My off-the cuff take on Episode 5 of Down to Earth with Zac Efron, featuring our hero’s visit to the CIP genebank.
A Genesys use case for the weekend
I figured today I’d tweet about a cool new feature of Genesys, the online portal to genebank accessions. And I did, but then I thought I should really put it on here too. So here goes.
The use case I’ll consider today is:
I have an accession I like, and I know where it was collected. Show me all other accessions anywhere in the world that come from a roughly similar climate.
Here’s what you do. Hang on to your butts.
When you have selected the accession you like in Genesys, go to Map, and look for this on the far left.
Click on Show Climate…
Then click on your accession on the map. You’ll get a summary description of the climate at that point.
If you then click on List Accessions (bottom left hand corner), you’ll get a list of all accessions from places which are roughly comparable in climate to that of the accession which you clicked. I can explain how that’s calculated separately if people are interested.
Or, you can choose one of those bioclimatic variables listed, decide on some max and min values, go to Filter Accessions on the left of the map, and insert your chosen values in the appropriate place on the menu that should appear (scroll down).
Click on Apply Filters at the top of the menu, and there’s a list of accessions again, this time from places with climates within your chosen limits.
Let me know in comments if you have any questions, or indeed ideas for improvement.
Here’s a PDF of the Twitter thread.
Visualizing the use of crop diversity
A couple of nice infographics for you today. Here’s one on forage genetic resources conservation and use, courtesy of the CGIAR Research Programme on Livestock. Click on the numbers to see the interactive elements.
And here, from Euroseeds, is an explanation of how gene editing could save beloved beloved grape varieties from fungal pests without (hopefully) changing their taste or wine-making features. This one is not interactive, though, so download the PDF to see it properly.
And yes, attentive readers will have noticed that both were included in Nibbles yesterday, but I thought they deserved re-upping, as the cool kids say.
Zac imagines a world without potatoes
If you’ve got Netflix and half an hour, you might want to watch episode 5 of Down to Earth with Zac Efron, in which our hero visits the genebank of the International Potato Centre in Lima, Peru.
Brainfood: Sled dogs, Chicken origins, Ancient livestock, Tenure and deforestation, Buckwheat, Soybean pangenome, Yam bean nutrients, Orphan legumes, Wild seeds, SeedGerm, Coconut conservation
- Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Sled dogs arose in Siberia, where they interbred with wolves.
- 863 genomes reveal the origin and domestication of chicken. It was Gallus gallus spadiceus from southwestern China, northern Thailand and Myanmar that was domesticated, possibly by rice and millet cultivators, according to Dorian Fuller, who disagrees with the domestication dates but likes the rest of the paper.
- Fodder for Change: Animals, Urbanisation, and Socio-Economic Transformation in Protohistoric Italy. In first-millennium BCE Italy, pigs grew in importance, cattle increased in size, sheep breeds differentiated according to use, and the chickens was adopted and adapted.
- Formalizing land rights can reduce forest loss: Experimental evidence from Benin. Randomized control trial shows land registration is associated with less deforestation.
- Buckwheat (Fagopyrum sp.) genetic resources: What can they contribute towards nutritional security of changing world? Not much until given the full -omics treatment, apparently.
- Pan-Genome of Wild and Cultivated Soybeans. The pan-genome is the new genome. Wait, did I use that before?
- Developing the role of legumes in West Africa under climate change. Lesser know, orphan legumes could step in for cowpea in some places, if only we knew more about them. Like a pan-genome, I guess.
- Evaluation of Nutritional and Antinutritional Properties of African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms.) Seeds. But we do know more about them! Lots of variation available to combat protein malnutrition, if only farmers grew more of the stuff. Oh so now it’s their fault?
- Conserving orthodox seeds of globally threatened plants ex situ in the Millennium Seed Bank, Royal Botanic Gardens, Kew, UK: the status of seed collections. Some decline in germinability for about 16% of samples. Includes successful germination protocols for 165 globally threatened seed plant taxa.
- SeedGerm: a cost‐effective phenotyping platform for automated seed imaging and machine‐learning based phenotypic analysis of crop seed germination. Fancy kit and maths can match seed specialists in scoring radicle emergence. But will it work with wild seeds? MSB unavailable for comment.
- In Situ and Ex Situ Conservation of Coconut Genetic Resources. Beyond coconut-only genebanks. I’d like to see SeedGerm work on this lot. Check out the whole book.