GIS – Page 46 – Agricultural Biodiversity Weblog

June 8, 2017June 8, 2017

Some new germplasm databases, at least to me

Long-time readers may remember a post from 2012 summarizing some media reports of trouble at the Italian national genebank at the National Research Council (CNR), Bari. But maybe things are not as bad as were made out at the time. Or have got better.

I’ve just come across what seems to be a fairly new website for the genebank and it doesn’t give the impression of crisis. It lists 57,568 accessions from 184 genera and 834 species, which is more that was reported back in 1999 in WIEWS for ITA004, hopefully the correct code for the genebank in question (at least the address matches, if not the name of the institute). This is the geographic coverage of the collection:

Impressive. Unfortunately, data on these accessions are not available in the European genebank database, Eurisco, and therefore they’re not in the global portal, Genesys, either. Hopefully that’s being rectified.

Since I’m on the subject of germplasm databases, I’ve also recently come across the Legume Information System, which focuses on material in the US genebanks. It has all kinds of data, but I just looked for germplasm from Italy to compare with what’s in Bari. Here’s the map for Medicago spp, showing growth habit in different colours (click on it to see it better).

Compare and contrast with the ITA004 collection for the same species.

Which is why it’s a good idea to have all these data together in one place, i.e. Genesys.

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 5, 2017June 5, 2017

Who moved my rice?

In reply to our plea for a definitive crop distribution dataset, Andy Nelson, who used to work at IRRI and is now at the University of Twente, had this to say in a comment.

Well, this may be one way to go.

Compiling the best expert information with subnational statistics as a first cut and then using that to guide further detailed mapping with remote sensing/big data.

I’d like to see more efforts in crowdsourcing for crop mapping as well.

“This” is “RiceAtlas, a spatial database of global rice calendars and production.” ((Laborte, A. G. et al. RiceAtlas, a spatial database of global rice calendars and production. Sci. Data 4:170074 doi: 10.1038/sdata.2017.74 (2017).))

Because of the need to develop a spatially explicit global database of rice calendars that includes detailed information on rice areas with more than one rice crop in a year, we compiled the most detailed available datasets of rice planting and harvesting dates by growing season in all rice-producing countries, and linked the database to subnational production data. ‘RiceAtlas’ provides a spatial and seasonal distribution of the world’s rice production. RiceAtlas contributes to the GEOGLAM (Group on Earth Observations Global Agricultural Monitoring) initiative and regional partnerships, such as the Asian Rice Crop Estimation and Monitoring initiative (Asia-RiCE), by providing information for agricultural monitoring requirements, satellite data acquisition plans, and global crop outlook.

Here’s what it looks like.

With regards to crowdsourcing, there are various initiatives out there that could be relevant, including Geo-Wiki‘s Field Size Campaign.

Anyway, no doubt the RiceAtlas will eventually end up on the website of the CGIAR’s Consortium for Spatial Information. One bit of this, the SRTM 90m Digital Elevation Data, made a recent list of Top 15 Free GIS Data Sources.

May 17, 2017March 4, 2018

Mapping crops: Are we there yet?

I ran across a bunch of nice crop maps on the internet ((Though there are some strange things about a couple of them. Check out the shea one, for example.)), so I made a GIF for you (click on it to get it cycling).

You’re welcome.

I’m reliably informed the source is Monfreda et al. (2008). You can download the data in multiple formats, but I don’t think I’ve ever seen the headline maps displayed all together as The Decolonial Atlas has done, albeit without attribution, which is naughty.

Anyway, people have obviously taken the trouble to download and play around with the data. For example, they have been ably mashed up by Bioversity to get a global crop diversity map.

Which, in turn, it is instructive to compare with the one from the Lancet Planetary Health map we blogged about a few days ago.

But which dataset to use to do this kind of stuff? Monfreda’s is only one of many.

I see that we now, after a long wait, have WordClim 2, thanks to the work of our friend Robert Hijmans and his colleagues. ((Not to mention climate surfaces going back 20,000 years.)) Is it too much to hope for that he’ll now turn his hand to producing the definitive crop distribution dataset? ((Yes, we’ve blogged about this before. More than once.)) Maybe something for the CGIAR’s Big Data Platform, just launched, to think about organizing, convening, and/or inspiring.

May 8, 2017May 8, 2017

Brainfood: Cannabis roundup, Citrus genomes, Mapping Africa, Maize diversity, Qat diversity, Language diversity, Apple taste, Coconut diversity, Napier grass review, Rangeland management, Chinese goats, Arabica evaluation, Bangladeshi chickens, Seed endophytes

Cannabis Domestication, Breeding History, Present-day Genetic Diversity, and Future Prospects. The weed is in trouble, man. Just one of the papers in a very special issue of Critical Reviews in Plant Sciences. And for a historical perspective…
Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Apomixis is down to a “miniature inverted-repeat transposable element insertion in the promoter region of CitRWP.”
Automated cropland mapping of continental Africa using Google Earth Engine cloud computing. Croplands increased by 1 Mha/yr between 2003 and 2014.
Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. Three groups: Mexico + southern S. America, lowland Mesoamerica + Caribbean, Andes.
Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation. Centres of origin in Kenya and Ethiopia, with limited movement between the two, but some hybrids in N. Kenya; the Yemeni stuff came from Ethiopia.
Process-based modelling shows how climate and demography shape language diversity. If you assume human groups split after reaching a certain population size, and rainfall limits population density, you can predict language diversity in Australia.
Volatile Compound Profiles of Malus baccata and Malus prunifolia Wild Apple Fruit. Look at the esters.
Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers. I can’t see much new here. Please, coconut experts, tell me what I’m missing.
Opportunities for Napier Grass (Pennisetum purpureum) Improvement Using Molecular Genetics. Could do better.
Heterogeneity as the Basis for Rangeland Management. Gotta mix it up.
Analysis of genetic diversity of Chinese dairy goats via microsatellite markers. The locally developed breeds are all derived from a single European breed.
Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.). You can’t use morphology to predict taste.
Breeding for the improvement of indigenous chickens of Bangladesh: evaluation of performance of first generation of indigenous chicken. I don’t understand this much, but I liked the names of the genotypes: Naked Neck, Hilly and Non-descript Desi.
Persistence of endophytic fungi in cultivars of Lolium perenne grown from seeds stored for 22 years. It’s a record!