1 / 11

Progress on sequencing tomato chromosome 12

Progress on sequencing tomato chromosome 12. Mara Ercolano. Distanza in cM. Selected BAC. Overgo probes. 12. LeHBa140M01. TM14B. At4g03280. 12.5. LeHBa026C13. cLPT6E9. 14.0. TG180. LeHBa206G16. 7.4. T1487. 24.0. LeHBa075C18. T1481. 32.0. LeHBa163O04. 6.4. T0028.

naomi
Télécharger la présentation

Progress on sequencing tomato chromosome 12

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Progress on sequencing tomato chromosome 12 Mara Ercolano

  2. Distanza in cM Selected BAC Overgo probes 12 LeHBa140M01 TM14B At4g03280 12.5 LeHBa026C13 cLPT6E9 14.0 TG180 LeHBa206G16 7.4 T1487 24.0 LeHBa075C18 T1481 32.0 LeHBa163O04 6.4 T0028 33.0 TG68 LeHBa032K07 36.0 T0989 LeHBa0146I19 T1667 39.0 14.4 LeHBa180O10 cLET-8-K4 41.0 LeHBa161H10 T1045 51.0 CT79 LeHBa021L02 T1211 53.0 4.3 CT211A o 5.5 T1185 57.8 SEED BAC CT219 cLET-8-G15 60.0 C 2.2 TG360 0.8 CD6A 1.6 TG394 68.0 TG283 BAC BAC in progress TG367 4.5 68.5 TG394 T1266 71.0 TG468 85.7 13.4 T1676 86.0 Short arm 6 4 T0882 97.0 CT287A T0770 101.0 6.3 TG28A 1.0 CT239B 2.0 Long arm 1 7 T1504 111.0 TG296 2.4 CT156 7.2 CT80B 6.1 CT276 5.8 TG473 1.8 CD2 Seed BACs sequencing status BAC submitted CT19A BAC in progress BAC near centromere LeHBa009J11 LeHBa266F15 LeHBa165B12 LeHBa302G23 LeHBa193C03 LeHBa326K10 LeHBa115G22 LeHBa093P12 LeHBa183M06 LeHBa147G13

  3. 2° cycle extension 1° cycle extension 1° cycle extension 2° cycle extension 3° cycle extension cM Seed BAC Overgo probes 12 LeHBa140M01 TM14B Eco038P06 Mbo103K08 HBa120K04 Eco072J06 HBa211M21 Mbo047B04 HBa010C08 Eco062N07 HBa133N05 HBa061F16 Mbo126D24 HBa071M19 HBa073O10 HBa090D09 HBa040O03 Eco097H19 Eco082A18 HBa189E08 Mbo123M18 HBa149G24 Eco124D18 HBa011D12 HBa224N06 HBa122A15 HBa165F06 Eco004H16 At4g03280 12.5 LeHBa026C13 cLPT6E9 14.0 TG180 LeHBa206G16 7.4 T1487 24.0 CT19A LeHBa075C18 T1481 32.0 LeHBa163O04 6.4 T0028 33.0 Eco032P11 TG68 LeHBa032K07 36.0 T0989 HBa093E12 LeHBa0146I19 T1667 39.0 14.4 LeHBa180O10 cLET-8-K4 41.0 HBa215O16 LeHBa161H10 T1045 51.0 CT79 LeHBa021L02 HBa029N13 T1211 53.0 4.3 CT211A o 5.5 LeHBa009J11 T1185 57.8 CT219 cLET-8-G15 60.0 C LeHBa266F15 2.2 TG360 0.8 CD6A LeHBa165B12 1.6 TG394 68.0 TG283 TG367 LeHBa302G23 4.5 68.5 TG394 T1266 71.0 LeHBa193C03 LeHBa326K10 TG468 85.7 13.4 LeHBa115G22 T1676 86.0 LeHBa093P12 T0882 97.0 CT287A LeHBa183M06 T0770 101.0 6.3 TG28A 1.0 CT239B 2.0 LeHBa147G13 T1504 111.0 TG296 2.4 HBa067C22 CT156 7.2 CT80B 6.1 HBa004A15 CT276 5.8 TG473 1.8 CD2 Extension BACs sequencing status

