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Parkin et al. 2005 (Genetics) 1 Collinearity defined: - mosaic of segmental blocks Brassica A + C genomes: B. napus 234 5 A B C D E A B B C Arabidopsis.

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Presentation on theme: "Parkin et al. 2005 (Genetics) 1 Collinearity defined: - mosaic of segmental blocks Brassica A + C genomes: B. napus 234 5 A B C D E A B B C Arabidopsis."— Presentation transcript:

1 Parkin et al. 2005 (Genetics) 1 Collinearity defined: - mosaic of segmental blocks Brassica A + C genomes: B. napus 234 5 A B C D E A B B C Arabidopsis A B C D E A B C E

2 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

3 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

4 Brassica linkage maps, in GERMINATE with CMAP (GMOD) viewer Loci will link to genomic resources

5 CKDH sensu Parkin et al., Sharpe et al. NIAB LGs NIAB chromosomes NVITS, Japan (Suwabe) LGs Chiifu (CNU) chromosomes sensu Koo et al CNU CK LGs R1 - R10 = N1 - N10 Kim et al.Lim et al.Choi et al. R1LG10Chr86 LG9 R2LG3Chr68 LG6 R3LG1Chr21 LG7 R4LG4Chr310 LG2 R5LG7Chr53 LG8 R6LG5Chr42 LG1 R7LG6Chr74?KooR2LG5 R8LG9Chr97?KooR9LG10 R9LG2Chr15KooR1LG4 R10LG8Chr109 LG3 Rosetta Stone for Brassica linkage group/chromosome assignments 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

6 Selection of markers for diversity screening Reactions performed on subset 1 with 12 markers highlighted in pink Analysis will be performed using BioGene GeneMarker software to replace ABI GeneMapper

7 Testing fidelity of GenomiPhi TM amplification Line nameSourceNa12A07Na10A08 MarinkaNGB53 NiklasBAZ43 Two lines showing high allelic diversity with two SSR markers have been identified 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 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 No. of alleles detected in a sample of 8 plants per line:

8 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

9 TN Population 2005 field bulking at WHRI of core set of 50 lines For QTL analysis really want 100 lines bulked - RRES may sow additional 75 lines Remainder of TN population is being regenerated in the GH Harvesting in progress

10 BnaDFFS Microspore culture

11 Microspore culture progress Line NameNo. of plants produced 4nDH1nColchicine doubling No. awaiting ploidy analysis Plants still in jars Plants still in plates Fido412263 8 2 Duplo60 2219 231511 Couve nabica41181181353 Emerald923 34 Cubs Root6 2 4 Global11 21 827 Matador1 1 0 Apex1 1 023 Judzae8 15 2 Jet Neuf2 1 113 Abukuma Natane8 1243 3 Hanna3 2 131 Guelzower5 1 4 3 Brutor3 1 244 Bronowski41 1 2 Ceska1 144 Canard7 661416 Sarapta 128 Moana Moana Rape 182 Dippes 130 Brauner Schnitkohl 21

12 LineColchicine - yes Colchicine - no 1n2n4n1n2n4n Apex 1 Bronowski 11 Brutor 1 Couve nabica 101881 Cubs Root 2 Duplo518 141 Emerald 2 2 Fido 22233 Global 2 1 Guelzower 1 Hanna 2 Jet Neuf 1 Judzae11 4 Matador 1 Effects of colchicine treatment in the initial medium

13 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?

14 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

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