Agricultural Biodiversity Weblog

February 18, 2014February 19, 2014

CGN18108 it is

Simon Foster very kindly took the trouble to post a comment setting the record straight on the source of that blight gene:

Apologies, a previous tweet from ourselves erroneously confirmed the accession as CGN18000. It is in fact CGN18108 which is still listed in the database as Solanum okadae (was subsequently found to be S. venturii in DNA fingerprinting studies).

The origin of Rpi-vnt1 is detailed in the original research paper describing the cloning and characterisation of the gene and which is cited in the Roy. Soc. paper published yesterday. All acknowledgement of sources was published in that paper.

Foster SJ, Park T-H, Pel M, Brigneti G, Sliwka J, Jagger L, van der Vossen E, Jones JDG. 2009 Rpi- vnt1.1, a Tm-2(2) homolog from Solanum venturii, confers resistance to potato late blight. MPMI 22, 589 – 600. (doi:10.1094/MPMI-22-5-0589)

Here’s the relevant bit of that paper:

Accessions of S. venturii and S. okadae were obtained from the Centre for Genetics Resources in Wageningen, the Netherlands (CGN) (Table 1). The S. venturii accessions were originally listed as S. okadae in the CGN database but have recently been reclassified based on work using amplified fragment length polymorphism (AFLP) markers to study the validity of species labels in Solanum section Petota (Jacobs 2008; Jacobs et al. 2008).

So my apologies to Dr Foster. There is indeed a very full and proper acknowledgement of the source of the gene in the earlier paper. However, I do still think that it would not really have taken much effort to also include an acknowledgement in the later paper. The confusion over which accession was actually used that I fell into, admittedly without taking the trouble of following the references, is evidence of why it’s important to do so.

Now to suggest to CGN that they may want to change the species name of CGN18108 in their database…

LATER: Just realized we started talking about all this quite a while ago.

February 18, 2014February 18, 2014

Credit where credit is due

You may have been following the reaction to the media frenzy about the announcement yesterday of a new way of making potatoes resistant to blight, cause of the Irish Famine a century and a half ago. I won’t add to the confusion, beyond saying that, as in everything in life, there are always alternatives, and wouldn’t it be nice if we gave them all a fair go?

No, what I want to talk about here is where the gene in question came from, the gene for blight resistance that was inserted into the popular British variety Desiree to such apparently good effect. We know from the paper that the gene is called Rpi-vnt1.1 and that it came from the potato wild relative Solanum venturii, but that’s all. I think that’s insufficient. There may be a reference in the paper or the supplementary material ¹ to the source of the Solanum venturii germplasm that was used in this work, but I was unable to find it. Apologies to the authors if I missed it, and thanks to whoever it was at the Sainsbury Lab that tweeted a response to my request for information:

@AgroBioDiverse @Cipotato Seed was from: http://t.co/XLC5Ud82mh

— The Sainsbury Laboratory (@TheSainsburyLab) February 17, 2014

It turns out that the germplasm was obtained from the Centre for Genetic Resources, the Netherlands, which has often been mentioned on this blog. Most recently, as coincidence would have it, yesterday, and on the subject of potatoes to boot. CGN is at the very forefront of genebank documentation, so it was very easy to find that there are 3 accessions of the species in question at CGN, that only one of those is resistant to blight, that it is CGN18000, that it was collected in 1972 in Argentina at an elevation of 3200m and that it came to CGN via the Institut fur Pflanzenbau und Pflanzenzuchtung Bundesforschungsanstalt, Braunschweig, Germany. There are more accessions out there (although apparently not at CIP, the International Potato Center, at least according to Genesys), and also herbarium specimens. Enough in fact to come up with an estimate of the overall geographic distribution of S. venturii, and perhaps identify some gaps.

Or am I wrong? It’s an informed guess. If there had been more than one accession with resistance, it would have been difficult to know which one was actually used in the paper. Anyway, I look forward to the day when even the authors of whizz-bang biotech papers will spend five minutes to do what I just did and properly acknowledge, perhaps even link to, the genebank, and the specific accession, whose existence ultimately allowed them to do their work.

February 17, 2014

Calling users of lettuce and potato genetic resources

An interesting announcement from our friends at CGN.

In the field of PGR documentation, we have seen, over the last decades, dramatic improvements: from card box files only mentioning the name of the variety and the location in the seed-storage, to internet accessible databases, sometimes with possibilities to order PGR on-line including click-wrap SMTA. However, the access to PGR information was always ‘supply driven’ saying: this is what we have, choose!

Here at CGN we have also been thinking about this, and decided that we might try to turn the situation towards a ‘demand driven’ PGR information access. Based on our experience interacting with users of our genebank, we have identified their first priorities where it concerns PGR: access to material and access to information, and on that basis experimented with creating web sites that could accommodate questions such as ‘where can I find a blue potato’, ‘where can I get material without having to sign a SMTA’, or ‘what has been done regarding the search for Bremia resistance in lettuce’. Some of such sites already exist, we wanted to find out if a genebank or the PGR conservation community would also be able.

We are proud to release two ‘PGR Crop Portals’ one aimed at potential users of lettuce germplasm, the other aimed at potential users of potato germplasm. These sites are not the same as the target audiences are neither, but, as you can see if you visit the sites, both ask frequently for feedback from the users, to add information, to share experiences.

This approach fits in a philosophy, where the data sources (genebanks) do the data collection and curation, whereas anyone can create an interface to the data (and thus the material) in these combined sources serving a specific target group. This target can be ‘lettuce breeders’ but also ‘anyone interested in crop wild relatives in the Balkan’, ‘the malting barley industry’ or ‘Dutch hobby gardeners interested in old vegetable varieties’. This approach requires (1) proper access to the PGR data, possibly via EURISCO or GeneSys, and (2) creators of interfaces who know their target audience very well and are willing to establish a communication link with this audience.

