Genetic diversity

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 9, 2018July 9, 2018

Brainfood: Phenotyping, Genotyping, Perennial Hordeum, Communicating PGRFA, Participatory breeding, Sri Lankan homegardens, Traditional Slovak landscapes, Ecosystem services, LWR double, African cassava, Labelling fish

Translating High-Throughput Phenotyping into Genetic Gain. More to it than cool drones. Although those are not to be sneezed at.
A guide to sequence your favorite plant genomes. Someone may already have what you need.
Towards the Development of Perennial Barley for Cold Temperate Climates—Evaluation of Wild Barley Relatives as Genetic Resources. H. bulbosum is the best bet. So far.
Communicating plant genetic resources for food and agriculture to the public — A study of grant-receivers with demonstration-projects in the Danish Rural Development Programme. It can be done.
Farmers’ participatory selection of new rice varieties to boost production under temperate agro-ecosystems. It can be done.
Assessing the Impacts of Agrobiodiversity Maintenance on Food Security Among Farming Households in Sri Lanka’s Dry Zone. Help the poor.
Contribution of Traditional Farming to Ecosystem Services Provision: Case Studies from Slovakia. Traditional systems more diverse and balanced in provision of ecosystem services than intensive modern systems. The problem is that pesky production service. Yeah, but about that…
Bright spots in agricultural landscapes: Identifying areas exceeding expectations for multifunctionality and biodiversity. Small is beautiful.
Why should we save the wild relatives of domesticated animals? Because we can.
Tracking trends in the extinction risk of wild relatives of domesticated species to assess progress against global biodiversity targets. And because we should.
Single nucleotide polymorphism (SNP) diversity of cassava genotypes in relation to cassava brown streak disease in Mozambique. Some Mozambican landraces are very similar to resistant Tanzanian landraces.
Generic names and mislabeling conceal high species diversity in global fisheries markets. DNA barcoding reveals that 300 “snapper” samples are in fact 67 species from disparate fisheries. Use Latin names, folks!

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 26, 2018July 13, 2018

Nibbles: Cordillera rice, Farmer seed, Toddy audio essay, Eat This Newsletter, Coconut conservation, Australian genebank, Sweet potato diversification, Mungbean income, NERICA impact, Bing cherry, TFP, Conservation evidence, NordGen matters

Conserving heirloom rice in the Philippines.
A seed production company run by farmers.
Tapping toddy. With audio goodness.
Lots of goodness in Jeremy’s latest newsletter.
Australia gets serious about coconut conservation in the Pacific and beyond.
Australia’s own genebanks are very serious. Oh yes indeedy.
Will sweet potatoes get young people into farming in Kenya? If my nephews are anything to go by, the answer, alas, is no.
Maybe they should try mungbeans.
Or NERICA.
The Bing cherry didn’t help Ah Bing much though.
Whatever the crop, it’s total factor productivity that you have to watch for.
And then don’t forget to include whatever intervention you come up with in subject-wide evidence synthesis.
Prize for best title of the week: “Nordic cooperation on genetic resources – what’s the point?” Nice video.

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.