Brainfood: Agroecology, Bioinformatics, Brazilian cassava, Cypriot wine, Swiss poppies, Pollinators, Groundnut breeding, Sorghum pangenome, Crop origins, Sparing vs sharing, Language diversity, Watermelon origins
- Crop origins explain variation in global agricultural relevance. What explains which crops are most important globally? For seeds, an origin in seasonally dry regions. For root, leaf and herbaceous fruit crops, an origin in the aseasonal tropics. But if you account for all that, basically age.
- Linguistic diversity and conservation opportunities at UNESCO World Heritage Sites in Africa. There’s a correlation between linguistic and biological diversity. Has anyone done crop diversity and languages?
- Sparing or sharing land? Views from agricultural scientists. If you look at synergies between nature and nurture (as it were), and beyond crop yield, you realize it’s the wrong question.
- Can agroecology improve food security and nutrition? A review. Yes, in 78% of 55 cases. But will it scale? And does it need to? Anyway, at least it’s looking beyond yield.
- Global effects of land-use intensity on local pollinator biodiversity. Intensification is bad for pollinator biodiversity for most land uses, but cropland intensification is only bad in the tropics. Can’t help thinking this needs to be mashed up with the above.
- Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. In particular, integrating the phenomics and genomics of landraces and wild relatives at the extremes of habitable ranges. Well, there’s a lot more to it than that, but this is what stuck with me.
- Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. 54% duplicates out of 3354 clones, the remaining 1536 arranged in 5 ecoregional ancestral groups.
- A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Not from southern Africa after all. Nice bit of work.
- Preliminary investigation of potent thiols in Cypriot wines made from indigenous grape varieties Xynisteri, Maratheftiko and Giannoudhi. Cypriot grapes are more drought tolerant than varieties grown in Australia, but produce the tastes Aussie wine drinkers really like.
- A morphometric approach to track opium poppy domestication. Fancy math says Swiss Neolithic farmers were involved in the domestication of the opium poppy. Enough to drive one to drink.
- Registration of GA-BatSten1 and GA-MagSten1, two induced allotetraploids derived from peanut wild relatives with superior resistance to leaf spots, rust, and root-knot nematode. Sequencing paying off.
- Extensive variation within the pan-genome of cultivated and wild sorghum. Sorghum next?
Nibbles: Small farms, DivSeek, Wheat gene atlas, Tannin synthesis, Pest/diseases, Food/feed, Korean vault
- Small farms are not just beautiful. Yes, the original paper was in Brainfood back in March, but this website seems to be new.
- DivSeek has a new strategic plan to “improve the generation and sharing of information about global plant genetic resources”: accelerate, add value, educate. Small farms unavailable for comment.
- Speaking of sharing information on global PGR, we need to do that for wheat genes, wheat gene scientists say.
- Probably for tannins too, come to think of it.
- FAO says climate change will make pests and diseases worse.
- FAO also says that livestock are not as bad as many people think.
- The sincerest for of flattery on display in South Korea.
The making of GapAnalysis.R
A big thank you to Colin Khoury, Julian Ramirez, Chrystian Sosa, and Dan Carver for this guest post, reminding us of the history of conservation gap analysis work at CIAT and other CGIAR centres during the past decade and more.
Maps have helped people find their way for at least 2500 years, so it’s no surprise that geographic methods have been part of the portfolio of tools used to try to understand patterns and distributions of crop diversity, and, more recently, crop genetic erosion, ever since these topics began to garner the interest of scientists and conservationists. Innovations in digital mapping tools, made possible by developments in computer processing and the internet, have enabled continual leaps in the power and efficiency of such methods throughout the past few decades.
CGIAR embraced geographic information system (GIS) research tools about as soon as they were developed. At the International Center for Tropical Agriculture (CIAT), the International Potato Center (CIP), the International Plant Genetic Resources Institute (IPGRI, now Bioversity International), and the International Rice Research Institute (IRRI), among others, scientists began to apply available GIS tools to genetic resources conservation, and then develop their own suite of methods, programs, and datasets, often in collaboration with national partners and academics (e.g. wild potatoes, peanuts, chile pepper, and peanut/potato/cowpea, as well as climate data). Some of these developments, such as FloraMap and DIVA-GIS (and more recently CAPFITOGEN, by other researchers), have been aimed at making these tools easier to use by those in genetic resources community without extensive GIS experience: an important effort toward greater accessibility, even if it has met with mixed success.
By the 2000s, crop wild relatives were gaining attention as important genetic resources for crop breeding, and would soon be specifically targeted for conservation both by the Convention on Biological Diversity (CBD’s Aichi Target 13), and the Sustainable Development Goals (SDG Target 2.5). It was increasingly important, therefore, that conservation research tools were applied to these useful wild plants, and fortunate that the groundwork for GIS applications had already been laid by a decade or so of research. Through the second phase of a cross-CGIAR initiative called the Global Public Goods Project 2 (GPG2), run from 2007-2010, the distributions of the wild relatives of ten CGIAR mandate crops were mapped, with priorities for further collecting for ex situ conservation identified.
Liveseed mixing it up with genebanks
We’ve Nibbled Liveseed before, but I think it’s time for a little bit more. It’s an EU-funded Horizon 2020 project with the objective “…to improve transparency and competitiveness of the organic seed and breeding sector and encourage greater use of organic seed.”
Though the main focus is breeding, there is also some work on cultivar mixtures, which is actually what prompted this post. Because a nice poster by Emma Flipon (ITAB) and Véronique Chable (INRAE) has just been made available on “How to create diversified variety mixtures based on gene bank resources.”
Always great to see different ways of using genebanks, including ones that don’t necessarily include breeding.