- Not so pristine after all.
- Farming the sturgeon.
- Colony Collapse Disorder 101. And how floral scents affect pollinator behaviour.
- Presentation on how mobile phones are changing rural livelihoods.
- Urban food gardens to combat high food prices in South Africa. And a different approach in Madagascar.
- Getting dates in Saudi Arabia is becoming difficult.
- “Winged” cats.
- The importance of taro in Hawaii. Thanks, Tevita.
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.
Nibbles: Poppies, Gardening, Milk, Grapes, Genebanks, Meat, Biotech, IK, Plant health
- Dropping the poppy.
- Gardening on windowsills and along roadsides.
- Cooling camel milk. Via.
- Fingerprinting grapes.
- “The seed banks that are run by agribusiness corporations would be a costly pursuit for the government and farmers.” Where to start responding to this? Thanks, Jeff.
- Further evidence of food price crisis.
- “What does biodiversity mean to Syngenta?“
- Traditional healer goes online. Via.
- Videos from Global Plant Clinic.
SINGER maps crop wild relatives
Putting the new SINGER interface through its paces, I find that it can do something interesting that GRIN cannot. Or at least I can’t see a way of doing it, let me know if you can. Below is a screenshot from SINGER showing a Google Map of the distribution of all wild Arachis accessions that the database knows about which have geographic coordinates. Very useful, I think. GRIN does map localities, but I could not manage to get it to do so for multiple species like this.
Tangled Bank 112
There was a bit of a mix up over the blog carnival Tangled Bank, which was supposed to appear last week, while its organizer was swanning around the Galapagos, presumably with other things on his mind. Well it is up now, with a couple of treats. One, alas, is broken. Tangled Banks says that “insects have been selecting hotter hot peppers for some time now. Andrew Bernardin at the Evolving Mind blog points out that “Mexican Food was Not Intelligently Designed.†Alas, Andrew’s blog at Evolving Mind seems to be a bit broken. And it is neat; the heat in chillies protects them from a fungus that destroys the seeds, but is ignored by birds, who disperse the seeds. My question: do birds detect chilli heat, but fail to be put off by it? Or are they completely oblivious to its presence? I mean, could you teach a bird to distinguish seed with chilli from seed without chilli?
The other treat is GrrlScientist, who takes that gray horse paper we blogged a while ago and really goes to town on it, complete with photos, graphs, and movie allusions.