Category: DNA

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The error of genebanks’ ways

ResearchBlogging.orgThe Crop Science paper by Mark van de Wouw, Rob van Treurena and Theo van Hintum ((Wouw, M., Treuren, R., & Hintum, T. (2011). Authenticity of Old Cultivars in Genebank Collections: A Case Study on Lettuce Crop Science, 51 (2) DOI: 10.2135/cropsci2010.09.0511)) of the Centre for
Genetic Resources, the Netherlands (CGN) probably deserves more than the rather cryptic Nibble we gave it yesterday. It certainly seems to be eliciting some interest in the media.

What van de Wouw and friends did was look in detail at alleged duplicates in a collection, the Dutch collection of old lettuce cultivars to be precise. I say alleged because when the researchers DNA fingerprinted plants from accessions which by all rights should have been identical, they weren’t. Known duplicates turned out to be unknown something elses. About 20% of accessions with the same cultivar name (out of a total of 283 accessions in 124 name groups) were in fact significantly different at the DNA level, and they shouldn’t have been. So, for example, 3 of the 12 accessions labelled Maikönig (or similar) in the collection are probably no such thing:

Lettuce is inbreeding, and “[d]iversity within accessions and accidental crossing is not a major issue for cultivars of a self-pollinating crop…” The researchers therefore blame “mislabeling and seed contaminations during processing and handling of the accessions,” mostly “from the period before uptake in the CGN collection.” Better procedures and better documentation systems now exist, and similar problems are much less likely, at least in properly run genebanks.

But what to do with the existing errors? Just remove the erroneous name from the database? Or get rid of the seeds too?

Removing the seeds might be the preferred option, as maintaining a collection is a costly operation and funds are limited… However, if the nonauthentic accession has been extensively evaluated and shown to have valuable characteristics it might be worthwhile to keep the accession, without the cultivar name, in the collection, provided it is confirmed that the accession was already nonauthentic at the time the evaluations were performed. Alternatively, a seed sample could be reacquired in case authentic material is still available elsewhere.

Was it all worth it? Does the significance of this study go beyond the fact that some accessions of old lettuce cultivars in the Dutch genebank may have got mixed up in the past? Well, there are 7.4 million odd accessions in the world’s genebanks, but they’re not all different. Some have no duplicates at all, others dozens. Maybe only about 2 million are unique. That adds to costs, so it would be worthwhile getting rid of a few duplicates. But only if they are in fact truly duplicates, and can easily be identified as such. As the cost of genotyping declines, detecting duplicates (at least in inbreeders and vegetatively propagated species) is becoming cheaper than maintaining them. That may be the most important message to take home from this thought-provoking paper.

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More on ancient Roman pills

What I missed when I wrote about the 2000-year-old Roman pills a couple of days back is that the research was highlighted by Discover magazine as one of the Top 100 Stories of 2010. In addition, Emanuela Appetiti, one of the researchers involved, kindly pointed me to a story at AoLNews which has lots more photos and another one in the Washington Post. She also gave me this nice bit of news:

…I am happy to inform you that Alain Touwaide and myself, along with Rob Fleischer, the geneticist who did the DNA analysis of the ancient medicines, will be in Rome in mid-May 2011 (on the occasion of the “Night of the Museums”) to present at “La Sapienza” University this research. For the first time, we’ll be all there: the three of us and the staff of the Soprintendenza di Firenze, who did the archeaological digging and first analysis. The event in Rome will be on May 14, 2011, at the faculty of Letters.

Looking forward to that. In the meantime, here’s a very recent interview with Alain Touwaide, courtesy of the BBC. Thanks, Emanuela.

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Radicchio diversity

Following in Luigi’s footsteps, the botanic gardens at Padua beckoned. The oldest botanic gardens in the Old World (Wikipedia is wrong; the New has older) they have operated continuously in the same place since 1545. A freezing February day was not ideal to see plants, and precious few of the labels denoted anything directly edible as food. I was not, however, entirely disappointed, for in a sunny bed in the lee of a building was a display of perhaps the region’s most famous crop: radicchio.

The picture above shows an old local variety, Variegato di Castelfranco, and Otello, a modern cultivar. Which, naturally, sent me scurrying to discover more about their history and breeding. There isn’t, actually, a huge amount. One study, of which I’ve seen only the abstract, examined DNA diversity of the five major types. Turns out that if you compare pooled bulk DNA from six individuals of each type, the different types are easy to distinguish. If, on the other hand, you look at DNA from individuals, the distinctions disappear. The variation within a single type is much greater than the variation among the different types. This, the researchers say, indicates that the types have maintained their “well-separated gene pools” over the years. An earlier paper (available in full) had come to a similar conclusion about the populations, with what seems like an ulterior motive: ((Although they were also concerned to enable breeders “to select inbred lines suitable for the production of commercial F1 hybrids”.))

The molecular information acquired, along with morphological and phenological descriptors, will be useful for the certification of typical local products of radicchio and for the recognition of a protected geographic indication (IGP) mark.

And lo, it came to pass. Four types (I think early and late Rosso di Trevisos are included in one designation) got their Protected Geographical Indication in 2008 and 2009. That’s late — tardivo — in the photograph below.

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Nibbles: Vegetables training, Genebanks and genomics, Kew and CWR, AnGR ABS