Agricultural Biodiversity Weblog – Page 130 – Agrobiodiversity is crops, livestock, foodways, microbes, pollinators, wild relatives …

May 6, 2019May 6, 2019

The very political genetics of wheat

A massive EU study looked into the DNA of 487 different kinds of wheat, including wild relatives, close domesticated cousins, old landraces, old cultivars and modern elite varieties. All bread wheat falls into one of three separate clusters. There is a founder population that represents primitive landraces originating in the Fertile Crescent and modern varieties that came about as part of the green revolution. It includes older varieties from Western Europe. A separate cluster contains varieties from Eastern European countries, developed after about 1955 during the cold war. The third cluster contains mostly varieties developed after about 1985 that mix DNA from the founder population and the Warsaw Pact cluster, reflecting a greater exchange among breeders after 1989.

There’s more, especially for wheat nerds such as myself.

The nerd in question is Jeremy, and his further thoughts are on his newsletter. I have his permission to reproduce the piece in full here, but I suggest you subscribe to the newsletter, it’s always full of interesting food-related stuff.

For one, Asian and European cultivars are much less similar than one might expect. Farmers in the two regions, while pursuing the same overall goal of greater productivity, seem to have done so by selecting different genetic targets for their work. Breeders now have more specific information about the stretches of DNA that they might want to target as they go about creating new varieties that can cope with changing climates.

Overall, the current picture of the evolution of wheat remains the same – complex – albeit with stronger support for some of the putative pathways. Personally, that’s a great relief. It means I don’t have to scrap any of the episodes of Our Daily Bread devoted to the evolution of wheat.

The original research paper Tracing the ancestry of modern bread wheats is behind a paywall, a scandal for taxpayer-funded research, but that’s another story. I suspect that anyone who needs more detail will have access, but if you just want more details, drop me a note.

You can also leave a comment below.

May 6, 2019May 7, 2019

Brainfood: Thlaspi domestication, WDPA, PA benefits, Oil palm benefits, Stunting, Production synchronicity, Bean nutrients, Caprine domestication, Roots of tuber eating, Cassava shovelomics, Intensification, Extinction prediction, Pistachio genome

Progress toward the identification and stacking of crucial domestication traits in pennycress. Thank goodness it’s closely related to Arabidopsis.
Sixty years of tracking conservation progress using the World Database on Protected Areas. Will increasingly expand to informally protected ares and link to other databases.
Evaluating the impacts of protected areas on human well-being across the developing world. Pretty positive impacts for communities living near protected areas, with some tourism.
Does oil palm agriculture help alleviate poverty? A multidimensional counterfactual assessment of oil palm development in Indonesia. Not in remote, mainly subsistence villages. So I guess that means the best outcomes come from oil palm plantations near protected areas?
Perspective: What Does Stunting Really Mean? A Critical Review of the Evidence. Not as much as some think, but not nothing.
Synchronized failure of global crop production. Lower production synchrony within crops, but higher among crops, meaning calorie production very vulnerable to climate change.
Comparative analysis of perennial and annual Phaseolus seed nutrient concentrations. Ca, Cu, Fe, Mg, Mn, and P higher in wild annuals.
Urine salts elucidate Early Neolithic animal management at Aşıklı Höyük, Turkey. May show the transition from hunting caprines to keeping them penned up about 10,000 years ago outside the Fertile Crescent.
Cooked starchy food in hearths ca. 120 kya and 65 kya (MIS 5e and MIS 4) from Klasies River Cave, South Africa. Earliest evidence of parenchyma as food, apparently.
Phenotypic variation of cassava root traits and their responses to drought. Phancy phenotyping.
Conventional land‐use intensification reduces species richness and increases production: A global meta‐analysis. Especially in mid-intensity systems, but in low- and high-intensity systems you can get closer to win-wins.
Projecting impacts of global climate and land‐use scenarios on plant biodiversity using compositional‐turnover modelling. All the intensification in the world is not going to help if climate change isn’t curbed.
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Salinity tolerance related to jasmonic acid synthesis pathway.

April 29, 2019April 11, 2019

Brainfood: Grazing behaviour, XW, Swedish Neolithic, Apple genome impact, Mango diversity, Blueberry quality, Durum genome, Ancient sorghum, Nordic rye, Tomato flavour, Diets & health, CGIAR & ITPGRFA

