Domestication

July 10, 2018

African rice roundup

It struck me that our friends at AfricaRice genebank and their partners have been particularly busy genotyping and phenotyping these past couple of years, so here’s a quick roundup of recent papers on the crop for easy reference.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes
Genetic control of seed shattering during African rice domestication
A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication
Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq
Domestication history and geographical adaptation inferred from a SNP map of African rice
Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity
Screening African Rice (Oryza glaberrima) for Tolerance to Abiotic Stresses: II. Lowland Drought

And I’m sure I’m missed a few, these are just the ones that we have included in Brainfoods…

There’s also this more popular piece on African rice in the New World.

July 2, 2018July 13, 2018

Brainfood: Italian hotspots, Spanish apples, ICRISAT proso, Scattered trees, Underutilized Malaysian fruit, Saudi chickens, AnGR, Double dates, European threatened plants, Pepper origins, Intensification outcomes, Breeding & diversity, Cold storage, African rice

A methodological approach to identify agro-biodiversity hotspots for priority in situ conservation of plant genetic resources. Interestingly, the centre of Italy comes out on top.
Genetic diversity and core collection of Malus × domestica in northwestern Spain, Portugal and the Canary Islands by SSRs. There is material in common between Galicia and the Canary Islands.
Diversity and trait-specific sources for productivity and nutritional traits in the global proso millet (Panicum miliaceum L.) germplasm collection. Out of 200, 26 were high in at least 2 nutrients.
The importance of scattered trees for biodiversity conservation: A global meta‐analysis. It’s pretty high.
Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae). The germplasm collections are not too bad, at least for the cultivated form.
Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers. The 6 breeds are diverse and show no inbreeding. Yet.
Conservation of breeds and maintenance of biodiversity: justification and methodology for the conservation of Animal Genetic Resources. Ah, so that’s why they did the above.
What are palm groves of Phoenix? Conservation of Phoenix palm groves in the European Union. Feral can still be useful.
Date Palm Agrobiodiversity (Phoenix dactylifera L.) in Siwa Oasis, Egypt: Combining Ethnography, Morphometry, and Genetics. Some locally recognized and named types are in fact collections of genetically distinct clones that somehow go together anyway: call them “ethnovarieties” if you wish. But not feral.
How to meet the 2020 GSPC target 8 in Europe: priority-setting for seed banking of native threatened plants. 62.7% of European threatened species are already in genebanks, but the others won’t collect themselves. No word on what to do about dates.
Evolutionary history of the chili pepper Capsicum baccatum L. (Solanaceae): domestication in South America and natural diversification in the Seasonally Dry Tropical Forests. Probably originated in Bolivian Amazonia and inter-Andean valleys.
Social-ecological outcomes of agricultural intensification. Win-wins are like hen’s teeth.
Plant breeding and diversity: A troubled relationship? There may be another bottleneck coming.
Rapid loss of seed viability in ex situ conserved wheat and barley at 4°C as compared to −20°C storage. 4°C is not cold enough for long-term conservation.
Genetic control of seed shattering during African rice domestication. Multiple genes lead to a range of non-shattering phenotypes.

June 25, 2018June 25, 2018

Brainfood: Rationalizing acquisition, Empowering women, Breadfruit domestication, Rice hybrid sterility, Long-distance crop dispersal, Diversification, African leafy greens, GIAH, Silkworm cryo, Bean in situ

Molecular markers as a tool for germplasm acquisition to enhance the genetic diversity of a Napier grass (Cenchrus purpureus syn. Pennisetum purpureum) collection. Win-win for the ILRI and Embrapa genebanks.
Women’s empowerment in agriculture and agricultural productivity: Evidence from rural maize farmer households in western Kenya. 1% increase in women’s empowerment led to a 6-16% increase in maize yields, depending on fanciness of math.
A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). Evidence of selection in 1000 genes.
A selfish genetic element confers non-Mendelian inheritance in rice. Pollen toxin-antidote genetic system controls hybrid sterility in wild-cultivated crosses.
Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age. It’s not all demic diffusion.
Determinants of crop diversification in rice-dominated Sri Lankan agricultural systems. Not everyone can diversify.
Improving food-system efficiency and environmental conservation using agricultural biodiversity in Busia County: a pilot study. Giving farmers nutritional data increased their cultivation of traditional vegetables, and their income.
The impacts of farmers’ livelihood endowments on their participation in eco-compensation policies: Globally important agricultural heritage systems case studies from China. Giving farmers money increased their income.
Conservation of wild silkworm genetic resources through cryopreservation: Standardization of sperm processing. It’s best to recover sperm from the bursa copulatrix and spermatheca of the female moth after mating.
Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity. 3 years of multiplication of heritage varieties in contrasting organic farms leads to genetic changes: it takes a network to truly conserve.

June 13, 2018

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.

June 11, 2018June 11, 2018

Brainfood: Sustainable Brazil, Epigenetic variation, Global conservation, Rice nutrition, Austronesian societies, Saharan domestication, GM wheat, Smallholders, Bos introgression

Sustainable diet from the urban Brazilian consumer perspective. Healthiness, basically.
Comparison of the Relative Potential for Epigenetic and Genetic Variation To Contribute to Trait Stability. Genetic >> epigenetic.
Global mismatch of policy and research on drivers of biodiversity loss. Except for climate change.
Carbon dioxide (CO2) levels this century will alter the protein, micronutrients, and vitamin content of rice grains with potential health consequences for the poorest rice-dependent countries. And not in a good way. But some variation among varieties = breeding opportunity?
Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy. Among Austronesian-speaking societies, no evidence that agricultural intensification drives social complexity; if anything, it’s the other way around.
Plant behaviour from human imprints and the cultivation of wild cereals in Holocene Sahara. Weediness has been good to humans in the past.
Gene Flow in Genetically Modified Wheat. Would probably only be a problem within fields.
How much of the world’s food do smallholders produce? FAO: 70%. New paper: 30-34%.
Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Miscegenation has been rampant.