This document summarizes plans to construct a whole-genome variant catalogue for the tomato clade. It will sequence over 100 accessions from cultivated tomatoes and wild relatives to identify alleles underlying phenotypic diversity across the entire genome. Reference genomes will be developed for some accessions. Variants will be identified by mapping reads from each accession to the appropriate reference. Data will be released in 2013 through a public-private partnership to enable further breeding efforts.

1. Construction of a whole-genome variant
catalogue for the tomato clade
http://www.tomatogenome.net
27 August 2012, Richard Finkers (@rfinkers)

2. Consortium
Funding partners (Academia & Industry): Funding agencies:
Genebanks & Heirloom enthusiasts:
Acknowledgements / Collaborators:

3. Rationale
 Genetic diversity in commercial tomato germplasm
relatively narrow.
 Introgression breeding from related wild species.
 Un(der)exploited genetic diversity in tomato land races?
 Aim:
● Identify alleles underpinning phenotypic diversity
across the entire genome and entire tomato clade

4. Rationale

6. Acknowledgement: Sjaak van Heuden, Paris market

7. EU-SOL core collection
 https://www.eu-sol.wur.nl
> 7000
 Information:
landraces
1000
landraces
 Marker data
 Phenotype data
200
landraces
 Passport data
 Markers
 20 (7000 -> 1000)
 384 (1000 -> 200)
Selected landraces for
(re-)sequencing  7500 ( 200 -> 34)
Acknowledgement: Dani Zamir et al. & Keygene N.V.

8. Landraces & old cultivar collection

9. Improving with exotic genetic libraries
Wild tomato species
are valuable candidate
for novel alleles
Dani Zamir, Nature Reviews Genetics 2, 983-989 (December 2001)

10. (re-)sequencing collection
52
Lycopersicon group
4
7
2
2 Arcanum group
2
1
1
2 Eriopersicon group
2
7
2 Neolycopersicon group
Tree according to Anderson et al. (2010), redrawn from Moyle 2008

11. Genome Alignment
 Read mapping to
cv. Heinz
 Genome structure
wild tomato
relatives?

12. Reference genomes
 Contribute to or de novo assemble:
● S. arcanum LA2157
● S. habrochaites LYC4
● S. pennellii LA716
 Rationale:
● (Nearly) homozygous accessions
● Inbred over a few generations
● One accession for re-seq read mapping / group

13. Now we are ready to sequence

14. Sequencing output
 De novo genome assembly
● 170bp, 2 x 100bp Paired-end sequencing (Illumina)
● 2kb, 2 x 100bp mate-pair sequencing (Illumina)
● 8kb matepair (454)
● 20kb matepair (454)
● On average, 205x coverage produced
 DNA re-sequencing
● 500bp, 2 x 100bp Paired-end sequencing (Illumina)
● On average, 41x coverage produced

15. Current & Future work
 Read mapping all accessions against S. lycopersicum c.v.
Heinz
 Construction of the new reference genomes
 Read mapping accession to reference from the same
group
 Extract allelic (and structural) variants
 Data release plan: Second half of 2013
● Public Private Partnership

16. Cherry picking
 En Tibi Perpetuis Ridentum
Floribus Hortum
 Ferrara, Italy (1542-1544)
 Salunca, Puma Amoris

17. Relevant URL’s
 Project site (lists selected accessions):
● http://www.tomatogenome.net
 Phenotype data & Images:
● https://www.eu-sol.wur.nl
 SOL100:
● http://solgenomics.net or http://solgenomics.wur.nl