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.
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.
- 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.
- Impacts of Global Food Systems on Biodiversity and Water: The Vision of Two Reports and Future Aims. It’s all connected, and not in a good way.
- On‐Site Capabilities of a Mobile Laboratory for Aquatic Germplasm Cryopreservation. Not so easy for plants, alas.
- Biogeography and conservation status of the pineapple family (Bromeliaceae). The Atlantic Forest, the northern Andes and Central America.
- A review of types of risks in agriculture: What we know and what we need to know. Very few studies look beyond production risk, largely ignoring four other types of risk, and the prevalence of multiple risks.
- Visual and olfactory floral cues related to ambophilous pollination systems in Poaceae. Insects can facilitate pollination in some grasses.
- Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding. Women select on quality, men on agronomy.
- Phenotypic and physiological responses to salt exposure in Sorghum reveal diversity among domesticated landraces. Salinity tolerance was acquired early in domestication and then maintained or lost depending on prevalent soil conditions.
- Combining Focused Identification of Germplasm and Core Collection Strategies to Identify Genebank Accessions for Central European Soybean Breeding. Pre-core FIGS subset based on adaptation to high-latitude cold regions, followed by coring using genotype data: from >17,000 to 366 accessions.
- Adaptive introgression during environmental change can weaken reproductive isolation. Reverse speciation is upon us.
- The future of legume genetic data resources: Challenges, opportunities, and priorities. Centralize and standardise. Good luck with that.
- Application of Mixed Methods to Identify Small Ruminant Disease Priorities in Ethiopia. National disease controls programmes may be on the wrong track.
- Tartary buckwheat (Fagopyrum tataricum Gaertn.) landraces cultivated by Yi people in Liangshan, China. 13 landraces, but not very well differentiated as to use.
- The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley. More genes, more alleles in known genes.
- The endemic ‘sugar canes’ of Madagascar (Poaceae, Saccharinae: Lasiorhachis) are close relatives of sorghum. Closer than some actual Sorghum spp.
- Large genetic yield potential and genetic yield gap estimated for wheat in Europe. Long way to go to match the potential, modelled yield of ideotypes.
- A suite of global accessibility indicators. How long it takes to get from anywhere in the world to settlements of different size. Or took, in 2015.
- A method for computing hourly, historical, terrain‐corrected microclimate anywhere on Earth. Why you might want to move in the first place.
- Genetic strategies for improving crop yields. “Valuable genetic diversity for increasing crop resilience resides in cultivated landraces, heirloom varieties and the wild relatives of crops.”
- A low-cost aeroponic phenotyping system for storage root development: unravelling the below-ground secrets of cassava (Manihot esculenta). But sometimes you have to work hard to get at it: case in point.
- High SNP diversity in the non-toxic indigenous Jatropha curcas germplasm widens the potential of this upcoming major biofuel crop species. And here’s another.
- Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. In China and Pakistan anyway.
- Plant populations of three threatened species experience rapid evolution under ex situ cultivation. So don’t cultivate, store seeds instead. Or as well.
- Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. Polyploidy pre-adapts plants for domestication.
- Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria. Case in point.
- A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. The rhizosphere protects.
- Do selfing species have greater niche breadth? Support from ecological niche modeling. Yes indeed.
- Modelled distributions and conservation status of the wild relatives of chile peppers (Capsicum L.). 50% are high priority for conservation. No word on their mating systems.
- Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. From 893 to 100, in 4 geographical clusters.
- A taxonomic monograph of Ipomoea integrated across phylogenetic scales. A whole bunch of new species, and evidence that some 60 species independently developed storage roots before humans were even around. Yes, even sweetpotato.
- Supermarket food purchases and child nutrition in Kenya. Not a bad thing.