How long have you worked at KeyGene and what is your main focus at this moment?

I have been employed at KeyGene since November 2004 and my focus has been on developing and boosting a number of new innovations, breakthrough technologies and traits. These are integrated and grouped in three proprietary platform technologies:

• the Accelerated Molecular Breeding platform,
• the new Molecular Mutagenesis platform and
• the Lead Discovery Bio-informatics platform.

The combined platforms are now being used to discover high impact plant traits in our Trait Platform. This platform currently focuses on the identification and improvement of trait genes. Especially new insect and fungal resistance genes, plant reproduction genes and herbicide tolerance genes.

With its newly developed technology and trait portfolio KeyGene is ready to give a new dimension to the genetic improvement of plants in a fast, cost effective and socio-economically acceptable manner.

We call this new way of molecular genetic improvement of crops the GreenGene Revolution and expect that the resulting breakthrough seed innovations will greatly benefit our customer seed and breeding companies.

One of our newest breakthrough innovations was recently announced at the Plant & Animal Genome conference in San Diego (January 2009) and is called “Whole Genome Profiling”.

Could you explain what Whole Genome Profiling is all about and why is it so interesting?

Every breeding company is interested in having whole genome sequence assemblies for the crops within their seed sales portfolio. However, the investments necessary to develop a comprehensive whole genome physical map and corresponding sequence assembly are for many of these crops economically unfeasible.

Therefore we developed a new cost effective method to construct high quality sequence-based physical maps. Such a DNA map is constructed using large DNA fragments clones of 120.000 base pair that can be fingerprinted by placing short, 30 base pair sequence tags spaced 2000 – 3000 base pair across these large DNA fragments.

Subsequently the large DNA fragments are ordered into contigs (continuous coverage) by using overlapping regions with identical sequence profiles. Unlike other profiling methods the Whole Genome Profiling map has ordered sequence-based anchor points.

Our new technology does all of this work in an efficient manner and at an affordable price and is applicable for plant, animal and human genome assembly.

How can a breeding company use the results of Whole Genome Profiling?

The availability of a sequence-based map allows very efficient and low cost whole genome sequencing of your crop of interest whereby the quality of the Whole Genome Sequence Assembly dramatically increases. On the one side a breeding company could decide to deep sequence a specific region of the crop genome that is of special commercial interest.

This could be for instance an important set of resistance genes or an interesting introgression segment from a wild relative.

The data from Whole Genome Profiling can focus the deep sequencing efforts to one or more 120.000 base pair fragment clones. Alternatively a sequence-based map might also be used as a starting point to quickly identify, clone, patent and commercialize interesting genes.

Whole Genome Profiling can also be used to characterize inbred lines at a relatively large scale. Whole Genome Profiling offers an array of applications all of which are geared towards identifying and characterizing economically important genomic regions or genes in real crops that often have large complicated genomes.

Did you use the technology already for crops?

Yes, KeyGene began developing this technology two years ago using Arabidopsis with its 120 million base pair genome as a model to proof Whole Genome Profiling works. Subsequently we used melon, which has a genome size of around 450 million base pair, to generate a de novo sequence based physical map.

This map was combined with the results of Whole Genome Sequencing and we have obtained a high quality genome assembly.

We also have successfully applied Whole Genome Profiling in a 2600 million base pair plant genome. Again this will be combined with Whole Genome Sequencing to yield a high quality map and a high quality genome assembly ready for targeted regional sequencing or for gene cloning.

How do you offer this technology?

We offer Whole Genome Profiling together with our strategic partner Amplicon Express Inc, (Pullman, Washington USA). Amplicon Express has great expertise in isolating DNA from crops and cloning large DNA fragments in BAC library systems.

KeyGene will be responsible for placing the sequence tags on these fragments in a high throughput mode and aligning the fragments using bio-informatics approaches.

Using our combined sales forces KeyGene and Amplicon Express Inc will distribute Whole Genome Profiling for world-wide as a service for researchers in plant, animal and human fields.

In conclusion, what would you like to tell the SeedQuest readership?

I would like to tell the SeedQuest readers that the KeyGene™ Whole Genome Profiling method is just one example of the new approaches we have developed for sequence based molecular breeding applications.

Other applications we have developed are CroPS® for High Throughput SNP discovery and KeyPoint™ for High Throughput mutation detection and cost effective resequencing (genomic DNA, cDNA etc; cf www.keygene.com).

I am convinced that with the use of such technologies we are entering into an era of “Sequence Based Breeding”.

In my opinion within the next 5 – 10 years plant breeders will be directly using DNA sequences rather than molecular markers for the genetic improvement of their crops. The use of Sequence Based Breeding can be combined with automated phenotyping.

This combined approach will enable dramatic improvement and molecular breeding of crops offering exciting new possibilities for fulfilling the growing demand for better and more Food, Feed, Fuel and Fibre.

Arjen van Tunen can be contacted at arjen.van-tunen@keygene.com

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