Information

June 8, 2017June 8, 2017

Getting to grips with rice in Europe

A little more on that RiceAtlas that I blogged about a couple of days ago. I managed to download the shapefile of rice growing areas, and open it in Google Earth. I then imported the Genesys rice dataset, and zoomed in on Europe. Here’s what those two things together look like.

Definitely a few issues. I’m not too worried about the accessions in northern Europe. Those are probably just wrong passport data. But what about all those in Turkey which are also outside putative rice growing areas? Are those passport data mistakes too, or is RiceAtlas missing something?

June 6, 2017June 6, 2017

Seed banking resources

Did not realize that BGCI have a very useful Seed Conservation Hub on their website where they have collated resources and provided training modules on the basics of seed banking (in 4 languages).

June 6, 2017June 6, 2017

Unique digital identifiers everywhere

A recent letter in Nature:

Members of the Consortium of European Taxonomic Facilities have adopted a consistent citation system for an estimated 20 million biological and geological specimens from European collections. We encourage researchers, publishers and other institutions to engage with this initiative by citing the full specimen identifier in their publications and data sets. These specimens provide reference material for research on evolution, genetics, mineralogy, ecology and taxonomy — hence the need for a reliable identification system for citation (see A. Güntsch et al. Database 1, bax003; 2017). Our system assigns a unique and permanent Uniform Resource Identifier (URI) to each specimen. It follows Linked Open Data principles (see www.w3.org/tr/ld-bp) by including a redirection facility to human- and machine readable representations of the specimen. It also gives credit to the collectors and custodians. For example, the alpine plant specimen Leptinella scariosa Cass., held by the Royal Botanic Garden in Edinburgh, UK, and collected in Chile by Charles Darwin in 1834, is referred to by the URI http://data.rbge.org.uk/ herb/E00070244.

Quentin Groom, Botanic Garden Meise, Belgium.
Roger Hyam, Royal Botanic Garden Edinburgh, UK.
Anton Güntsch, Botanic Garden and Botanical Museum, Berlin, Germany.

Genebanks are doing something very similar.

June 5, 2017June 5, 2017

Brainfood: CWR prioritization, CWR data, Yam core redux, Traditional landscape value, African rice domestication, Digital conservation, First farmers, Revived breed, Mitigation targets, Zoonoses, Population, JEB on legumes

Broadening the Base, Narrowing the Task: Prioritizing Crop Wild Relative Taxa for Conservation Action. Use socioeconomic value of crop, and potential usefulness and threat status of relative.
Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives. Useful in determining the second of the above.
Re-defining the yam (Dioscorea spp.) core collection using morphological traits. Cleaning up the core.
“Things are different now”: Farmer perceptions of cultural ecosystem services of traditional rice landscapes in Vietnam and the Philippines. 73 indicators for the contribution of landscapes to culture, aesthetics, and local knowledge.
A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. You want no shattering? You also get smaller seeds. Like it or edit it.
Digital conservation: An introduction. Brave new world… Special issue of Ambio.
The Genomic History Of Southeastern Europe. Souther Greek Neolithic farmers not same as other European Neolithic farmers.
Genomics of a revived breed: Case study of the Belgian campine cattle. Racial impurities are confined to a few farms.
Reducing emissions from agriculture to meet the 2 °C target. We’re doomed.
Conservation of biodiversity as a strategy for improving human health and well-being. By keeping animals and their nasty diseases away from people, we’re not talking communing with Nature here.
The interaction of human population, food production, and biodiversity protection. Minimise the interaction.
Nature’s pulse power: legumes, food security and climate change. Special issue of Journal of Experimental Botany on legumes. Eat up your beans!

May 29, 2017May 18, 2017

Brainfood: Iron beans, Citrus evolution, Ethiopian co-ops, Farmer evaluation app, Exotic breeding, Cost of doing business, Plummy, Italian pears, Chinese cowpea, Breadfruit phylogeny, Seed collecting

Iron beans in Rwanda: crop development and delivery experience. 800,000 households, discontinuation rate 11%. But the health outcomes? Too early, I guess.
Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. It’s so VERY complicated.
Seed producer cooperatives in the Ethiopian seed sector and their role in seed supply improvement: A review. Sitting between the formal and informal seed systems, they “play a key role in meeting seed demand and contribute greatly to seed supply improvement through high-volume production of seed, crop, and variety diversification, and seed delivery to farmers.”
Gamification of farmer-participatory priority setting in plant breeding: Design and validation of “AgroDuos”. Based on pairwise ranking. I remember doing it by hand, but it’s nice to have the app. And there’s more.
Emerging Avenues for Utilization of Exotic Germplasm. It comes down to the collections being better characterized and understood.
Genetic resource policies in international collaborative research for food and agriculture: A study of USAID-funded innovation labs. Transaction costs are rising. Well, yeah.
Plums: A Brief Introduction. Will keep you regular.
Characterization and phylogenetic analysis of ancient Italian landraces of pear. Some synonyms found, some unknown things identified. All very worthy.
Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. The Chinese stuff is different to the African stuff.
Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae). Yeah but how many can you eat?
Effective seed harvesting strategies for the ex situ genetic diversity conservation of rare tropical tree populations. “…fewer seeds from each of a larger number of trees, … from peripheral subdivided regions of the population.”