Author: Luigi Guarino

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Credit where credit is due

ResearchBlogging.orgYou may have been following the reaction to the media frenzy about the announcement yesterday of a new way of making potatoes resistant to blight, cause of the Irish Famine a century and a half ago. I won’t add to the confusion, beyond saying that, as in everything in life, there are always alternatives, and wouldn’t it be nice if we gave them all a fair go?

No, what I want to talk about here is where the gene in question came from, the gene for blight resistance that was inserted into the popular British variety Desiree to such apparently good effect. We know from the paper that the gene is called Rpi-vnt1.1 and that it came from the potato wild relative Solanum venturii, but that’s all. I think that’s insufficient. There may be a reference in the paper or the supplementary material 1 to the source of the Solanum venturii germplasm that was used in this work, but I was unable to find it. Apologies to the authors if I missed it, and thanks to whoever it was at the Sainsbury Lab that tweeted a response to my request for information:

It turns out that the germplasm was obtained from the Centre for Genetic Resources, the Netherlands, which has often been mentioned on this blog. Most recently, as coincidence would have it, yesterday, and on the subject of potatoes to boot. CGN is at the very forefront of genebank documentation, so it was very easy to find that there are 3 accessions of the species in question at CGN, that only one of those is resistant to blight, that it is CGN18000, that it was collected in 1972 in Argentina at an elevation of 3200m and that it came to CGN via the Institut fur Pflanzenbau und Pflanzenzuchtung Bundesforschungsanstalt, Braunschweig, Germany. There are more accessions out there (although apparently not at CIP, the International Potato Center, at least according to Genesys), and also herbarium specimens. Enough in fact to come up with an estimate of the overall geographic distribution of S. venturii, and perhaps identify some gaps.

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Or am I wrong? It’s an informed guess. If there had been more than one accession with resistance, it would have been difficult to know which one was actually used in the paper. Anyway, I look forward to the day when even the authors of whizz-bang biotech papers will spend five minutes to do what I just did and properly acknowledge, perhaps even link to, the genebank, and the specific accession, whose existence ultimately allowed them to do their work.

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Calling users of lettuce and potato genetic resources

An interesting announcement from our friends at CGN.

In the field of PGR documentation, we have seen, over the last decades, dramatic improvements: from card box files only mentioning the name of the variety and the location in the seed-storage, to internet accessible databases, sometimes with possibilities to order PGR on-line including click-wrap SMTA. However, the access to PGR information was always ‘supply driven’ saying: this is what we have, choose!

Here at CGN we have also been thinking about this, and decided that we might try to turn the situation towards a ‘demand driven’ PGR information access. Based on our experience interacting with users of our genebank, we have identified their first priorities where it concerns PGR: access to material and access to information, and on that basis experimented with creating web sites that could accommodate questions such as ‘where can I find a blue potato’, ‘where can I get material without having to sign a SMTA’, or ‘what has been done regarding the search for Bremia resistance in lettuce’. Some of such sites already exist, we wanted to find out if a genebank or the PGR conservation community would also be able.

We are proud to release two ‘PGR Crop Portals’ one aimed at potential users of lettuce germplasm, the other aimed at potential users of potato germplasm. These sites are not the same as the target audiences are neither, but, as you can see if you visit the sites, both ask frequently for feedback from the users, to add information, to share experiences.

This approach fits in a philosophy, where the data sources (genebanks) do the data collection and curation, whereas anyone can create an interface to the data (and thus the material) in these combined sources serving a specific target group. This target can be ‘lettuce breeders’ but also ‘anyone interested in crop wild relatives in the Balkan’, ‘the malting barley industry’ or ‘Dutch hobby gardeners interested in old vegetable varieties’. This approach requires (1) proper access to the PGR data, possibly via EURISCO or GeneSys, and (2) creators of interfaces who know their target audience very well and are willing to establish a communication link with this audience.

Please have a look at the site, and let us know what you think!

Finally, I would like to thank Rob van Treuren (lettuce), Roel Hoekstra (potato) and Frank Menting (both), for all their efforts to get the initiative to this stage, and express my hope that the user community will help to take it further.

A most welcome initiative, I think, finally moving beyond databases. Hard to fault the theory, let’s all see how the practice pans out. Leave comments here, or send them to Theo van Hintum at CGN.

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Brainfood: Value of Chiloé, Zimbabwe sorghum, Rosa karyotypes, PSM diversity, Pear diversity, Medic clines, Wild rices, Barley adaptation, Coffee agroforesty

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Nibbles: New potatoes, Wild species, Native maize, Conservation course, Indigenous fishery, Yield trends