Genetic diversity

August 7, 2018August 8, 2018

A focus on West Africa

A paper just out on the domestication of pearl millet gives me the chance to acknowledge the terrific amount of work on domestication of West African crops going on in Yves Vigouroux‘s lab.

Yam: Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes.
African rice: The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. More here.
Pearl millet: A western Sahara centre of domestication inferred from pearl millet genomes.
Fonio: High selfing rate inferred for white fonio [Digitaria exilis (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs.

August 6, 2018August 6, 2018

Brainfood: Ecology of domestication, Citizen soybeans, Silkworm domestication, Barley spread, Indigenous management, Maize domestication, Temperate maize, Nutrient yields, Amazon history double, Women & diets, Online classification, Charred breadcrumbs, Wheat drought

Crop domestication: anthropogenic effects on insect–plant interactions in agroecosystems. Domestication can upset trophic webs. Poor dears.
The soybean experiment ‘1000 Gardens’: a case study of citizen science for research, education, and beyond. 2492 gardens, in fact.
The evolutionary road from wild moth to domestic silkworm. Domestication in China, followed by multiple independent spreads and differentiation.
Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes. 3 taxa, 8 genepools, multiple routes for spread. A bit like silkworm but in the opposite direction.
A spatial overview of the global importance of Indigenous lands for conservation. 40% of all terrestrial protected areas.
Maize domestication and gene interaction. More than just the headline 5 genes.
Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize. Need to go back to tropical germplasm for adaptation to temperate conditions.
Moving beyond calories and protein: Micronutrient assessment of UK diets and land use. Roots, tubers and vegetables are the most land-efficient producers of 23 nutrients.
The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon. It is still with us.
Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre. And not just in the east.
Does women’s time in domestic work and agriculture affect women’s and children’s dietary diversity? Evidence from Bangladesh, Nepal, Cambodia, Ghana, and Mozambique. Yes, but varies with socioeconomic status.
Remap: An online remote sensing application for land cover classification and monitoring. Use your training set to detect habitat type(s) in Google Earth.
Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan. Before domestication.
Drought tolerance during reproductive development is important for increasing wheat yield potential under climate change in Europe. The good news is that germplasm close to the optimized ideotype for 2050 is already out there.

July 31, 2018July 31, 2018

Nibbles: Carrot breeding, BIEN, Protected areas databases, Brazilian genebanks, Endangered coconut genebank, DSI, ABS, Climate pix, Botanical pix double, Potatoes galore, Pandanus language, Archaeological double, Palestinian seed saving

Putting the polyacetylene back into carrots.
The Botanical Information and Ecology Network gets an upgrade. Any CWRs among its 18,844,855 more observations?
And any is protected areas? This will tell how well they’re managed. Mash up with this spatial database on indigenous lands?
Otherwise, there are genebanks, though not enough in Brazil, apparently.
And not always safe.
What to do with Digital Sequence Information? Would be nice to be clear on what it is.
ABS broken down by ISF. And the CGIAR. Not DSI though.
Need climate visuals? Well, who doesn’t.
The Columbian Exchange has visuals also.
And the Royal Horticultural Society too.
Speaking of Columbian Exchange: frites. And Vavilov, chefs, etc.
Speaking about nuts in PNG. Comment by Jim Croft, who would know: “Except the species illustrated is the widespread oceanic strand species, Pandanus tectorius, not the endemic highland crop ‘karuka’, Pandanus julianettii.”
5000-year-old brewery in Egypt.
14,000-year-old bread.
Fast forward 14,000 years.

July 30, 2018July 30, 2018

Brainfood: Community forests, Pepper CWR, Banana spread, Blight plasticity, VIR wheat

Research frontiers in community forest management. Trends are for hybrid business models, REDD+ interactions and the use of secondary data.
Production of embryo rescued hybrids between the landrace “Friariello” (Capsicum annuum var. annuum) and C. baccatum var. pendulum: phenotypic and cytological characterization. Another crop wild relative enters the arena.
Earliest Musa banana from the late Quaternary sequence at Fahien Rock Shelter in Sri Lanka. People used wild bananas for 40,000 years before domesticated triplods arrived 6000 years ago.
Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen. “…17 genes are not expressed in one of the two…isolates despite apparent absence of sequence polymorphisms.”
Novel sources of resistance to Septoria nodorum blotch in the Vavilov wheat collection identified by genome-wide association studies. The collection that keeps on giving.

July 23, 2018July 11, 2018

Brainfood: African rice domestication, Barley evaluation, Al & sorghum, Potato seed systems, Yield trends, Arachis resynthesis, Potato breeding, Lupinus evolution, Helianthus invasiveness, Wild cassava, Beaked maize return, Amaranth breeding, Vegetables, American dogs

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Domesticated in northern Mali as a result of the decline of wild species due to the drying of the Sahara.
Unlocking historical phenotypic data from an ex situ collection to enhance the informed utilization of genetic resources of barley (Hordeum sp.). Don’t throw away that historical data from regenerations.
Exploiting sorghum genetic diversity for enhanced aluminum tolerance: Allele mining based on the AltSB locus. It’s more prevalent in guinea sorghums.
Unearthing unevenness of potato seed networks in the high Andes: a comparison of distinct cultivar groups and farmer types following seasons with and without acute stress. Potatoes are not just potatoes. And farmers are not just farmers.
Global patterns of crop yield stability under additional nutrient and water inputs. Higher variability in yield expected under higher fertilizer inputs.
Segmental allopolyploidy in action: Increasing diversity through polyploid hybridization and homoeologous recombination. Domesticating peanuts, the right way this time.
Applications of New Breeding Technologies for Potato Improvement. Humble no more?
Pleistocene glacial cycles drive isolation, gene flow and speciation in the high‐elevation Andes. In Lupinus, phylogeny does not recapitulate orogeny.
Evolution of invasiveness by genetic accommodation. In a crop wild relative, no less.
Manihot takape sp. nov. (Euphorbiaceae), a new tuberous subshrub from the Paraguayan Chaco. A crop wild relative too.
Back to beaked: Zea mays subsp. mays Rostrata Group in northern Italy, refugia and revival of open-pollinated maize landraces in an intensive cropping system. Title of the week. Alternative: Polenta Power.
From zero to hero: the past, present and future of grain amaranth breeding. Runner up.
Issues and Prospects for the Sustainable Use and Conservation of Cultivated Vegetable Diversity for More Nutrition-Sensitive Agriculture. Still neglected.
The evolutionary history of dogs in the Americas. They came over from Siberia with people, rather than evolving from local wolves, but all that’s left of them is a cancer.