An inexpensive and open‐source method to study large terrestrial animal diet and behaviour using time‐lapse video and GPS. GoPro used to figure out what species grazing cows eat throughout the year. Could be useful to gauge forage value of different plants.
The risk posed by Xanthomonas wilt disease of banana: Mapping of disease hotspots, fronts and vulnerable landscapes. Northern Mozambique and central lowland DR Congo are the gateways. Extension is the key.
Maritime Hunter-Gatherers Adopt Cultivation at the Farming Extreme of Northern Europe 5000 Years Ago. Migrating farmers drew the line at Sweden.
Apple whole genome sequences: recent advances and new prospects. Great insights into domestication and diversity of collections. Next step: genomic prediction.
Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method. The collection at the USDA Subtropical Horticulture Research Station could be half the size.
Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Including candidate genes for fruit quality.
Durum wheat genome highlights past domestication signatures and future improvement targets. Mutation for high cadmium accumulation common in domesticated material, but a variant allowing better growth in zinc-deficient soils and less accumulation available in wild populations.
A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Genomes from archaeological specimens suggest that decrease in diversity over time in sorghum was not due to an initial one-off domestication bottleneck, but rather to repeated sequential founding episodes. Doesn’t seem like much of a difference to me.
Population genetic structure in Fennoscandian landrace rye (Secale cereale L.) spanning 350 years. Just one big happy, old family.
Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Breeders could breed for flavour. But will they?
Health effects of dietary risks in 195 countries, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. People should eat more of the above grains and fruits.
CGIAR Operations under the Plant Treaty Framework. Non-monetary benefits are not to be sneezed at, but all too often are.

April 22, 2019April 3, 2019

Brainfood: GI, Collection representativeness, Miracle tree, Brave new world, Wheat roots, Dry beans, Seedling roots, Ecotourism, Citrus evolution, Mango evolution, Aboriginal translocation, Carrot cores, Potato breeding

Impact of Geographical Indication schemes on traditional knowledge in changing agricultural landscapes: An empirical analysis from Japan. GI encouraged sharing of traditional knowledge.
Genetic diversity in British populations of Taxus baccata L.: Is the seedbank collection representative of the genetic variation in the wild? Yes, though marginal populations could be collected more.
The miracle mix of Moringa: Status of Moringa research and development in Malawi. Needs breeding.
New plant breeding technologies for food security. Genome editing, basically. Meet the new boss…
Evolutionary agroecology: Trends in root architecture during wheat breeding. In China, wheat breeding has involved unconscious group selection for simpler, less branched, deeper roots in higher-yielding modern varieties.
Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.). Deeper-rooted, and more drought-tolerant, wild beans are found in dry regions.
Seedling traits predict drought-induced mortality linked to diversity loss. Species with longer seedling roots survive drought better.
Is ecotourism a panacea? Political ecology perspectives from the Sundarban Biosphere Reserve, India. Well, what do you think?
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. Citrus evolution in one beautiful diagram. I just wish I could remember the details from one day to the next.
Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication. Two genepools, and no bottleneck. No cool diagram though.
Aboriginal Translocations: The Intentional Propagation and Dispersal of Plants in Aboriginal Australia. More than just replanting tubers after harvest, although plenty of that.
Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection. It’s a numbers game.
Potato Breeding by Many Hands? Measuring the Germplasm Exchange Based on a Cultivated Potatoes Database. Most use of varieties in breeding is within countries.

April 15, 2019March 29, 2019

Brainfood: Green Revolution, Pear diversity, Spider plant, Mexican maize erosion, Wheat yield, Salty carrots, Salinity tolerance, Diversification, Ancient farmers, Genebank training, Grapevine diversity, Dietary diversity, Wild chickpeas, Hulless barley

From Green Revolution to Green Evolution: A Critique of the Political Myth of Averted Famine. Did not avert famine, but it was still important.
Comparative transcriptomic analysis provides insight into the domestication and improvement of pear (P. pyrifolia) fruit. Much diversity was lost during domestication, but some was gained during improvement, though in different parts of the genome.
Association between vitamin content, plant morphology and geographical origin in a worldwide collection of the orphan crop Gynandropsis gynandra (Cleomaceae). It’s the E and S African stuff you want.
The abandonment of maize landraces over the last 50 years in Morelos, Mexico: a tracing study using a multi-level perspective. Don’t blame the youth.
Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential. Landraces and synthetics can be used to increase yield potential.
Variation for Salinity Tolerance During Seed Germination in Diverse Carrot [Daucus carota (L.)] Germplasm. 4 cultivated accessions from Turkey out of 273 were best, and the wilds were no good, for a change.
Salt stress under the scalpel – dissecting the genetics of salt tolerance. Need to break it down into its component parts. See above for an example, I guess.
Ecological-economic trade-offs of Diversified Farming Systems – A review. Need to take the long view.
Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Until the next one comes along.
Training in Plant Genetic Resources Management: A Way Forward. I hope so.
Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. “The network of the domesticated grapevine cultivars is an indication of a highly complicated breeding history of European domesticated grapevines that started thousands of years ago.”
The Minimum Dietary Diversity for Women of Reproductive Age (MDD-W) Indicator Is Related to Household Food Insecurity and Farm Production Diversity: Evidence from Rural Mali. Women from food insecure households less likely to reach MDD-W.
Novel sources of resistance to root-lesion nematode (Pratylenchus thornei) in a new collection of wild Cicer species (C. reticulatum and C. echinospermum) to improve resistance in cultivated chickpea C. arietinum. Goon news for hummus.
Determining factors for the diversity of hulless barley agroecosystem in the Himalaya region — A case study from Northwest Yunnan, China. Religion helps.