Agricultural Biodiversity Weblog

December 6, 2019December 6, 2019

The world’s largest sorghum genebanks

USDA … Plant Genetic Resources Conservation Unit located in Griffin, Ga., is home to over 100,000 accessions of preserved plant germplasm including the largest collection of sorghum germplasm in the world.

Well that’s the kind of statement that I just have to fact-check. It’s a little difficult to be entirely sure, Genebank Database Hell being what it is, but I think perhaps the ICRISAT genebank edges it. At least if you go by what’s in Genesys. IND002 is ICRISAT, USA016 the USDA Griffin genebank.

But, of course, it’s not just about the numbers. Only 20% or so of the accessions are geo-referenced, but mapping what data there is does suggest that there are interesting complementarities between the two collections (ICRISAT in red, USDA in blue — click on the map to see it better).

Anyway, do read the rest of the article in Seed World, there’s interesting stuff in there, and what’s a couple thousand sorghum accessions between friends anyway.

December 6, 2019December 6, 2019

Deconstructing crop TED

TED-Ed has a bunch of videos on the history of different crops: cacao, tea, and maize for a start. They’re cute, and do provide some interesting information. But a pinch of salt is recommended with your corn on the cob.

December 4, 2019December 4, 2019

Yes, we have plenty of banana information, take 2

A new version of the Musa Germplasm Information System (MGIS) is out. There’s more data, tools for better curation, a way to search for accessions cited in the literature, and re-organized menus. Do check it out. MGIS data eventually makes its way to Genesys.

And since I’m here, it’s worth noting that the banana is uniquely well-endowed with information resources. In addition to MGIS, there’s a whole slew of other databases and assorted information products, thanks to the wonder that is ProMusa.

ProMusa is a network of people promoting scientific discussions on bananas.

In alliance with the International Society for Horticultural Science (ISHS), the network organizes scientific symposia (reported in proceedings) to help its members stay up-to-date on the latest research developments and encourage collaborations within and between disciplines.

When not meeting face-to-face, ProMusa members stay in touch using the network’s mailing list.

This website is the network’s online platform, which offers news, knowledge and information on bananas.

The centrepiece is Musapedia, “an online, collaboratively built compendium of knowledge on bananas.” But there are also databases of scientific literature, images and contacts. And an excellent news area — InfoMus@.

You can follow — and interact with — ProMusa on Facebook and Twitter. I can’t think of a crop that has anything similarly comprehensive. It really should be your first port of call for anything to do with bananas.

Gabe Sachter-Smith laid out in a spiral a sample of the more than 100 types of bananas documented during the collecting mission to West New Britain, PNG. They include the ever mysterious Fe'i banana, photographed next to its possible ancestor, Musa maclayi. pic.twitter.com/HahIXm1P4K

— ProMusa (@promusa_banana) October 11, 2019

BTW, the title of this post refers to a previous foray into banana information resources.

December 3, 2019December 4, 2019

Old vines in a new catalogue

Who doesn’t love old trees? I, for one, could read about them for days. And, alas, have occasionally done so. Especially if they are cultivated species. The internet is full of old, attractively gnarled olive trees, for example. Old grapevines, not so much. There was recently that piece in The Economist about recreating Leonardo’s vineyard, but that’s not quite the same thing.

So it was a pleasant surprise to come across the Old Vines Register, curated by wine expert Jancis Robinson. Turns out there are some 400-year-old vines out there. Which I’d really like to see some day.

Anyway, since I’m talking grapes, I might as well highlight the work of the Vitis Working Group of the European Cooperative Programme for Plant Genetic Resources (ECPGR). Note in particular their “On-farm inventory of minor grape varieties in the European Vitis Database.” There must be some pretty old vines among those.

As for genebanks, there are 16,000 accessions of cultivated Vitis out there (plus 2,400 wild relatives), according to Genesys, though only about 1,900 are geo-referenced (see map below). Genesys, remember, brings data from ECPGR’s European genebank database, Eurisco, together with that from genebanks in other parts of the world. There is also a separate European Vitis Database, though I’m not sure of the exact overlap with Eurisco.

What of the future? Well, we’re probably going to need all that diversity given what climate change is already doing to the crop. A recent Twitter thread by Dr Sarah Taber analyzed the depiction of vineyards in an episode of Star Trek: The Next Generation set in the year 2367. We’ll just have to see if her decidedly critical view of twenty-fourth century management practices is borne out in the forthcoming series, which does seem to feature, at least according to the trailer, somewhat better kept, though not particularly old-looking, vines. No word yet on what varieties the Picards grew, and will grow.

https://www.youtube.com/watch?v=Ishyf14_yx0

December 2, 2019December 2, 2019

Brainfood: Cassava diversity, Landrace diversity double, Soybean oil quality, Cucurbit domestication, Carrot colours, Pharaonic emmer, Teosinte RILs, Chinese pigs, Brazilian apples, Teosinte diversity, Forests & diets, Forest productivity, Agricultural productivity

A global overview of cassava genetic diversity. The African germplasm is different from the Latin American, but not by that much.
Genetic variability in landraces populations and the risk to lose genetic variation. The example of landrace ‘Kyperounda’ and its implications for ex situ conservation. Better genetically to conserve landraces as sub-lines. But financially?
Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs. Above goes for pigs too.
Selection and Molecular Characterization of Soybeans with High Oleic Acid from Plant Germplasm of Genebank. 3 accessions have interesting variants in the relevant gene.
Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology. Lots of different paths to domestication, but all involve loss of flesh bitterness, one way or another.
Changing Carrot Color: Insertions in DcMYB7 Alter the Regulation of Anthocyanin Biosynthesis and Modification. How the carrot lost its purple.
A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Most closely resembles modern material from Turkey, Oman and India.
TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize. With added teosinte goodness.
Adaptive phenotypic divergence in an annual grass differs across biotic contexts. The rhizosphere affects adaptation of teosinte along an altitudinal gradient. We’ll need a Nested Association Mapping Population for that too now, no doubt.
Population genetics assessment model reveals priority protection of genetic resources in native pig breeds in China. Most breeds have low diversity; Tibetan pigs are an exception.
A brief history of the forty-five years of the E’AppleBP apple breeding program in Brazil. 27 new varieties seems like pretty good going.
Testing the Various Pathways Linking Forest Cover to Dietary Diversity in Tropical Landscapes. Sometimes there’s a direct pathway (e.g., consumption of forest food), sometimes an income pathway (income from forest products used to purchase food from markets), and sometimes an agroecological pathway (forests and trees sustaining farm production). And sometimes there isn’t.
Evolutionary diversity is associated with wood productivity in Amazonian forests. “…greater phylogenetic diversity translates into higher levels of ecosystem function.” No word on its effect on diets.
Anatomy and resilience of the global production ecosystem. Plenty of words on its effect on diets.