Category: Vegetables

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Lost in genebank database hell

Navigating around germplasm databases can be a frustrating experience. A posting on the CropWildRelativesGroup alerted me to a Science Daily piece on tomato genomics which mentioned the wild relative Lycopersicon pennellii (or Solanum pennellii, but I’m not going there, at least not today). But how many accessions of this species are conserved ex situ? And where is it found in the wild?

Ok, so SINGER first, as that’s been much on my mind — and on this blog — of late. SINGER shows 61 accessions of L. pennellii, all from the AVRDC collection. Most of them are from Peru, although 7 accessions have USA, Mexico, Poland (?) or “unknown” as source country. None of these accessions seem to have geo-references, so no nice map from SINGER this time. Pity. But SINGER does give very neat summaries for your query results. ((Incidentally, AVRDC has its own Vegetable Genetic Resources Information System online, which has 65 records for L. pennellii.))

GRIN returns 51 accessions. I can’t find any easy way of working out the duplication between these and the AVRDC material, but I imagine it is significant. Again, most of the accessions are from Peru, but it’s kind of difficult to get summary information across all accessions in GRIN at the moment, though I know they are working on this. Now, tomato germplasm is conserved at the C.M. Rick Tomato Genetic Resources Center (GRIN tells you so), and they have a database of their own. Querying it results in 45 hits, but again there’s no easy way I can see of looking at summary information across all these. You have to look at each individual accession in turn to find out where they’re from, and if you do you get a little map too. The thing I don’t quite understand is why the accessions are geo-referenced in the Tomato Genetic Resources Center database, but not in GRIN. Maybe they’re upgrading the data gradually at the Centre and haven’t passed the latest version on to GRIN? That may also explain the discrepancy in accession numbers. It looks like they’re working on the geo-spatial part of the database, and it may well be possible to get a map of all the accessions of a particular species eventually.

You can of course do that in GBIF right now, but GBIF only has 8 geo-referenced L. pennellii records: from the Missouri Botanical Garden, the Dutch genebank and the European germplasm database, EURISCO. Too bad the Tomato Genetic Resources Center is not a GBIF data provider. And, indeed, that its geo-reference data is not included in GRIN, which is a GBIF provider.

So the answers to the questions I started with are: at least, and probably not much more than, 112, but that probably includes duplicates; and Peru. But I cannot produce a decent map of the distribution of L. pannellii online. I would have to mess around and download the data from the Tomato Genetic Resources Centre database, and then map it myself. Which I may well do, just to show it can be done. But this little exercise does show that there’s a lot of work to be done to improve the data in — and fully integrate — existing agrobiodiversity databases.

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Tasteful breeding

A couple of days ago the Evil Fruit Lord complained — a little bit — about an article in a Ugandan newspaper which extolled the virtues of traditional crops and varieties over new-fangled hybrids. While not doubting the many attractive qualities of landraces and heirloom varieties, he quite rightly pointed out that there’s nothing to stop modern varieties and hybrids tasting just as good:

I get really sick of the tendency to talk about plant breeding as a process which makes crops into finicky, crappy tasting garbage in exchange for yield. You absolutely can create varieties which taste as good (or better) than traditional varieties, produce more, and resist pests. In fact, plant breeding is the only way to get to that.

Now there’s an article by Arthur Allen in Smithsonian magazine which basically says — not very surprisingly, I suppose — that both those things have happened in the tomato:

Flavor … has not been a goal of most breeding programs. While importing traits like disease resistance, smaller locules, firmness and thicker fruit into the tomato genome, breeders undoubtedly removed genes influencing taste. In the past, many leading tomato breeders were indifferent to this fact. Today, things are different. Many farmers, responding to consumer demand, are delving into the tomato’s preindustrial past to find the flavors of yesteryear.

Allen has a good word to say for the wild relatives:

The architect of the modern commercial tomato was Charles Rick, a University of California geneticist. In the early 1940s, Rick, studying the tomato’s 12 chromosomes, made it a model for plant genetics. He also reached back into the fruit’s past, making more than a dozen bioprospecting trips to Latin America to recover living wild relatives. There is scarcely a commercially produced tomato that didn’t benefit from Rick’s discoveries. The gene that makes such tomatoes easily fall off the vine, for instance, came from Solanum cheesmaniae, a species that Rick brought back from the Galapagos Islands. Resistances to worms, wilts and viruses were also found in Rick’s menagerie of wild tomatoes.

And he also plugs genebanks:

…we can take comfort in the tomato’s continuing, explosive diversity: the U.S. Department of Agriculture has a library of 5,000 seed varieties, and heirloom and hybrid seed producers promote thousands more varieties in their catalogs.

Not quite sure where he got that number, as the C.M. Rick Tomato Genetic Resources Center seems to have about 3,500 accessions, but anyway.

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Improved varieties in West Africa

This just in from FAO’s Seed and Plant Genetic Resources Service (AGPS).

Please find below links to the West African Catalogue of Plant Species and Varieties (COAFEV). This document was prepared in the framework of the West African Seed Regulation Harmonization, which was supported by AGP. This process involved 17 West and Central African countries of the West African Economic and Monetary Union (WAEMU), the Economic Community of West African States (ECOWAS) and of the Permanent Interstate Committee for Drought Control in the Sahel (CILSS) and has led to the adoption of a harmonized seed regulatory framework by the ECOWAS Council of Ministers on 18 May 2008 in Abuja.

This framework provides for the establishment of the COAFEV, which is the list of varieties whose seeds can be produced and commercialized in the member states without restriction. The objective of such a system is to facilitate West African farmers’ access to a greater diversity of varieties and to foster cross-border seed trade.

English version.

French version.

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