Genebanks

February 11, 2015June 3, 2021

What does it cost to conserve crop diversity in Europe?

There’s a document on the NordGen website entitled Towards a European Plant Germplasm System — The third way ¹ which advocates setting up a “European Plant Germplasm System” along the lines of the US National Plant Germplasm System. Written by Lothar Frese, Anna Palmé, Lorenz Bülow and Chris Kik — all from big European genebanks — the paper “builds on the results of the PGR Secure project funded under the EU Seventh Framework Programme.”

This is what the European system would look like:

What, no Svalbard? Even the NPGS uses that. Also, there are separate germplasm committees for each crop in the US, rather than one committee to rule them all. That makes more sense if the idea is to have input from the users, as in the US; but maybe that’s not it, as in the diagram the committee is not linked to the users. So what is it for? Anyway, how much would this all cost?

As a rule of thumb, the ex situ conservation including related research costs approximately 60 € / accession and year (personal communication of Dr. U. Lohwasser of 23 May, 2014 and Dr. P. Bretting of 22 May 2014). 1,725,315 accessions are kept in European genebanks resulting in an assumed total annual costs for ex situ conservation of 103,518,900 € per year for the whole of Europe. In view of the 34 billion € spent for agri-environmental measures within the EU-28 a budget of 100 million € / year is not unreasonable. The question rather is whether the stakeholder groups and policy makers feel that having a European Plant Germplasm System is worth this amount.

Well, let’s fact-check that. The operating budget for the NPGS is $44,600,000 per year, for 569,000 accessions, which is about $78 per accession, or about €70 at today’s exchange rate. That’s probably a conservative estimate, I’m reliably informed, as the NPGS gets a lot of in-kind support from the universities with which it cooperates — but it’s the right ballpark anyway. The international genebanks of the CGIAR get around $20 million a year to maintain and make available their ca. 700,000 accessions, which seems very cheap, but includes very little of those “related research costs.”

What we don’t know — or at least I don’t — is what European countries are actually spending on their genebanks at the moment. It seems maybe the authors don’t know either, because another of the 12 recommendations they make, besides establishing the system, is to inventory the money available. Here are all the recommendations, conveniently filleted out for you. Look at number 6:

1. We suggest the establishment of a European Plant Germplasm System.
2. Establish a legal basis for conservation of plant genetic resources for food and agriculture in the EU.
3. Establishment of a technical EU infrastructure for the organisation of conservation of plant genetic resources for food and agriculture measures.
4. Establishment of an EU information infrastructure for conservation of plant genetic resources for food and agriculture.
5. Disentangle juridically and financially genebank tasks from plant breeding research and plant breeding tasks at the national level.
6. Inventory of financial means available to genebanks and estimation of financial means needed for a fully functioning European network of genetic resource collections (ex situ, in situ and on-farm).
7. Increase the visibility of plant genetic resources collections on the internet.
8. Develop a European platform for long-term crop specific pre-breeding programmes.
9. Clear uncertainties concerning Access and Benefit Sharing (ABS) rules so that breeding companies can take economic decisions on a safe legal basis.
10. Research should be strengthened to better understand the amount and geographic distribution of genetic diversity present in priority crop gene pools.
11. The European agro-NGOs and their influence should be strengthened.
12. Establishment of a European Network of Private-Public-Partnership programmes for evaluation of plant genetic resources in Europe.

My own recommendation would be to start with that inventory of financial means. It would be nice to know how close to that €100 million we in fact are — and how much of it, if any, would need to be new money.

February 11, 2015February 11, 2015

Nibbles: Old breweries, Old grape seeds, New beer, Sheep breeds, Indian rice landraces, GM rice in China, Barley breeding, Botanical tipple, Mata Atlantica conservation, Quinoa

There are some really old breweries out there.
And some really old grape seeds in Sardinia.
The beauty of hops. New and old.
Some very photogenic old sheep breeds in the Lake District.
Someone has discovered some old salt-tolerant rice landraces. Also medicinal and aromatic rices. Well I never.
Meanwhile, at the other end of the rainbow, the Chinese dip a toe into gourmet GM rice.
Brit boffins breed flood-proof barley.
Botanical gin. Two of my favourite things, combined.
Saving the Pau Brasil is, well, complicated. But what else was it going to be?
Yet another roundup of the pros and cons of quinoa.

February 10, 2015February 10, 2015

New version of banana genebank information system goes live

Great to see a new version of the Musa Germplasm Information System (MGIS) released. The URL is unchanged. The key improvements are listed as follows (slightly edited):

1. All information on a single accession can be viewed in one page
2. Taxonomic content of each collection is summarized graphically.
3. Easier data filtering and export functions.
4. Users can share comments on any accession.
5. Accessions can be requested online via the Musa Online Requesting system (MORS) with a modified interface.

