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Parkin et al. 2005 (Genetics)

Arabidopsis. 2. 3. 4. 5. A. A. A. B. A. C. B. C. B. B. B. C. C. D. D. E. E. E. Collinearity defined: - mosaic of segmental blocks. 1. Brassica A + C genomes: B. napus. Parkin et al. 2005 (Genetics). Database developments. adopt GERMINATE as public-domain repository

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Parkin et al. 2005 (Genetics)

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  1. Arabidopsis 2 3 4 5 A A A B A C B C B B B C C D D E E E Collinearity defined: - mosaic of segmental blocks 1 Brassica A + C genomes: B. napus Parkin et al. 2005 (Genetics)

  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. 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 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: • 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

  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 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

  10. BnaDFFS Microspore culture

  11. Microspore culture progress

  12. 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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