Please have a look at the site, and let us know what you think!

Finally, I would like to thank Rob van Treuren (lettuce), Roel Hoekstra (potato) and Frank Menting (both), for all their efforts to get the initiative to this stage, and express my hope that the user community will help to take it further.

A most welcome initiative, I think, finally moving beyond databases. Hard to fault the theory, let’s all see how the practice pans out. Leave comments here, or send them to Theo van Hintum at CGN.

February 17, 2014January 27, 2014

Brainfood: Value of Chiloé, Zimbabwe sorghum, Rosa karyotypes, PSM diversity, Pear diversity, Medic clines, Wild rices, Barley adaptation, Coffee agroforesty

Valuing cultural ecosystem services: Agricultural heritage in Chiloé island, southern Chile. Willingness to pay at US$50.5 per person per year, and not related to distance from site.
Assessments of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm. New sources of resistance (for the US) in even a moderately diverse collection.
Karyotype Analysis of Wild Rosa Species in Xinjiang, Northwestern China. It’s just amazing to me that people still do karyopypes.
Explaining intraspecific diversity in plant secondary metabolites in an ecological context. Trait variance in these things is considerable, partly genetic and can evolve, maybe even faster than mean trait values.
Identifying genetic diversity and a preliminary core collection of Pyrus pyrifolia cultivars by a genome-wide set of SSR markers. Close relationship between China and Japan, and Sichuan a bit of a nexus.
Genomic Signature of Adaptation to Climate in Medicago truncatula. Found genes associated with position along 3 environmental clines in a set of populations, then were able to predict performance of other populations based on genotype.
Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Yes, and from these particular places.
An efficient method of developing synthetic allopolyploid rice (Oryza spp.). Should make using those wild relatives a bit easier.
Can barley (Hordeum vulgare L. s.l.) adapt to fast climate changes? A controlled selection experiment. Maybe not. Not even the landrace.
Coffee landscapes as refugia for native woody biodiversity as forest loss continues in southwest Ethiopia. “Coffee farms could support a considerable portion, though not all, of the woody biodiversity of disappearing forests.” No word on what it does to the coffee, though.

February 14, 2014April 30, 2015

A plateful of Camargue Red Rice

How far back into the mists of time, do you suppose, have the French versions of the fabled gnarled rustics of Sicily been nurturing the equally fabled red rice of the Camargue? The question occurred to me as I walked past a shop window in Bonn recently, and saw this delectable display of various products of that region, including said rice. Well, it turns out that although rice has been grown in the Camargue for centuries, this particular, trendily healthy variety is of somewhat more recent vintage.

A chance cross between the wild rice and a short grain rice was discovered in 1983 by a René Griotto (died 1989.) He found it growing at the foot of the Montmajor Abbey. Development of the cross was pursued in conjunction with the French “Institut national de la recherche agronomique” (INRA.) They’d grow plants, select seed from certain plants, then grow those, till finally they settled on the plant breed known today as Camargue Red Rice.

Wild rice? What wild rice grows in France? I asked my go-to guy for everything Oryza:

Must be weedy rice introduced with a crop. France is way outside the known limits of distribution of wild rice. 100 years ago a red rice introgression would have been rigorously weeded out. In the 1980s Europeans were becoming aware of the health benefits of non-white food. I wonder if they actually thought red rice = anti-oxidants = anti-cancer, which is today’s mantra.

Here’s some more from an FAO publication on weed management:

The seeds of most weedy biotypes of O. sativa and O. glaberrima have a pigmented pericarp resulting from the presence of a variable content of different antocyanins, cathekins and cathekolic tannins (Baldi, 1971).

The red pigmentation is a dominant character and is controlled by more than one gene (Leitao et al. 1972; Wirjahardja et al. 1983)

The red layer of the weed grains harvested with the crop should be removed with an extra milling but this operation results in broken grains and grade reduction (Smith, 1981; Diarra et al. 1985a, 1985b).

Weedy biotypes of O. sativa have been differentiated into indica or japonica types, on the basis of the morphological and physiological traits, isozymes, RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and AFLP (Amplied Fragment Length Polymorphism) markers.

According to a study funded by the European Community, weeds collected in Mediterranean rice fields belonging to the japonica group and weeds from Brazil were close to the indica group (Ghesquière, 1999). In this study no specific allele of weeds were found which can serve as a diagnostic marker to easily determine the varietal origin of the weedy forms. Nevertheless, a great deal of evidence would seem to show that the primary origin of red rice can come from distant crosses between indica and japonica varieties.

Vaughan et al. (2001) pointed out that the several samples of weedy biotypes collected in the United States belong not only to the indica and japonica subspecies, but also to the O. rufipogon and O. nivara species.

Anyway, before you ask, I can’t find a reference to the red rice of the Camargue in any of the genebank databases that I know. It’s definitely not in IRRI. There’s no data at all on any rice collections in France on Eurisco, although other countries do have substantial collections of French rice, in particular Russia. WIEWS does list a number of important rice collections in France, but they seem to be international, with only some 9 samples from France itself. GRIN also has significant holdings of French rice, but nothing that I can see on Camargue Red Rice specifically, ² at least going by passport information. We know INRA have been having trouble with their grape collection. Do they even have a collection of local rices? Or are they relying on those gnarled Camargue rustics, and clever niche marketing to hip, health-conscious foodies of course, ³ to keep them going?