I particularly like the ability to comment, though you do have to register for that. The data cover 2,281 accessions from six genebanks around the world, ² including 1,456 in the International Transit Centre (ITC) managed by Bioversity International in Belgium:

The ITC data are also in Genesys, which shows 1,529 accessions rather than 1,456. I assume MGIS is the more up to date, but I’m unclear why there should be a difference. ³

You can search among the 2,281 accessions on name or number; or by filtering by any combination of genebank, species, subspecies, genome group (AAB, say), subgroup (Cavendish, say), country of origin, ploidy, whether there’s a photo, whether it’s been included in a molecular study, and availability. Searching is pretty fast.

Each accession gets a nice page summarizing all the pertinent information.

Screen Shot 2015-02-10 at 9.33.10 AM

That information can include morphological characterization data, and illustrations, as you can see above, but I could not find a way of searching the database based on a particular descriptor or combination of descriptors. You get a map when collecting locality is known, but you can’t map multiple accessions, as far as I could see. You’d have to do that in Genesys, I guess.

If you want to download data, you have to cut and paste accession numbers into a form on another page, and then you get a CSV or XLS. It didn’t look to me like you could export either morphological characterization data or molecular data. I have to say I was disappointed by the whole export thing.

So, some good things, some not so good things in this new version of MGIS. I’ll be keeping an eye on it for further developments. And continue playing with it, of course. Maybe I missed something.

February 9, 2015February 9, 2015

Brainfood: Cassava descriptors, Core collections, Oat breeding, Indigenous fruits, Sandalwood in Fiji, Eggplant diversity treble, Globally important mushrooms, High amylose rice, Chickpea diversity, Finger millet diversity, Lethal yellowing, Spanish peppers, Local potato experts

Selection of the most informative morphoagronomic descriptors for cassava germplasm. From 51 to 32. Hardly seems worth it. And dropping descriptors can be dangerous.
Advances in core collection of plant germplasm resources. In Chinese, alas, but it sounds intriguing.
Trends in breeding oat for nutritional grain quality – An overview. You want high β-glucan, and you can get it by breeding for high yield, luckily. A. atlantica has high β-glucan.
Indigenous Fruit Trees of Tropical Africa: Status, Opportunity for Development and Biodiversity Management. Need for “exploiting the under-tapped treasuries of IFT.” Still? People have been saying that for years. They’ve even designated agroforestry systems as globally important and everything.
Promoting Santalum yasi Seeman (Sandalwood or yasi) in agroforestry systems to reverse agrodeforestation in Fiji. An attempt to introduce a high value species into a threatened agroforestry system. Not just fruit, then.
Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: Implications for conservation. Quite a lot of geneflow.
The potential for crop to wild hybridization in eggplant (Solanum melongena; Solanaceae) in southern India. Transgenes from the crop could spread to the wild relative.
Variation in Antioxidant Activity and Flavonoid Aglycones in Eggplant (Solanum melongena L.) Germplasm. So, the leaves are good for you. But I suspect they taste like crap.
The Qingyuan Mushroom Culture System as Agricultural Heritage. Would pay money to see that.
Selecting High Amylose Rice Germplasm Combined with NIR Spectroscopy at the RDA Genebank Conserved. From 9481 to 14 with high amylose and decent agronomy. But why bother?
Field response of chickpea (Cicer arietinum L.) to high temperature. There are some heat tolerant lines in the ICRISAT genebank.
Genetic diversity in East African finger millet (Eleusine coracana (L.) Gaertn) landraces based on SSR markers and some qualitative traits. The diversity is high, mainly within countries, and missing from the ICRISAT minicore. Naughty.
Analyses based on the 16S rRNA and secA genes identify a new phytoplasma subgroup associated with a lethal yellowing-type disease of coconut in Côte d’Ivoire. The international genebank is threatened.
New Insights into Capsicum spp Relatedness and the Diversification Process of Capsicum annuum in Spain. Limited genetic diversity has differentiated in Spain into pungent, elongated peppers in the South and Center, and sweet, blocky and triangular types in the North.
Knowing native potatoes: finding local experts through innovative methods in the Peruvian Andes. Community Biodiversity Register methodology applied to potato landraces. Don’t see anything much new here, but good to have it nicely documented.

February 8, 2015February 7, 2015

Nibbles: Biltong, Coco de mer, PGRFA course, Poplar genebank, IRRI genebank, African agriculture, Hybrid chickens, American food

Professor wants to copyright the name biltong, should be forced to eat nothing else until he takes it back.
Getting to the bottom of coco de mer.
PGRFA course at Wageningen. Expensive, but worth it, and you can apply for a NFP/MENA Fellowship, check on the course overview PDF.
The IRRI genebank manager has seen the future of genebanks: “…we need to work on building the system to estimate breeding value from genotype, and then we will be able to feed more detailed knowledge to the breeders.” He probably means DivSeek. Now IRRI really need to get a different stock image of him and his genebank.
The UK now has a National Black Poplar Clone Bank. Not quite as big as the above.
A different take on Bill’s Big Bet. And more along the same lines.
Hybrid Kuroiler chickens a big hit in Uganda. Bill may be onto something after all.
“As American as apple pie” is just the beginning. I want to see Kuroilers at KFC.