platforms for molecular breeding: KeyGene’s Whole Genome
Arjen J. van Tunen
is CEO of KeyGene NV.
He serves as board member on
several associations including EuropaBio, the
European Biotechnology Association, NIABA, the
Dutch Biotechnology Association and Food Valley,
a consortium for Food Innovations in the
Netherlands. Furthermore Arjen van Tunen is a
professor of Plant Biochemistry at the
Swammerdam Institute for Life Sciences,
University of Amsterdam and Visiting Professor
at the Shanghai Institute of Biological
KeyGene is developing and applying molecular
genetic technologies and traits for the
improvement of crops. KeyGene performs contract
research all over the world in co-development
projects with seed and Agro Biotech companies
including its four strategic shareholder
companies which are leaders in vegetable
breeding. KeyGene employs 135 staff in its
headquarters in Wageningen, the Netherlands and
in its subsidiary Keygene Inc in Rockville, USA.
Additionally, KeyGene operates a joint lab with
the Shanghai Institutes for Biological Sciences
in Shanghai, China
interview with Arjen J. van Tunen, CEO of
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
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
- the Accelerated Molecular Breeding
new Molecular Mutagenesis platform and
- the Lead Discovery
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
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
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
How can a breeding company use the results of Whole Genome
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
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
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.
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
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.
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.
conclusion, what would you like to tell the SeedQuest
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
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
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
No part of
this interview may be reproduced,
distributed, transmitted, displayed, published or broadcast
form or by any process without prior written permission from