Agricultural Biodiversity Weblog

June 24, 2019

CGIAR gets its data together

GARDIAN, the Global Agricultural Research Data Innovation & Acceleration Network, is the CGIAR flagship data harvester. GARDIAN enables the discovery of publications and datasets from the thirty-odd institutional publications and data repositories across all CGIAR Centers to enable value addition and innovation via data reuse.

Among the goodies that GARDIAN harvests are two geo-referenced datasets: genebank accession localities from Genesys and 2005 crop production, harvested area and yield. I’ve often advocated here for the mashing up of these datasets. Here, for example, is irrigated harvested area (grey-black) and genebanks accessions (dark green) for rice in part of Asia.

The colour scheme needs work, I guess, but it’s a start.

There are also about 250 documents featuring the word “genebank” for you to explore.

GARDIAN is a product of the CGIAR Platform for Big Data in Agriculture.

June 24, 2019June 24, 2019

Brainfood: Macadamia domestication, Middle Eastern wheat, ART virus, Open science, Red Queen, Food system change, Chinese Neolithic booze, Dough rings, Making maps, Biofortification, Endophytes, African maize, Switchgrass diversity, Ancestral legume

Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing. One tree is the basis of the industry.
The Israeli Palestinian wheat landraces collection: restoration and characterization of lost genetic diversity. Bringing it all back home.
Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae). There’s always something…
Plant health emergencies demand open science: Tackling a cereal killer on the run. …but openness will get us through it.
Rapid evolution in plant–microbe interactions – a molecular genomics perspective. Until the next one.
Understanding food systems drivers: A critical review of the literature. Spoiler alert: urbanization, raise in consumer income, population growth, attention paid to diet & health issues, technological innovations, intensification and homogenization of the agricultural sector, increase in frequency and intensity of extreme events, general degradation in soils and agro-ecological conditions, improved access to infrastructure and information, trade policies and other processes influencing trade expansion, internationalization of private investments, concerns for food safety. I guess diversity is in there somewhere.
The origins of specialized pottery and diverse alcohol fermentation techniques in Early Neolithic China. So good, they invented fermentation twice.
The Hoard of the Rings. “Odd” annular bread-like objects as a case study for cereal-product diversity at the Late Bronze Age hillfort site of Stillfried (Lower Austria). Unbaked, tarallini-like dried wheat/barley dough rings may have been used ritualistically. No, not like that.
EviAtlas: a tool for visualising evidence synthesis databases. Everybody likes a map.
Editorial: Improving the Nutritional Content and Quality of Crops: Promises, Achievements, and Future Challenges. A review of reviews of biofortification, and more.
Fungal endophyte diversity from tropical forage grass Brachiaria. 38 fungi isolated from 9 Brachiaria species, but unclear if any are beneficial.
Characteristics of maize cultivars in Africa: How modern are they and how many do smallholder farmers grow? Out of 500 samples in 13 countries, about half were in some way improved, covering about half of the surveyed planted area.
QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. You can combine alleles which are locally advantageous in different places to get a
super-biofuel.
Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. The wild ancestor of peanut, pigeonpea, soybean, beans, mungbean, chickpea, lotus and medics was closest to wild peanuts. Maybe they can synthesize it?

June 21, 2019June 21, 2019

Europeans working on European crop working groups

‪The European crop conservation network — ECPGR — has a couple of new crop working groups, on maize and on berries. All the working groups have very informative pages on the ECPGR website, including details of all members and a mailing list, a link to relevant germplasm, and meeting and project reports. Worth exploring, if you’re interested in those crops. Start with berries.

A reminder that you can explore data from the European genebank network on the Eurisco website, and also mashed up with genebanks from other parts of the world on Genesys. As an example, here’s the Eurisco Ribes data on Genesys. Unclick the “EURISCO” tab to see what’s available in genebanks outside Europe.

LATER: Oh, and by the way, European genebanks have also started to review each other. The CGIAR genebanks have also all been reviewed by external experts in the past few years.

June 17, 2019June 25, 2019

Brainfood: Seed viability double, Forest reserves, Biodiversity value, Hunter-gatherers, Seed concentration, Past CC, Hot lablab, Mungbean adoption, Climate smart impacts, Tree threats, Chicken domestication, Top sorghum, Ancient wines, Plant extinctions

Variation in seed longevity among diverse Indica rice varieties. 8 major loci associated with seed longevity.
Seeds and the Art of Genome Maintenance. Viability is about the DNA repair response. Snap.
Are Mayan community forest reserves effective in fulfilling people’s needs and preserving tree species? Sure they are.
The power of argument. People don’t respond to utilitarian arguments when it comes to biodiversity. In the Netherlands.
Do modern hunter-gatherers live in marginal habitats? Nope. What can I tell ya?
New evidence on concentration in seed markets. Not as bad as some people think.
Climate change has likely already affected global food production. From 2003 to 2008, there’s been a ~1% average reduction in consumable food calories in barley, cassava, maize, oil palm, rapeseed, rice, sorghum, soybean, sugarcane and wheat.
Selection of Heat Tolerant Lablab. 6 out of 44 accessions from the WorldVeg genebank are heat tolerant. Seems a lot.
Counting the beans: quantifying the adoption of improved mungbean varieties in South Asia and Myanmar. 1.2 million farmers reached by WorldVeg varieties. Lablab next?
Climate smart agricultural practices and gender differentiated nutrition outcome: An empirical evidence from Ethiopia. They work, but they’re better in combination.
Pests and diseases of trees in Africa: A growing continental emergency. Into Africa…
Genetics of adaptation in modern chicken. Not much of a domestication bottleneck; that came later.
Multi-Trait Diverse Germplasm Sources from Mini Core Collection for Sorghum Improvement. From 40,000 in the genebank, to 242 in the mini-core, to 6 really cool ones (from Yemen, USA, China, Mozambique, and India x2 if you must know).
Palaeogenomic insights into the origins of French grapevine diversity. Ancient DNA from 28 pips dating back to the Iron Age provides pretty good matches to grapes grown today.
Global dataset shows geography and life form predict modern plant extinction and rediscovery. Almost 600 plants went extinct in modern times, at least, and I count about 20 crop wild relatives among them.

June 14, 2019June 14, 2019

Extinct CWR mapped

Following yesterday’s promise, here are extinct crop wild relatives mapped. Your job is to match dots to names.