- A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. One strong candidate gene, from 6 possible regions. And here’s the light version.
- Yeast culture collections in the twenty-first century: New opportunities and challenges. Pretty much the same as plant genebanks.
- Genetic variation in sorghum as revealed by phenotypic and SSR markers: implications for combining ability and heterosis for grain yield. Possible parents for hybrids identified.
- Actionable knowledge for ecological intensification of agriculture. Look at the landscape, articulate trade-offs and don’t forget the social dynamics.
- Taxonomic and functional diversity in Mediterranean pastures: Insights on the biodiversity–productivity trade-off. Somebody mention trade-offs?
- Are the major imperatives of food security missing in ecosystem services research? Pretty much.
- Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion. Agriculture got you laid, but then killed you.
- High carbon and biodiversity costs from converting Africa’s wet savannahs to cropland. Bad idea all round.
Talking non-biotech strawberries and citrus
If the recent post on the UC Davis Strawberry Wars whetted your appetite, the Talking Biotech podcast can help with a leisurely run-through the history of the crop and efforts to breed it from Kevin Folta and his guest, Dr Jim Hancock, strawberry breeder from Michigan State University. Where things are not as wild as at Davis, apparently. It’s a fascinating story of global interdependence in genetic resources, and the importance of crop wild relatives. And, it turns out the first scientifically bred crop variety was a strawberry. Since I’m at it, the episode on citrus was pretty good too. But Kevin, how about some more explicit recognition of the importance of genetic resources collections (i.e. genebanks) in all this work?
Following Brassica into Genebank Database Hell
Scientists at The Genome Analysis Centre (TGAC) have released the first web repository for Brassica (mustard plants) trait data to tackle reproducibility, user controlled data sharing and analysis worldwide. Scoring the versatile crop’s beneficial traits will assist Brassica breeders in improving their crop yields, increased nutritional benefits and reduce our carbon footprint through biofuel production.
Very worthy, of course. But also, alas, an opportunity missed. How so? Come with me to Genebank Database Hell.
Let’s start with a random germplasm line from the Brassica portal: DEU146_BRA_02028. That’s a weird but somewhat familiar name. People in the know will recognize DEU146 as the code for the German national genebank, IPK. But the organization is given in the portal as CGN, the Dutch national genebank. What’s going on? Stay with me, don’t panic. The portal does provide the following metadata for the material in question:
Provenance: Brassica.xls file downloaded from http://documents.plant.wur.nl/cgn/pgr/brasedb/, March 3rd 2010
Comments: Line name concatenated from resource collection code and genetic resource collection “accession” number; associated data availabel from European Brassica Database of Genetic Resource Collections
Entered by: graham.king@bbsrc.ac.uk
Entry date: 2010-03-03
One’s first instinct of course is to look for the BRA_02028 bit of the name among the DEU146 material in Genesys, but that would be too easy. You have to strip out the assorted underscores, and indeed the leading zero, and that gets you to the right accession, which happens to be from Ethiopia. Breathe.
You could also Google the European Brassica Database of Genetic Resource Collections, as per the metadata, which is hosted by CGN, hence the reference to that organization in the portal. If you search for BRA 2028 you get to the same thing as in Genesys, and eventually to the original record at IPK.
So, to recap: a British guy entered into the Brassica portal some data hosted (as part of a European project) by the Dutch genebank, pertaining to an accession in the German genebank collected in Ethiopia and originally conserved in the old West German national genebank. The actual URL quoted in the metadata returns a 404 error.
Look, I’ve said it before, and no doubt I’ll say it again. It’s great that gene-jockeys like the ones at TGAC build their own databases with all kinds of fancy genotypic and phenotypic data for breeders and other researchers to use. It’s really great, I mean it. It’s what’s going to get the stuff in genebanks used, and we all want that. But please, please, make sure that those breeders and researchers don’t have to go through what I’ve just described to actually get their hands on the seeds. Because I’m pretty sure they won’t. Go through it, I mean. They have better things to do.
Baby oil steps
Is anyone looking for resistant material?
That’s what we asked back in August last year, at the height of the Italian Xylella olive plague panic.
Then in March this year there was news of some 10 cultivars being tested. Now comes this:
An experimental olive plot with almost twenty different olive cultivars (24 replicates for each cultivar) has been set last week in the Xylella-infected area of the province of Lecce (Apulia, southern Italy). The 2-years old plants will be exposed to the natural infective vectors throughout the entire project duration. This plot extends the experimental field established in 2015 within a specific EFSA pilot project and including 10 different olive cultivars, whose evaluations will be followed and continued through the project POnTE.
Which is great and all, but why didn’t they put 50 or 100 cultivars out in the first place?
LATER: Oh, and BTW, did you know you can adopt an olive tree?