Prof. Evert Jacobsen
Scientific Director
Plant Research International and Wageningen University, Plant Sciences*

How can information technology make seed companies more successful, and what specific solutions does your company offer?

While it may be fair to say that the use of information technology has not always been given the highest priority in the seed business, the last decade has offered a number of fresh perspectives. When it comes to mathematics, the evaluation of field trials and of the value of trial fields have become more effective. Total quality management in seed production has only become possible thanks to the automation in logistics. In addition, the seed business had (and still has) to take into account the way its partners and customers have integrated IT within their businesses. Research in Wageningen has certainly contributed to some important new IT-angles for the seed business. Here, I would like to focus on current and future perspectives.

Opening up black boxes for breeders

For an effective breeding process, breeders often had to focus on the phenotype of the progeny. Indeed, the general and specific combing ability are included in the choice of parents. However, breeders often have very little idea about the genetic background of certain traits, and certainly not of the metabolic background. The plants were like a black box: we saw the effects, but we didn’t know their source.

Wageningen has been at the forefront of the development and application of genomics and bioinformatics. As well as serving fundamental research, this work benefits plant breeders at institutes and private enterprises worldwide. Once we know the origin of the trait, we can multiply the possibilities for its exploitation. An exciting example is the future combination of different pest or disease resistance mechanisms in a single variety. I expect some dramatically positive effects on the durability of the resistance.

User-friendly genetic mapping

From the outset of gene mapping using molecular markers, Wageningen has been developing genetic mapping software. JoinMap®, a co-production of Plant Research International and Wageningen University, now has thousands of users at breeding companies and institutes around the globe. Various publications and informal responses from our users make clear that the programme remains an essential ingredient for success. Since 1993, we have continuously adapted the programme to user requirements and to new techniques in mathematics and molecular analysis.

As a result, our latest version, JoinMap® 3.0, can handle a wide range of mapping populations and offers data export to other platforms. The user interface can be regarded as one of the best in genetic mapping software. Our partnership with Kyazma, a software company in Wageningen, guarantees continuation of the development and support.

Combining breeding and mapping? FlexQTLTM!

In the 1990s, molecular techniques reached the point where seed business and research institutes could also map quantitative traits. Wageningen filled the gap with the MapQTL® package. Version 5 combines multiple mapping techniques with attractive graphic presentation of results, a fast algorithm, a user-friendly windows interface and export to both Office software and JoinMap®. This allows thousands of users to include QTL-mapping in their existing work. Our collaboration with Kyazma again guarantees continuous development of the package.

Despite all of this, our customers and partners asked for more. Breeders told me they wanted to use their regular breeding programme for mapping purposes, rather than carrying out dedicated mapping experiments alongside the breeding programmes. They also explained how they would also like to include data from earlier trials, preferably including morphological data.

The Plant Research International response was to develop FlexQTLTM. Breeders can now commission us to use the data from their ongoing selection trials to also map quantitative traits by tracing important alleles across multiple generations. The cost reductions are substantial and the package brings new perspectives for breeders who were previously unable to carry out separate mapping experiments

SeedCalulator®: optimal seed testing

Seed companies, testing stations and researchers evaluating germination tests have adopted SeedCalculator as an easy to use package for effective evaluation of germination tests. Users only have to score the amount of seeds that have germinated and the time at which the scoring was done. The software performs the fit that describes the germination curve and the germination parameters are calculated and presented. Technicians do not need to be skilled in statistical analyses for these tests.

Other packages are not dedicated to fit germination data in an easy way. Furthermore, SeedCalculator makes it easy to compare germination tests from different testing sites, because the calculations are standardised. A new package, which also will include predictive information on germiniation under different temperatures and soil moisture contents, is now being developed at Plant Research International.

Setting up and evaluation

We know that mathematics and statistics are not the favourite disciplines of many of our breeding and seed production customers. Drawing conclusions without fooling oneself is essential for success, however. We therefore have specialised scientists advising customers based on their aims, trial set-up and data.

The impact of the customers’ IT

It is of course important to take into account the level and use of automation at one’s customers. Because produce quality and timing are crucial to the success of today’s growers, they are keen to explore the possibilities of steering their crops in a way that optimises economic yield. Computer-based decision support systems such as those developed in Wageningen allow growers to combine actual data from the market with the status of their crops. The computer then offers the grower suggestions regarding the use of growth conditions such as nutrition and temperature. This will be quite a challenge as it relies on varieties responding in a precisely predictable way. Imagine a cucumber variety for which the growth can be controlled in such a way that the grower can be certain of the duration of production, the production peaks and lulls , the position of the fruits in the crop and the quality of the produce.

Expecting the unexpected

Research institutes such as Plant Research International continuously push back the boundaries what is possible. Five years ago I could not have predicted the impact that the combination of up scaling of genomics technologies and developments in bioinformatics would have. Partners and customers can now ask questions they could not have thought of back then.

It is my firm belief that IT can help the seed business meet its goals and ambitions, and it might just be in an unexpected way.

*both Plant Research International and Wageningen University, Plant Sciences are part of Wageningen UR, The Netherlands.
The Plant Sciences Group of Wageningen UR is a collaboration of:
- Plant Research International B.V.
- Applied Plant Research (Praktijkonderzoek Plant & Omgeving B.V.)
- Wageningen University

Prof. Evert Jacobsen can be reached at evert.jacobsen@wur.nl
For more information about Plant Research International, Inc., please visit www.plant.wageningen-ur.nl

May 2004