  4. POTENTIAL EXTENDING BACs P1 P2 IL Mapping P1 P2 “BRIDGE” SEED BAC 1 2 3 4 5 6 7 Extending BAC validation protocol SEQUENCED SEED BAC 5’ 3’ ANCHOR MARKER Sequencing comparison 1p1 2 p2 3p3 4, 5parental genotypes 6,7IL lines

  5. Centromeric region T1211 IL mapping PCR 1BAC SL_MboI0127O07 2SEED BAC Le_HBa0021L02 3,4parental genotypes 5,6IL lines B 1 2 3 4 5 6 Multiple alignment of : S. pennellii, M82, IL 12-2, SEED BAC Le_HBa0021L02 end BAC SL_MboI0127O07. E

  6. New seed BACs through IL mapping PROTOCOL VALIDATION: 12 already sequenced BACs (1/ chromosome) chosen with both end sequences available on SGN and >500 bp. Primers amplifying approx. 400-500 bp product on each end with Tm approx 50°C Amplification from S.lycopersicum and S.pennellii DNA Sequencing and identification of SNPs/indels Sequencing of IL DNA and mapping of BACs Protocol automation GOAL: Mapping of 200 new seed BACS from “euchromatic” (Japan; France) sets.

  7. Mbo123M18 HBa120K04 Eco124D18 HBa149G24 Eco072J06 Eco004H16 HBa010C08 Eco124D1 LeHBa161H10 Mbo123M18 HBa029N13 HBa120K04 53,0 51,0 HBa149G24 LeHBa021L02 Eco004H16 SEED BAC HBa010C08 Seed BAC extension process 1° cycle extension 1° cycle extension 3° cycle extension 2° cycle extension 2° cycle extension Seed BAC LeHBa140M01 LeHBa026C13 LeHBa206G16 LeHBa075C18 LeHBa163O04 LeHBa032K07 LeHBa0146I19 LeHBa180O10 LeHBa161H10 LeHBa021L02 HBa029N13

  8. 52 BAC in sequencing pipeline

  9. Map position of overgo markers used for Chr. 12 Map Position (cM) Marker 12,5 C2_At4g03280 Map Position (cM) Marker 14,0 cLPT-6-E9 19,0 TG263 21,0 TG68 24,0 T1487 51,0 T1045 53,0 T1211 32,0 T1481 53,5 CT99 33,0 T0028 54,0 T1093 Near centromere 36,0 T0989 54,5 C2_At5g42740 39,0 T1667 55,0 T1078 41,0 cLET-8-k4 55,5 TG283 56,0 T1622 57,2 P62 57,5 T1451 65,0 T1947 57,7 cLET-8-E15 66,0 TG111 57,8 T1185 68,0 TG394 58,2 SSR20 68,5 TG367 59,0 CT189 71,0 T1266 60,0 SSR124 60,0 SSR44 60,0 cLET-8-G15 86,0 T1676 96,0 T1784 96,0 TG296 97,0 T0882 101,0 T0770 115,0 T1504 120,0 CD2

  10. Summary To date 20 seed BACs have been selected as starting points for sequencing. 7 seed BAC sequences (Phase 3) have been submitted to SGN repository. A total of 45 BACs are currently at different phases of the sequencing pipeline. In order to identify extending BACs to move out of starting points, a strategy that combine bionformatic analysis and molecular validation has been set up. A bioinformatic platform has been built at the Univ. of Naples to provide an Italian resource for supporting the annotation of the tomato genome. A Solanaceae resistance genes database (SRG) has been developed to perform functional annotation of this gene’class

  11. Participating Institutions Univof Naples ‘Federico II’ Luigi Frusciante Mara Ercolano Amalia Barone Maria Luisa Chiusano ENEA, Rome Giovanni Giuliano CNR-IGV, Portici (Naples) Silvana Grandillo CRIBI and Univ. of Padua Giorgio Valle Alessandro Vezzi Funding Agronanotech (Italian Ministry of Agriculture - started October, 2004) FIRB (Italian Ministry of Research - started October, 2005) EU-SOL (European Commission - started May 2006)

More Related