Transcript SOL Genome Project - University of California, Davis

The International Solanaceae Genome Project (SOL):
Systems Approach to Diversity and Adaptation
SOL Genomics Network
• Formed in 2003 to answer two questions:
– How can a common set of genes give rise to such
a wide range of morphologically and ecologically
distinct organisms that occupy our planet?
– How can a deeper understanding of the genetic
basis of plant diversity be harnessed to better
meet the needs of society in an environmentallyfriendly and sustainable manner?
More than 3,000 Solanaceae species world-wide. Major
evolutionary progress in South America unaltered by ice-ages
and fueled by extreme climates.
Lynn Bohs
2n=2x=24 950 Mb
2n=2x=24 950 Mb
2n=2x=24 1300 Mb
2n=4x=24 1800 Mb
2n=2x=24 3000 Mb
2n=2x= 22 ca. 1000 Mb
SOL Tomato Sequencing
• Genome size of 950 Mb. ~35,000 genes.
• 25% DNA lies in gene-dense euchromatin
regions.
• Anchor BACs to genetic map
(S. esculentum x S. pennellii F2) then choose
new BACs based on sequenced ends. Verify
physical location by FISH.
Comparable Maps
• Arabidopsis:
– Arabidopsis COSII
• Eggplant:
– Eggplant-LXM 2002
• Pepper:
– Pepper-FA03
– Pepper-AC99
• Potato:
– Potato-TXB 1992
• Tobacco:
– Tobacco SSR 2007
• Tomato:
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Tomato FISH map
Tomato-EXPIMP 2001
Tomato-EXHIR 1997
Tomato-EXPIMP 2008
Tomato-EXPEN 1992
Tomato-EXPEN 2000
Tomato IL map (2)
Tomato physical map
Tomato FPC map
Tomato AGP map
Chrom. 1
Mb* 24
2
3
4
5
6
7
8
9
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11
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26
26
19
11
20
27
17
16
10
13
11 T=220
Short arm
Italy
USA
USA
Spain
USA
France
UK
China
Korea
USA
Long arm
The Netherlands
USA
Centromere
euchromatin
heterochromatin
AT-rich satellite DNA
* Euchromatin portion
The 10 missions of SOL
1)
2)
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5)
Sequence the reference tomato genome using BAC minimal tiling paths.
Develop deep EST databases and shotgun genomic sequences for other Solanaceae
crops as well as SNP analysis of diverse germplasm.
Construct COS maps and interspecific introgression resources for all SOL crops
Establish a saturation set of mutagenesis lines and cloned gene specific tags (GST).
Construct a comprehensive phylogenetic and geographical distributional
information network.
6)
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8)
9)
Apply transcription, proteomic & metabolic profiling to explore chemical and
developmental evolution.
Apply non-destructive ‘Real Time’ physiology and phenotyping.
Improve the efficiency of plant breeding -- especially through use of natural
diversity.
Educate the public about the value of biodiversity, domestication and plant
improvement.
10)
Develop an international bioinformatics platform which will facilitate a systems
approach to SOL research.