Genebanks

June 17, 2013June 17, 2013

Stable identifiers for genebank accessions still a dream?

Natural history collections and herbaria contain many millions of specimens that are used for research. When scientists publish their results they cite which specimens they used so that other scientists can both check the work and build on what has been achieved.

Institutions that hold specimens are publishing increasing amounts of data about (and images of) their specimens on-line. We need to have a way for scientists to reference specimens so that someone reading research results can simply click a link to see the supporting data and perhaps an image. To make this happen we need stable web links to the specimens that the holding institutions commit to maintain for the long term and that are implemented in a similar way across many institutions. Once this mechanism is widely adopted machines will be able to exploit the links to specimens to help do entirely new kinds of research.

This meeting was about establishing a consistent mechanism that will work across institutions.

Yes! And genebank accessions? When can we have some movement on that?

June 17, 2013June 17, 2013

Brainfood: Maize rhizosphere, Climate change vulnerability, Heterosis squared, African forests, Sequencing genebanks

Diversity and heritability of the maize rhizosphere microbiome under field conditions. There’s a lot of it, but only measured in inbreds so far. One wonders about landraces.
The Vulnerability of Biodiversity to Rapid Climate Change. We should focus on increasing the adaptive capacity of species and ecosystems, but predictions are difficult, especially about the future.
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Sex is better with two.
Progress Toward Understanding Heterosis in Crop Plants & Genomic and epigenetic insights into the molecular bases of heterosis. It’s the allelic interactions, stupid. Now to make use of this.
Deforestation in an African biodiversity hotspot: Extent, variation and the effectiveness of protected areas. Protected areas have worked for the evergreen forest, but don’t forget the miombo! Would be intersting to know what this all means for crop wild relatives.
Comprehensive genotyping of the USA national maize inbred seed bank. Ladies and gentlemen, I have seen the future of genebanks.

June 14, 2013June 14, 2013

Nibbles: Public goods, Again, Tainted love, Strawberry Fare, Organic money, Organic unbuttered parsnips, Insect resistance, Cassava quakes, Gin and other botanics

A well-briefed Olivier De Schutter, UN Special Rapporteur on the Right to Food, reflects on biodiversity for food and agriculture as a public good. Video. Comments closed!
UK genebanks are wonderful, says chair of British Society of Plant Breeders.
Getting ready for a possible ban on pig castration, the Nordic Food Lab tells us how to deal with Boar Taint.
The things you can learn from strawberries (if you can hold off eating them).
More money for research on organic agriculture shock plea.
HRH Prince Charles didn’t use the R-word, but you know he might just possibly agree.
I wonder whether he realises that the evolution of resistance by insect pests is predictable.
If cassava is such a Rambo root, how come it quivers before a fly? Even a super-fly?
And if that isn’t enough to keep you busy over the weekend, how about celebrating World Gin Day tomorrow, with a good book (and a glass) in hand, natch.

June 11, 2013June 12, 2013

Playing around with new spatial datasets

Kai Sonder, CGIAR GIS geek extraordinaire, alerts us to the release of a couple of cool new global geospatial datasets, on roads and urban expansion. You need GIS software to get the full benefit of these, but at least for the city one some of the data ((present extent of urban areas, but not the changes in time, as far as I can see.)) are available in KML format. This is what you get when you map in Google Earth Yerevan’s present extent together with the location of wheat germplasm accessions from Genesys.

Clearly some of those samples must have been collected a while back, when the city was perhaps smaller. And this is what you get when you map Armenia’s roads, again with wheat, but this time in DIVA-GIS.

A nice enough illustration of a bias towards collecting germplasm near roads that has been looked at in quite a lot of detail in another part of the world. But I just can’t help thinking these resources should be easier to play around with. Especially together.

LATER: Spurred on by Cedric and Jeremy, let me spell it out in more detail. What I would have liked is for both datasets to be available in their entirety in a format allowing easy upload to Google Earth. You will tell me that if you’re really, seriously interested in analyzing these datasets, together with others (like that Armenian wheat stuff from Genesys, say), you can do it by downloading the shapefiles, which is the standard format for such things, and opening them in any decent GIS software. And you’d be right. But isn’t there another kind of user? The one who wants to just, well, play around. Maybe even as a preliminary to more serious analysis, but initially just play around. That user is not well served by these resources. I know because I am that user, and I don’t feel well served.

June 5, 2013June 5, 2013

Nibbles: Hot peppers, Job, Hippy scientist, Seed law considered, Old seed, Rice and recovery

Will the world ever tire of hot pepper stories?
Would you like to work at the Millennium Seed Bank?
The Guardian hymns Howard-Yana Shapiro, the “vegan hippy scientist” who wants to open orphan crop genomes.
Patrick links to Arche Noah’s response to the new EU seed laws.
Laws that don’t bother Gene Logsdon, planter of old seed.
IRRI claims that rice seed aids Bangladesh’s cyclone recovery, but frankly, I can barely read it.