- Enhancing the functioning of farm animal gene banks in Europe: results of the IMAGE project. Lots going on, but avian species in particular need more work.
- Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking. Over 1,000,000 samples from over 55,000 animals, representing 165 livestock and poultry breeds, collected over 60 years, more than 50% of rare breeds.
- Cryoconservation of Animal Genetic Resources in Europe and Two African Countries: A Gap Analysis. Out of the 2949 breeds registered in DAD-IS, 16% have material in genebanks, but only 4% have enough to allow breed reconstitution.
- Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. How we got to the above.
- Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.). 13 out of 16 taxa need in situ and ex situ work.
- Wild potato Genetic Reserves in Protected Areas: prospection notes from Los Cardones National Park, Salta, Argentina. Nice combination of in situ and ex situ.
- Agricultural intensification was associated with crop diversification in India (1947-2014). But only at country level, and not by much. At district level, crop diversity went down in rice/wheat areas and up in the south and west as oilseeds and vegetables replaced millet and sorghum. Doesn’t strike me as positive overall, diversity-wise.
- From population to production: 50 years of scientific literature on how to feed the world. Time for a bit of holism.
- Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time. 5 ecogeographic clusters, 4 related heading time groups.
- Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America. Domestication of northerly migrating wildish material in Mexico rather than 2-step domestication in S America and then Mexico.
- Enset‐based agricultural systems in Ethiopia: A systematic review of production trends, agronomy, processing and the wider food security applications of a neglected banana relative. Better data needed, for a start.
- Worldwide Genetic Resources of Duckweed: Stock Collections. 36 species, no less. Need more?
- Realizing hybrids between the cultivated peanut (Arachis hypogaea L.) and its distantly related wild species using in situ embryo rescue technique. You need to apply growth substances to the pollinated flowers.
- The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E. Genetics controls shape, environment size.
- Adaptation and development pathways for different types of farmers. Watch your context, and don’t forget governance.
- Golden Rice and technology adoption theory: A study of seed choice dynamics among rice growers in the Philippines. They forgot context. And governance. But let the author spell it out in a tweet thread.
Brainfood: Bean diversity treble, Edited tomatoes, Breeding strategies, Pseudocereals, American lost crops, Genotyping collections, Apple diversity, Rice domestication, Cotton domestication, Wheat & gluten, Rubus phylogeny, Cassava brown streak, Prices & migration, Edible caterpillars
- Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline. There’s a fairly straightforward way to select for larger beans as a key component of yield.
- Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity? Not as much as it could be.
- Diversity, use and production of farmers’ varieties of common bean (Phaseolus vulgaris L., Fabaceae) in southwestern and northeastern Ethiopia. There are more varieties per household in places where the overall number of varieties per community was lower.
- Rapid customization of Solanaceae fruit crops for urban agriculture. Gene editing for shorter tomatoes.
- The home field advantage of modern plant breeding. Public breeding programs should go for specialist varieties that perform reliably in narrow environments.
- Thinking Outside of the Cereal Box: Breeding Underutilized (Pseudo)Cereals for Improved Human Nutrition. The next quinoa awaits its 15 minutes.
- Experimental Cultivation of Eastern North America’s Lost Crops: Insights into Agricultural Practice and Yield Potential. There’s life in the old crops yet. And that’s before gene editing.
- Time for a paradigm shift in the use of plant genetic resources. Genotype everything.
- Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. 3 early modern cultivars had a disproportionate impact on modern apples.
- Machine Learning Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication. The indica and japonica sub-species have exchanged a lot of genetic material at different times, and you get different answers to the question of domestication depending on which bits you look at.
- Genetic Analysis of the Transition from Wild to Domesticated Cotton (G. hirsutum L.). There are fibre quality genes in the subgenome from the parent with unspinnable fibre. Go figure.
- A Comparative Study of Modern and Heirloom Wheat on Indicators of Gastrointestinal Health. Not much difference.
- Target Capture Sequencing Unravels Rubus Evolution. The taxonomy needs work. You don’t say.
- Expansion of the cassava brown streak pandemic in Uganda revealed by annual field survey data for 2004 to 2017. The history of a disease outbreak in excruciating detail.
- Crop prices and the individual decision to migrate. Decrease in the price of coffee in Vietnam (but not rice, which is mainly used for household consumption rather than export) resulted in increased chance of migration, but only for individuals of lower education.
