Towards an Integrated Physical Map of the Tomato

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Towards an Integrated Physical Map of the Tomato Genome Mingsheng Chen Institute of Genetics

Towards an Integrated Physical Map of the Tomato Genome Mingsheng Chen Institute of Genetics and Developmental Biology Chinese Academy of Sciences January 13, 2008

l Reassemble the fingerprint data of Hind. III and Mbo. I libraries generated by

l Reassemble the fingerprint data of Hind. III and Mbo. I libraries generated by Arizona Genomics Institute and Sanger l Manual editing and contig merging l Marker data generation: 3 D pool l FSD: Fingerprint Simulated Digest l Anchored contig information l Web. FPC

FPC build l Reassemble the fingerprint data of Hind. III and Mbo. I libraries

FPC build l Reassemble the fingerprint data of Hind. III and Mbo. I libraries l Cutoff value of e-12 tolerance 7 l Clone total 132, 541 l Total contigs 4360 (Compare > 7000 of Hind. III FPC build) l Genome coverage 658 Mb (avearge band size 4096 bp)

Manual Editing l Contig merging by BAC end searching combined with marker information l

Manual Editing l Contig merging by BAC end searching combined with marker information l 4156 contigs (we only merged the contigs with anchoring information) l 837 markers (781 framework)

Marker l Overgo marker (provided by Ying Eileen Wang) l PCR-based approach: 3 -D

Marker l Overgo marker (provided by Ying Eileen Wang) l PCR-based approach: 3 -D pool

The pooling strategy for the tomato Hind. III BAC library

The pooling strategy for the tomato Hind. III BAC library

l 985 markers l 245 markers of chr 1/5/12 (Chen) l 249 markers of

l 985 markers l 245 markers of chr 1/5/12 (Chen) l 249 markers of chr 3/7/9 (Li) l 247 markers of chr 4/6/10 (Ling) l 244 markers of chr 2/8/11 (Wang)

Example Marker Chr Plate Position C 2_At 1 g 09760 3. 1335 1 B

Example Marker Chr Plate Position C 2_At 1 g 09760 3. 1335 1 B 6 C 2_At 1 g 09760 3. 1335 1 E 6 C 2_At 1 g 09760 3. 1335 1 F 5 C 2_At 1 g 09760 3. 1335 1 G 12 C 2_At 1 g 09760 3. 1335 5 B 1 C 2_At 1 g 09760 3. 1335 5 E 6 C 2_At 1 g 09760 3. 1335 5 G 2 Computational BACs a 0035 B 06 a 0035 B 17 Positive BAC a 0035 B 17 a 0292 M 06

C 2_At 1 g 09760 -group 1 C 2_At 1 g 09760 -group 2

C 2_At 1 g 09760 -group 1 C 2_At 1 g 09760 -group 2 C 2_At 1 g 09760 -group 3 C 2_At 1 g 09760 -group 4 1 -B 6; 1 -E 6; 1 -F 5; 1 -G 12 C 2_At 1 g 09760 -group 5 Control 5 -B 1; 5 -E 6; 5 -G 2

Fingerprint Simulated Digest (FSD) l Compare the position of the original BAC clone with

Fingerprint Simulated Digest (FSD) l Compare the position of the original BAC clone with sd clone; check the integrity of the physical map l Identify additional clones for sequencing l 531 sd clones

26 kb 80% 107 kb 145 kb

26 kb 80% 107 kb 145 kb

Anchored Contigs l Chr 01 36 ctgs 10 Mb l Chr 02 29 ctgs

Anchored Contigs l Chr 01 36 ctgs 10 Mb l Chr 02 29 ctgs 6. 8 Mb l Chr 03 29 ctgs 10 Mb l Chr 04 26 ctgs 9 Mb l Chr 05 24 ctgs 7 Mb l Chr 06 29 ctgs 8. 4 Mb

Anchored Contigs l Chr 07 36 ctgs 9. 2 Mb l Chr 08 38

Anchored Contigs l Chr 07 36 ctgs 9. 2 Mb l Chr 08 38 ctgs 10. 2 Mb l Chr 09 27 ctgs 7. 5 Mb l Chr 10 11 ctgs 4. 7 Mb l Chr 11 14 ctgs 4. 6 Mb l Chr 12 19 ctgs 6. 6 Mb Total Coverage 187 Mb

Web. FPC http: //tomato. genetics. ac. cn/

Web. FPC http: //tomato. genetics. ac. cn/