Category: Genebanks

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Through the genebank looking glass

As a contribution to the ongoing discussion of genebank database hell, we’re pleased to provide a platform for Michael Mackay, the person responsible for the bioinformatics projects at Bioversity International. At least until he gets a platform of his own …

Many thanks to Dirk van Enneking (and others) for providing some constructive input into suggesting what sort of information and functionality users of plant genetic resources (PGR) might actually want to see to help them locate and select accessions for their research and plant improvement activities. My understanding of the situation is comparable to Dirk’s.

  • Is it a telling sign that there is only one response to my request for a profile of what germplasm users want from an information system in about four months?
  • Is it such a boring and useless endeavor (to provide an online PGR information system) that it does not really matter what information and functionality is provided?
  • Perhaps we have been socially engineered to accept mediocrity and now we are prepared to accept token systems?

In starting work on Global-ALIS (ALIS = Accession Level Information System), one component of the Global Information on Germplasm Accessions (GIGA) project that will build a single internet doorway to more comprehensive information on over 2 million accessions held in genebanks around the world, we are finding a lot of information to support Luigi’s original post Lost in genebank database hell and subsequent points raised in response — including Dirk’s contribution.

One thing we learn is that a lot of data has been accumulated but it is not all made available, possibly for reasons other than intellectual property issues. For example, several people involved in genebank PGR documentation have said that if no one uses the online systems (because they are not useful for the purpose of finding and selecting germplasm for research and plant improvement) then what is the sense in continually updating the data?

Another issue is the availability of characterization and evaluation data. At the moment it seems that only the GRIN system makes significant progress on this count.

A third issue is adding value to existing data. Luigi mentioned geo-referencing and implied spatial analysis as useful ways to better understand distribution and, perhaps, add value to existing data in term of quality and usefulness.

I am pleased to say that we are addressing these issues, and more, in the development of Global-ALIS. However, the eventual utility of this system (due to be deployed in early 2011) could reflect the input and suggestions of those who want to explore and utilize all that genetic variability buried deeply in the world’s genebanks.

We are about to build a Global-ALIS website where people will be able to make suggestions and comments on what genebank database heaven might be like, what features it would have and how people might use it. Dirk’s and everyone else’s positive comments are great stuff! We will certainly take these suggestions on board. The only caveat I need to make is that we cannot do everything at once, so please be prepared to prioritize your suggestions to help us address the issues that will have the most impact in the first instance.

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Genebanks not (yet) trendy

WorldFish has a new blog, focusing on spatial data. It’s only been going a few months, but it looks like it may well have some interesting stuff of relevance to agrobiodiversity. One of its early posts reminded me of something I’ve wanted to do for a while, and that is use Google Trends to look at interest in genebanks. In particular, I wanted to know whether all the news about the Svalbard Global Seed Vault has excited people about genebanks in general. Apparently, not.

trend

Click to enlarge.

The various spikes in interest in Svalbard do not seem to have resulted in increasing searches for “genebank” or “seed bank.” At least not that you can yet see clearly. Here’s hoping…

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Their enemies are time and money…

The (London) Times Life & Style (Women) section had a feature on the Millennium Seed Bank a few days ago and somehow or other we missed it. Slap wrist.

The jars of dried seed go into the cold store, an underground library full of sliding stacks of shelves, every one full of glass jars holding even tinier glass jars. The temperature is -20C but the air-conditioning system creates a further wind-chill.

In that room, the size of a corner shop, are seeds of 10 per cent of the world’s plants. Beyond is another, larger room that one day, Smith hopes, will hold the rest. Empty shelves stretch away into the gloom.

One quibble. The article makes the Svalbard Global Seed Vault sound like a purely Norwegian affair, which of course it isn’t.

Regarding the funding of the Seed Vault, the Norwegian government funded the construction of the Vault in its entirety (this cost $9 million), and will continue to fund the maintenance of the facility, for an annual cost of circa $150,000. The Global Crop Diversity Trust funds the operation and management of the Seed Vault, as well as the transport of the seeds from developing countries to the Arctic. This second component – the transport – is possible through our work with the United Nations Foundation, a partnership which is funded by the Bill & Melinda Gates Foundation.

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Turkey to get yet another genebank?

The news that a genebank will be built in Ankara in 2009, which we nibbled a couple of days ago, is problematic for a number of reasons. But let’s just deal with an error of fact first.

The ministry announced that it will set up Turkey’s first seed bank in Ankara in 2009. The bank, which will reportedly be named Noah’s Bin, will be the fourth largest of its kind in the world.

This will not in fact be Turkey’s first seed bank, as even a Turkish tourism site knows. ((Or did. The site sems to have disappeared.)) The Aegean Agricultural Research Institute (AARI) at Izmir has in fact housed a genebank since 1964, and contributes data to EURISCO, and thence Genesys, to the tune of some 13,000 accessions.

Am I missing something? Is the Izmir genebank going to close, in favour of a larger, newer facility in Ankara? If that is the case, it will not just contain Turkish material.

Some 160,000 wheat types and 27,000 maize types currently registered at the International Wheat and Maize Improvement Center (CIMMYT) will also be included in the gene bank. Turkey will be the third country to have such a center.

What is the metric according to which this genebank would be the third in the world? The only thing I can think of is that it would be the third place to house the CIMMYT collection, after CIMMYT itself and Svalbard. But what would be the rationale for that? Why would Turkey want to go to the expense of maintaining a triplicate of “160,000 wheat types and 27,000 maize types” when it could just get the ones it wanted from CIMMYT at any time at the drop of an email?

It is very laudable that the Turkish government is taking the threat of climate change to agriculture so seriously as to contemplate an expense of this magnitude on ex situ conservation, but the article does raise some interesting questions.