KeyGene delivers sequence-based physical map of the tomato genome to CBSG and international SOL Consortium
Interview with Marco van Schriek, team leader of KeyGene’s Solanaceae group.

December 2009

Congratulations Marco, this is an achievement with a successful collaboration. Could you tell us a little bit more about it?

“About five years ago, a public initiative started, the International SOL Consortium, to sequence the genome of a specific tomato line (Heinz 1706). The partners started with a relatively small physical map. KeyGene got involved in January 2009 and used the Whole Genome Profiling (WGP) technology to help the Consortium to physically map the tomato genome more accurately. This sequence-based physical map will be used as the scaffold to produce a superior tomato genome assembly. This will be finished at the end of 2009. The sequence will be publicly available for everyone interested.”

What kind of applications does this physical map and the genome sequence of tomato offer?

“The knowledge of the tomato genome is very valuable to plant breeders. It provides deeper knowledge on the genetic basis of its traits of interest, and can thereby give a competitive advantage. Breeders can take advantage of the candidate gene approach: if you know what genetic region is involved in a certain trait, you can look at the genes that are present in that region, what their functions could be and then you can make a prediction on what genes might be good candidates for your trait of interest. Of course, these predictions must be validated and tested afterwards.”

Click to enlarge

Can you tell me a bit more about the International SOL Consortium?

“The International Tomato Genome Sequencing Project aims to sequence the gene-rich euchromatic portions of the twelve tomato chromosomes. An international consortium of sequencing centers in 12 countries is performing most of the genomic sequencing. In each country, several research institutes work together to map that chromosome. In the Netherlands that is the Centre for BioSystems Genomics (CBSG). KeyGene and Wageningen UR are both part of CBSG. This is now further expanded with the whole genome sequence based physical map and random shotgun sequences to speed up the first draft genome sequence of tomato.”

KeyGene as part of the sequencing consortium.

“For KeyGene, co-operation and entering partnerships is key. We believe that that results in the best products. We are open to co-operate with future genome sequencing consortia and can bring our own partners in order to deliver a higher quality genome.”

What is so unique about the Whole Genome Profiling technology*?

“The traditional way of making a physical map of a genome uses a limited number of markers of which the sequence is often not known. Our proprietary Whole Genome Profiling technology uses hundreds of thousands of markers, and the sequence of each of those markers is known. That is why it can optimally be used together with next generation sequencing technologies, such as random shotgun sequencing. The physical map is the linking pin to map the sequence of the whole genome. The result is a very accurate sequence based physical map of an organism, in this case tomato, which can easily be linked to whole genome sequence information.”

What kind of applications does this technology offer to other companies?

“Whole Genome Profiling can be the linking pin to any genome sequencing project of any organism; plants and animals alike. We can help many companies and consortia to speed up and increase accuracy in obtaining their genome sequence. We also used our WGP technology to make a physical genome map of potato. And of course we work for specific clients on other crops, but that part is confidential.”

What will be the next steps for KeyGene with tomato?

“We are currently improving several traits of tomato, such as taste and other quality traits and we will keep doing this for the next years. Other topics of interest are traits such as stress and drought tolerance. We see that these are becoming important traits in crops. And on the longer term, who knows…”

Click to view the brochure "Whole Genome Profiling"