Squeezing olives

BTW, if you want to see what that “olive plague” we blogged about a few days ago looks like, here’s a despatch from the front lines by our intrepid photojournalist on the spot, Layla.

Incidentally, my attention has coincidentally recently been drawn to the Bioresources For Oliviculture (BeFOre) project (emphasis added):

The project aims at establishing a multi-lateral network of research and innovation staff active in OLIVE germplasm access, conservation, evaluation and exploitation, strengthening research capacities through the exchange of knowledge and expertise on a shared research programme focused on establishing integrated common protocols to phenotype and characterize plants at molecular, morphological and physiological level, and evaluating the olive oil quality related to varieties. Particular attention will be paid at establishing the international intellectual property rights for conserving and exchanging the olive genetic resources. The involvement of some Non Academic Organizations will allow the sharing of knowledge and ideas from research to all levels of the olive production chain, from plant propagation to fruit production and oil extraction (and vice-versa).

The bit about IPR is important because olives are not on Annex 1 of the International Treaty, at least for now, and one of the deliverables of the project is:

Core set of genotypes present in the main olive cultivar collections and grown under different agro-environmental conditions to evaluate their agronomical performance

Hopefully some of those genotypes are going to be of use against Xylella, either directly or through breeding.

Brainfood: Arracacha diversity, Mediterranean diet, Asian sheep & goats, Alpine flax, Breeding efficiency, Models, Domestication & seed size, Palm uses, CC & production, Insecticide & diversity

Some new germplasm databases, at least to me

Long-time readers may remember a post from 2012 summarizing some media reports of trouble at the Italian national genebank at the National Research Council (CNR), Bari. But maybe things are not as bad as were made out at the time. Or have got better.

I’ve just come across what seems to be a fairly new website for the genebank and it doesn’t give the impression of crisis. It lists 57,568 accessions from 184 genera and 834 species, which is more that was reported back in 1999 in WIEWS for ITA004, hopefully the correct code for the genebank in question (at least the address matches, if not the name of the institute). This is the geographic coverage of the collection:

Impressive. Unfortunately, data on these accessions are not available in the European genebank database, Eurisco, and therefore they’re not in the global portal, Genesys, either. Hopefully that’s being rectified.

Since I’m on the subject of germplasm databases, I’ve also recently come across the Legume Information System, which focuses on material in the US genebanks. It has all kinds of data, but I just looked for germplasm from Italy to compare with what’s in Bari. Here’s the map for Medicago spp, showing growth habit in different colours (click on it to see it better).

Compare and contrast with the ITA004 collection for the same species.

Which is why it’s a good idea to have all these data together in one place, i.e. Genesys.

Unique digital identifiers everywhere

A recent letter in Nature:

Members of the Consortium of European Taxonomic Facilities have adopted a consistent citation system for an estimated 20 million biological and geological specimens from European collections. We encourage researchers, publishers and other institutions to engage with this initiative by citing the full specimen identifier in their publications and data sets. These specimens provide reference material for research on evolution, genetics, mineralogy, ecology and taxonomy — hence the need for a reliable identification system for citation (see A. Güntsch et al. Database 1, bax003; 2017). Our system assigns a unique and permanent Uniform Resource Identifier (URI) to each specimen. It follows Linked Open Data principles (see www.w3.org/tr/ld-bp) by including a redirection facility to human- and machine readable representations of the specimen. It also gives credit to the collectors and custodians. For example, the alpine plant specimen Leptinella scariosa Cass., held by the Royal Botanic Garden in Edinburgh, UK, and collected in Chile by Charles Darwin in 1834, is referred to by the URI http://data.rbge.org.uk/ herb/E00070244.

Quentin Groom, Botanic Garden Meise, Belgium.
Roger Hyam, Royal Botanic Garden Edinburgh, UK.
Anton Güntsch, Botanic Garden and Botanical Museum, Berlin, Germany.

Genebanks are doing something very similar.