steve Barns, Advanta, subsequently sold to Limagrain – yes
Mike Kearsey, Birmingham – yes
Jo Bowman, Nickersons – yes
Monsanto – awaiting reply
TN Population
2005 field bulking at WHRI of core set of 50 lines
Remainder of TN population is being
regenerated in the GH
Harvesting in progress
For QTL analysis really want 100 lines bulked - RRES may sow additional
75 lines
BnaDFFS Microspore culture
Microspore culture progress
Line Name
No. of plants
produced
4n
DH
1n
Fido
41
2
26
3
8
Duplo
60
22
19
23
15
11
Couve nabica
41
18
11
8
3
5
3
Emerald
9
2
3
3
4
Cubs Root
6
2
4
Global
11
2
Matador
1
1
0
Apex
1
1
0
Judzae
8
1
Jet Neuf
2
1
Abukuma Natane
8
1
Hanna
3
2
1
Guelzower
5
1
4
Brutor
3
1
2
Bronowski
4
1
2
Ceska
1
Canard
7
1
Colchicine
doubling
1
1
No. awaiting
ploidy analysis
8
5
6
Plants still
in plates
2
2
7
2
3
1
3
2
1
2
Plants still
in jars
4
6
3
3
3
1
3
4
4
1
4
4
1
4
16
Sarapta
128
Moana Moana Rape
182
Dippes
130
Brauner Schnitkohl
21
Effects of colchicine treatment in the initial medium
Line
Colchicine - yes
1n
Apex
Colchicine - no
2n
4n
1n
1
1
1
Bronowski
Brutor
1
Couve nabica
10
Cubs Root
2
Duplo
5
18
18
Emerald
8
1
14
1
2
Fido
22
Global
2
2
2
3
1
Hanna
2
Jet Neuf
Matador
3
1
Guelzower
Judzae
2n
1
1
1
4
1
4n
Bulking of the founder lines
Founder lines being regenerated with a target of >10g seed per line at WHRI
In addition:
29 founder lines sent to Mark Nightingale, Elsoms for bulking this 2005/06
•
Will bag 2 plants/line – 25-100g seed for their seed
•
Collect unbagged seed from middle of 1.2 x 3 m plot – upto 1 kg
•
Seed yields expected to be lower for DFS lines
36 fixed lines sent to Neal Evans, RRES, to include in their 2005/06 field bulking
Possibility of distributing of seed through NASC - need to discuss further
with Sean May
MTA?
What next for OREGIN?
Some thoughts from WHRI
Plant resources
Want to maximise ability to utilise the BnaDFFS and mapping populations
• Complete fixation of the BnaDFFS
• Bulk up BnaDFFS, TN, DY mapping pops and TV substitution lines - breeders?
• Possibly extend BnaDFFS in association with Chinese
Marker analysis
• Complete genotyping of DFFS with 100 SSRs
• AFLP fingerprint DFFS – provides alternative diversity assessment and quick QC check –
fairly breeder friendly
• Generate sufficient marker density to enable association analysis (>1000) - other funding
sources for this
• EcoTILLING genes of interest
Pathogens
• UK core collection from existing collection
Trait analysis
• Oil analysis
• Screen pathogen core collection against BnaDFFS
• Others, e.g flowering time, water use efficiency, mineral use efficiency, virus resistance,
vernalisaiton requirement, other seed traits
Data management
• To include collation of published QTLs