1. Sequencing update of tomato chromosome 3 Chinese Academy of Sciences
Chuanyou Li
Chinese Academy of Sciences
2019/1/18

2. Physical map construction
FISH
BACs sequencing
Problems

3. BAC libraries Three BAC libraries of tomato were ordered
and duplicated.
(HindIII, EcoRI, MboI)
Manual editing of the available FPC data:
7000 contigs contigs

4. Physical map construction critical for whole genome sequencing
~1000 genetic markers don't have corresponding BACs
physical map coverage is very low
only ~50Mb of 950 Mb of tomato genome
physical map is not focused on the euchromatin region
no minimum tilling path could be developed at this moment
sequencing has to step-by-step, BAC-by-BAC

5. PCR screening of Positive BACs Containing the 986 Genetic Markers
PCR of Heinz
PCR of superpool
PCR of each pool
Data deconvolution
individual BAC confirmation
pool plate 1
pool plate 2
pool plate 3
pool plate 4
pool plate 5

6. Screening and confirmation of markers
Chr.
makers
Tested
confirmed 1
133
102 68 2
119 83 53 3 81 73 49 4
110 90 57 5 67 47 21 6 75 39 7 92 52 8 69 54 28 9 76 55 35 10 62 50 45 11 56 22 12 33
sum
985
756
480

7. Library quality
Too many hits
No hits
This effort provides little help to refine the physical map.

8. Tomato sequence
FISH
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

10. The borderlines on the short and long arm of tomato chromosome 3
The order of clones on tomato chromosome 3
Heterochromatin and euchromatin study on tomato chromosome 3

11. Chinese Group Target Tomato chromosome 3 Short arm cen Long arm

12. The clone of TG479 located at the end of short arm and the clone of T1540 on borderline between the short arm heterochromatin and euchromatin.

13. The clone of TG244 located at the end of long arm

14. The nearest clone of TG247 located on the long arm heterochromatin from centromere.

15. The clone of T0772 located on boundary between the heterochromatin and euchromatin of the long arm.

16. The order and distance of clones on tomato chr3
T cM
SSR cM
T cM
T cM

17. The order and distance of clones on tomato chr3
T cM
TG or 123.0cM

18. Based on FISH analysis, 47 seed BACs were confirmed.

19. BACs sequencing 3730 standard, 10-15X coverage
97 BACs were on the sequencing pipeline
44 BACs were finished.
15 BACs were submitted to SGN.

20. Problems:
Physical map?
Identification of more BACs?

21. Acknowledgment SOL project committee
The Ministry of Science and Technology of China.
Institute of Genetics and Development Biology, CAS
Wuhan Botanical Garden, CAS
National Center for Gene Research, CAS
Shandong Agricultural University, China
Mingsheng Chen, Zhukuan Cheng, Hongqing Ling,
Jianru Zuo, Yongbiao Xue,Ying Wang, Bin Han

22. Thanks for your attention！