- The contribution of ‘chitoumou’, the edible caterpillar Cirina butyrospermi, to the food security of smallholder farmers in southwestern Burkina Faso. It’s significant, but only during the caterpillar season. I guess they don’t keep. I spot an opportunity. Yeah, you guessed it, gene editing.
Visualizing broccoli
Zachary Stansell, who seems like a very interesting guy, had the top post on all of Reddit late last year with — wait for it — a picture of broccoli diversity. And rightly so. It is beautiful.
The coloured bars? They are based on ~10K SNPs, with varieties that share a given colour sharing more of these markers, and being more closely related genetically.
Tomato diversity did what?
I hope Jeremy won’t mind me copying here his take on tomato diversity from the last Eat This Newsletter of 2019. There’s interesting stuff there on coffee and wheat too, so wander over, and subscribe.
It is a truth universally acknowledged, that the modern crop is genetically less diverse than its predecessors. Universally acknowledged perhaps, but in at least one case, not a truth.
Dutch greenhouse tomatoes have been a poster-child for the loss of genetic diversity, the result of breeding for bumper production and good looks, rather than flavour or resilience. In the late 1980s, especially, German newspapers described them as Wasserbomben. Exports of these water bombs to Germany, previously their main destination, collapsed, and Dutch breeders began to pay attention. Their efforts are recognised in a new analysis of seven decades worth of tomato varieties, with a large jump in genetic diversity from the 1990s to the 2000s. An earlier jump, from the 1960s to the 1970s, reflects an effort to breed better disease resistance into existing varieties.
These genetic changes have been accompanied by changes much easier to recognise in the supermarket and on the plate. In the 1950s and 1960s, you would be hard pressed to buy a tomato that weighed less than 50 gm or more than 100 gm. Modern cherry tomatoes and big beefsteak types are newcomers to industrial greenhouses. Flavour profiles too, have changed, with tomatoes becoming both more flavourful and more diverse in their flavour profiles.
Of course, it is still possible to buy a water bomb if you try, but the key conclusion of this study is that tomato genetic diversity has seen “a nine-fold increase since the 1960s”. That’s not to say that things couldn’t be better. Other studies have shown that people generally consider heirloom tomatoes – pre-1950 and not subjected to focussed industrial-style breeding – tastier than modern varieties. Good though recent Dutch breeders have been, they could yet do better.
Brainfood: Food access, Rare species, Italian landraces, Forest status, CC & production, Myanmar nutrition, Super-pangenome, Plant pest priorities, Peanut resistance, Maize coring, EAT-Lancet costs, Sorghum tannins double, Dutch cattle core
- Food Access Deficiencies in Sub-saharan Africa: Prevalence and Implications for Agricultural Interventions. Income doesn’t necessarily translate into better nutrition, but keeping livestock does. Happy New Year.
- The commonness of rarity: Global and future distribution of rarity across land plants. Rare species are especially vulnerable to climate and land use change.
- Exploring on-farm agro-biodiversity: a study case of vegetable landraces from Puglia region (Italy). High vegetable landrace diversity may be linked to poor soils and distance from urban centres.
- Measuring Forest Biodiversity Status and Changes Globally. Combines biodiversity significance and intactness, and comes up with not that many places.
- Escaping the perfect storm of simultaneous climate change impacts on agriculture and marine fisheries. Business as usual means 90% of world’s population will see declines in both agricultural and fisheries production.
- Potential for smart food products in rural Myanmar: use of millets and pigeonpea to fill the nutrition gap. 2 weeks of inclusion had positive effect on wasting, stunting and underweight.
- Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement. Add up species pangenomes for a whole genepool. Would be cool to grow it.
- Plant Pest Impact Metric System (PPIMS): Framework and guidelines for a common set of metrics to classify and prioritise plant pests. Host crop value, market access, feasibility of management and reversibility are the most important ones.
- A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea). You have to cross it with another wild relative first.
- The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections. Different approaches to making cores tested with maize data from Seeds of Discovery.
- Affordability of the EAT–Lancet reference diet: a global analysis. US$2.84 per day, or more than household per capita income for at least 1.58 billion people.
- Allelochemicals targeted to balance competing selections in African agroecosystems. Levels of tannins in sorghum correlated with taste receptor variant in humans and presence of sparrows.
- Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population. Chilling tolerance associated with low tannin and short stature. No word on the role of sparrows.
- Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds. Almost optimized, at least for bulls.