- Genetic Identity in Genebanks: Application of the SolCAP 12K SNP Array in Fingerprinting and Diversity Analysis in the Global In Trust Potato Collection. 11 mismatches between 250 original samples and their putative in vitro counterparts.
- Maize seed cryo-storage modifies chlorophyll, carotenoid, protein, aldehyde and phenolics levels during early stages of germination. But do the effects last?
- Sharing aquatic genetic resources across jurisdictions: playing ‘chicken’ in the sea. Fish resources need cooperative governance too.
- Imminent extinction in the wild of the world’s largest amphibian. Because it’s a luxury food, believe it or not.
- Community structure informs species geographic distributions. Include coexisting species in niche models for better results.
- Increasing plant diversity with border crops reduces insecticide use and increases crop yield in urban agriculture. Planting soybeans, maize and vegetables around rice was bad for pests and good for profits in Shanghai.
- Where are Europe’s last primary forests? Mountains, mainly.
- Seeds in space. Orbiting Svalbard, anyone?
- Resistance Genes in Global Crop Breeding Networks. Networks for cassava, potato, rice, and wheat “are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs.”
- Plant Mating Systems Often Vary Widely Among Populations. One estimate is never enough.
Nibbles: Phenotyping drones, Citrus history, Potato museum, Mango database, Florilege, Endicott Pear, Landrace booze, Neolithic Revolution, Easy mapping
- Breeding grass while high. Probably not what you’re thinking.
- When life gives you ancient lemons.
- Potato Museum gets new website.
- Mango gets a database.
- So do France’s genebanks.
- The oldest living cultivated fruit tree in North America? I think not, but interesting nevertheless.
- Whiskey goes heirloom.
- Excerpt from Spencer Wells’ Pandora’s Seed on the Neolithic Revolution.
- Our occasional contributor Robert Hijmans sings the praises of mapping with R.
Brainfood: Cassava breeding, Teosinte gaps, Arabidopsis and CC, Urban pineapple, Minnesota apples, European CWR, Spiderplant review, British condiments, Yeast diversity, Diversity & productivity
- Toward improving photosynthesis in cassava: Characterizing photosynthetic limitations in four current African cultivars. The landraces are better at photosynthesis than the improved cultivars. Maybe because the aim of producing the latter was pest and disease resistance rather than yield.
- Ecogeography of teosinte. Only 11% in protected areas.
- A map of climate change-driven natural selection in Arabidopsis thaliana. Summer is coming.
- Urban backyards as a new model of pineapple germplasm conservation. Two thirds of citizen scientists did a really good job.
- Identification of unknown apple (Malus × domestica) cultivars demonstrates the impact of local breeding program on cultivar diversity. 330 unknown highly diverse trees in northern Minnesota, 264 unique genotypes, 76 matched to 20 named cultivars from local breeding program at the University of Minnesota, or imported Russian cultivars.
- Development of national crop wild relative conservation strategies in European countries. 30 countries: 13 in preparation stage, 14 with drafts, and 3 not yet started.
- Current knowledge and breeding perspectives for the spider plant (Cleome gynandra L.): a potential for enhanced breeding of the plant in Africa. I actually like the bitterness of the leaves.
- Condiments before Claudius: new plant foods at the Late Iron Age oppidum at Silchester, UK. Benefits of a customs union, I guess.
- Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Genetics linked to lifestyle differences.
- Plant spectral diversity integrates functional and phylogenetic components of biodiversity and predicts ecosystem function. About 50% of variation in productivity in the Cedar Creek biodiversity experiment explained by spectral diversity.
Brainfood: Genebanks genomics, Improving forages, 3000 rices, Sweet potato dispersal, Diversity on farm double, Herbaria double, Phenotyping box, Invasives, Meta-meta-analysis, Rice domestication, Soil depth
- Role of genomics in promoting the utilization of plant genetic resources in genebanks. Genebanks don’t need to do genomics themselves to benefit from genomics.
- Improving the Yield and Nutritional Quality of Forage Crops. Case in point.
- Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Case in point. Multiple independent domestications. Tomorrow, the world.
- Sweet potato dispersal or human transport? Maybe no evidence one way or another after all. Rebuttal of: Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia. And the counter to the rebuttal. This genomics stuff not so easy after all.
- Review: Meta-analysis of the association between production diversity, diets, and nutrition in smallholder farm households. It’s not always there. But that would have been a high bar.
- Agricultural diversification as an important strategy for achieving food security in Africa. Case in point. More diverse households and farming systems are more food secure, but only up to a point, and it depends on various factors. 43% of African cropland will be difficult to diversify.
- Using herbaria to study global environmental change. Have been used to monitor the effects of climate change, habitat change, pollution and invasives on plants.
- Green Digitization: Online Botanical Collections Data Answering Real‐World Questions. Gotta get the stuff digitized first though.
- The ‘PhenoBox’, a flexible, automated, open‐source plant phenotyping solution. Somebody mention digitizing?
- Dissecting the null model for biological invasions: A meta-analysis of the propagule pressure effect. The success of aliens is down to their numbers. Wonder if it works for pest and disease organisms too.
- Are systematic reviews and meta-analyses still useful research? We are not sure. All righty then. Scrap the above.
- Shattering or not shattering: that is the question in domestication of rice (Oryza sativa L.). From one of the authors, Debarati Chakraborty: Loss of shattering through sh4 is not a crucial step for rice domestication. Genetics, cultural anthropology and archaeology suggests that primitive agrarians were dependent on wild or semi-domesticated shattering rice.
- Rooting for food security in Sub-Saharan Africa. Sub-Saharan Africa probably hasn’t the rootable soil depth for monster maize yields.
More on cassava germplasm from Brazil
You might remember a post from a couple of weeks back comparing the localities of cassava accessions in Genesys (mostly conserved at CIAT) with cultivation of the crop in Brazil. I ended that little piece with the observation that when data from the national genebank system of that country finally makes its way into Genesys, which should not be long now, it will be possible to really figure out where the gaps are in the “global” collection of the crop. Well, as it happens, there was a Tweet just recently which included a photo of a map of where Embrapa’s cassava accessions come from:
Embrapa has collected germplasm from throughout the Amazon region and has characterised this using 20,000 SNPs. Main disease problem is soft rot during heavy rains in this rainforest zone. Working on identifying pathogens & finding genes linked to resistance @IITA_CGIAR @embrapa pic.twitter.com/7go8eipUhn
— James Legg (@jamesplegg) April 28, 2018
So, quick as a flash, I imported it into Google Earth as an image overlay, and after much fiddling to make it fit on top of the background provided by GE (only partially successfully), was able to compare it with the accessions in Genesys:
The two sets of accessions (red for Embrapa, yellow for CIAT) look nicely complementary at a glance. Maybe the gaps in one collection are adequately covered by the other, and vice versa (which of course then brings up the issue of safety duplication, but that’s another post). Or maybe not: this is a really crude way of looking at the data. But it does point to the importance of data sharing and the need for collaboration among genebanks, national and international.