Genetic diversity

October 7, 2020

How to sample for ex situ conservation

There was an intriguing tweet a few days ago from the redoubtable Sean Hoban about a presentation his lab is making at the Center for Plant Conservation meeting this week.

The @seanmhoban lab will present this poster at @CPCplants conference this week. Work by @Kaylee_rosen @koticneutralDNA @BailieMunoz building on vital work by @BethanyZumwalde @ScientistESS pic.twitter.com/SMfX3Qe4oM

— Sean Hoban (@seanmhoban) October 4, 2020

I was particularly taken with this bit.

Sampling more from bigger populations is somewhat different advice than has been given in the past, and it will be interesting to see the reaction.

The two references that Sean lists on the poster are as follows:

Toward the metacollection: Coordinating conservation collections to safeguard plant diversity.
Conservation through collaboration: Ensuring genetic diversity in garden collections.

October 7, 2020

Nibbles: Crop mapping, Sampling, Rice domestication, Coffee rust podcast, Wool dogs

Crop-Climate Suitability Mapping. Yes, another one. I feel a proper post coming on.
Tweet from Sean Hoban on ex situ sampling strategies. I feel a proper post coming on.
Proper blog post explains a really complicated rice domestication paper in about a page.
Proper podcast from Jeremy on, among other things, why coffee leaf rust is not why the Brits drink tea.
Not sure if this is blog post, but it’s a really good example of weaving together (see what I did there?) different pieces of work on the wool dogs (sic) of the Pacific NW.

October 6, 2020

Nibbles: Seeds4all, Seed keepers, African cattle book, Slavery & food podcast, Fonio cooking, Rabbit domestication

Seeds4all website launched to help make seeds available to all.
Why, you ask? Read this.
Beautiful book on the diversity of African cattle from ILRI.
The bloody history of food.
Decolonize your diet with fonio.
Domestic rabbits are pretty wild.

October 5, 2020October 8, 2020

Brainfood: Sorghum lodging, GR wheat, Wild potato core, Wild tomato structure, Protected areas, Biodiversity agreements, Malt archaeology, Hittite archeology, Seed traders, Peasant networks, Seed storage, Mesoamerican crop origins, Intensification, Cattle breeds, Pig domestication, Rice barcodes, Potato history, Rice spread

Large-scale genome-wide association study reveals that drought-induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation. To reduce lodging, better to select for stay-green (delayed leaf senescence) than for short stature and lodging resistance per se. Here’s a Twitter thread by one of the authors summarizing the findings.
Green revolution ‘stumbles’ in a dry environment: Dwarf wheat with Rht genes fails to produce higher grain yield than taller plants under drought. At least it doesn’t lodge, though, right?
A Core Subset of the ex situ Collection of S. demissum at the US Potato Genebank. From 149 to 38, keeping 96% of all marker diversity.
Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species. I guess if you were going to make a core collection for this you could do worse than sample ecogeographically diverse and isolated spots. Tricky to conserve in situ though.
DNA barcoding of Oryza: conventional, specific, and super barcodes. 6 hypervariable regions in the chloroplast genome can serve as rice-specific DNA barcodes. Assuming you agree on species concepts in the first place.
A “Global Safety Net” to reverse biodiversity loss and stabilize Earth’s climate. The 50% of the Earth to save to save the Earth.
Three Key considerations for biodiversity conservation in multilateral agreements. Plan, model, assign responsibility.
Mashes to Mashes, Crust to Crust. Presenting a novel microstructural marker for malting in the archaeological record. Aleurone cell breakdown in archaeobotanical remains is a robust indicator of beer-making. I bet they find it everywhere now.
The agroecology of an early state: new results from Hattusha. Huge underground grain silos, with each container holding grain from multiple sites, which could be evidence of tax-paying. But no word on beer.
Informal Seed Traders: The Backbone of Seed Business and African Smallholder Seed Supply. Lots of room for engagement, and considerable upside. If I were to pick out just one high-potential intervention, it would be providing training in seed testing.
Restoring cultivated agrobiodiversity: The political ecology of knowledge networks between local peasant seed groups in France. I’m sure they’re testing their seeds.
A Protective Role for Accumulated Dry Matter Reserves in Seeds During Desiccation: Implications for Conservation. Cells must have >35% dry matter to be able to withstand desiccation.
Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico. It looks like we — inexplicably — missed this the first time around. Chilli, maize and beans originated in different parts of Mexico.
Ecological intensification and diversification approaches to maintain biodiversity, ecosystem services and food production in a changing world. Though you can change one thing at a time, it’s better to redesign the whole system. But is the better the enemy of the good?
Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle. 2 groups among Italian breeds: North-Central breeds linked to Alpine and Iberian breeds, and Podolian-Sicilian breeds with links to the Balkans.
The Archaeology of Pig Domestication in Eurasia. Independent domestication in northern Mesopotamia by 7500 BC (extensive management) and China by 6000 BC (maybe intensive); failed to take off in Japan, for interesting reasons.
Vegetative States: Potatoes, Affordances, and Survival Ecologies. The potato has both helped to underpin and resist state coercion. The Hittites would have worked something out, though, I feel.
Holocene coastal evolution preceded the expansion of paddy field rice farming. Rice only moved south from the lower Yangtze 2-3000 years ago, once costal land opened up. No word on affordances.

October 1, 2020October 1, 2020

Nibbles: Apple museum, Colonialism museum, Mohawk seeds, India2Africa, DivSeek vid

A cool apple museum in Wenatchee, Washington.
Cool museum exhibit on German colonial exploitation of agricultural raw materials, in Hamburg.
Mohawk culture and teaching embodied in seeds. And not in a museum.
Indian legumes a hit in Ghana, via genebanks, not museums.
Long video from IPK on using data to use genebanks. You mean like above?