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Progress on sequencing tomato chromosome 12

Progress on sequencing tomato chromosome 12. Mara Ercolano. Summary BACs in sequencing pipeline. Chromosome 12 short arm sequencing status. Chromosome 12 pericentrometric area sequencing status. Chromosome 12 long arm sequencing status. POTENTIAL EXTENDING BACs. P2. P1. IL Mapping.

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Progress on sequencing tomato chromosome 12

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  1. Progress on sequencing tomato chromosome 12 Mara Ercolano

  2. Summary BACs in sequencing pipeline

  3. Chromosome 12 short arm sequencing status

  4. Chromosome 12 pericentrometric areasequencing status

  5. Chromosome 12 long arm sequencing status

  6. POTENTIAL EXTENDING BACs P2 P1 IL Mapping “BRIDGE” SEED BAC Extending BAC validation protocol 5’ SEQUENCED SEED BAC 3’ ANCHOR MARKER Sequencing comparison

  7. 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 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

  8. “De novo” BAC mapping Choice of BACs with good end sequences on SGN PCR primer design on BAC ends Amplification of S. lycopersicum and S. pennellii DNA Amplification and sequencing of 72 ILs (single pass, SP6 end) Polymorphism detection and mapping of SP6 end Confirmation of T7 end on selected ILs

  9. Results * Mapped on one end

  10. Summary validation

  11. Genes Strategy used to identify genomic differences between two tomato genotypes Driver Tester c b a • Chromosome of S. lycopersicon • Chromosome of S. pennelii IL line • Fragment present only in the driver genotypes

  12. SRG Database

  13. Telomero 5 esoni 11 esoni Risultati coincidenti Fgenesh Arabidospis Fgenesh tabacco Database EST Annotation results Centromero Marker Le_HBa BAC estension SP6 BAC estension T7 (SEED-BAC) 0 100000 45000 95000 112743 30000 20000 35000 40000 70000 75000 5000 85000 15000 50000 90000 55000 80000 25000 10000 65000 60000 3 esoni 5 esoni 2 esoni 4 esoni 10 esoni 2 esoni 3 esoni 5 esoni 8 esoni 3 esoni 14 esoni 9 esoni 7 esoni 3 esoni 8 esoni 7 esoni 3 + 2 esoni 6 esoni 2 esoni 11 esoni 1 esoni 2 esoni 2 esoni 4 esoni 2 esoni 5 esoni 15 esoni 4 esoni SRG

  14. Summary A total of 68 BACs are currently at different phases of the sequencing pipeline. Nine seed BACs and 1 extending BAC have been submitted to NCBI database and SGN repository. A strategy that combine bionformatic analysis and molecular validation to identify extending BACs, has been set up. In order to select new starting points for sequencing a IL mapping effort has been being. A bioinformatic platform to provide an Italian resource for supporting the annotation of the tomato genome has been built up. Resources useful to analize data provided from sequencing project have been developed.

  15. Participating Institutions ENEA, Rome Giovanni Giuliano Marco Pietrella Giulia Falcone Univof Naples ‘Federico II’ Luigi Frusciante Mara Ercolano Amalia Barone Maria Luisa Chiusano 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)

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