Information

February 10, 2015February 10, 2015

Livestock mapping comes of age

For your information, we have been beavering away since then, collecting more recent and detailed sub-national livestock statistics and disaggregating these using a slightly modified modelling approach, and 1 km multi-temporal, Fourier-processed MODIS imagery from the University of Oxford. We hope in time to produce global coverage for the most important livestock species, and make these publically available, but we have focussed our initial efforts on poultry and pigs in Asia.

That was Timothy Robinson in a comment on a post of ours back in 2012, and he’s been true to his word. There was a paper last year ¹, and there’s a wiki for the data.

pigs

I suggested in my earlier post that it was possible to get the impression that a lot of different players were working in parallel, if not in actual competition, on livestock distribution mapping. If that was indeed the case, and perhaps it was just an impression, it all seems to have been resolved in the intervening couple of years, thank goodness. According to the wiki:

In a multi-partner collaboration centered on the International Livestock Research Institute (ILRI), the Food and Agriculture Organization of the United Nations (FAO) and the Université Libre de Bruxelles (ULB-LUBIES), global maps of livestock distributions and production systems are being revised and updated.

Only fair to add that I landed on this via a blogpost on Vox, of all places, which has been getting quite a lot of attention on Twitter, for some reason. It seems to have escaped my early warning system last year.

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 10, 2015February 10, 2015

Nibbles: Avocado rising, Cynobiofuel, Ginseng in situ, MGIS, Strawberry breeding, Maca biopiracy, Certification

The avocado was once quinoa.
Cyanobacterium found in an algal collection at the University of Texas in Austin will save us all.
You need the cops on your side if you want to save American ginseng.
Banana genetic resources get a new website.
Peace breaks out in UC Davis strawberry dispute.
How did maca get from Junin to Yunnan?
Philippines may label biodiversity-friendly products.

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.