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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.

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Getting to grips with rice in Europe

A little more on that RiceAtlas that I blogged about a couple of days ago. I managed to download the shapefile of rice growing areas, and open it in Google Earth. I then imported the Genesys rice dataset, and zoomed in on Europe. Here’s what those two things together look like.

Definitely a few issues. I’m not too worried about the accessions in northern Europe. Those are probably just wrong passport data. But what about all those in Turkey which are also outside putative rice growing areas? Are those passport data mistakes too, or is RiceAtlas missing something?

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Chasing melons in Central Asia

I’ve been meaning to post a link to Eric Hansen’s entertaining “In Search of Ibn Battuta’s Melon” for ages. Published in 2015 in AramcoWorld, its title says it all. Intrigued by a wonderful, and wonderfully expensive, Mirza melon from California, Hansen recalls the following passage from the celebrated Moroccan traveller, and resolves to find the melons in question — “the best of all dried fruit” no less — in their native Uzbekistan.

There are no melons like Khorezmian melons maybe with the exception of Bukharian ones, and the third best are Isfahan melons. Their peels are green, and the flesh is red, of extreme sweetness and firm texture. Surprisingly, they cut melons into slices, dry them in the sun, put them into reed baskets as it is done with Malaga figs, and take them from Khorezm to the remote cities in India and China to sell. They are the best of all dried fruit.

Needless to say, he finds them, or something that he decides is much like them, though he also comes to see the pointlessness of the quest.

In the closing hours of my quest, I realized that over the 681 years since Ibn Battuta’s visit to Khorezm, Uzbek farmers had been hard at work perfecting the art of melon breeding and growing. By saving old local melon seeds, creating and improving new varieties and passing down specialized horticultural practices according to regional water quality, soil types and climatic conditions, they had no doubt improved the disease resistance, shelf life, yield, texture, degree of sweetness and complexity of flavors of melons throughout the different growing areas. And then there was the issue of random variations due to natural hybridization in the melon fields to consider. With all of these factors in mind, it would not be surprising—even likely—that Ibn Battuta’s melon had evolved into something quite different, disappeared entirely, or simply fallen out of favor because other, more recent varieties were better.

Hansen has helpful guides in Uzbekistan, not least the authors of the book Melons of Uzbekistan. He doesn’t however, link to the book, which is available online. I’m happy to rectify that oversight here.

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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.