DNA – Page 12 – Agricultural Biodiversity Weblog

January 26, 2021January 26, 2021

Tweeting beans

Twitter is often a hellsite, but every once in a while, it really comes through. Case in point is this cool summary of a recent paper on the genetics and physiology of seed dormancy in common beans posted by one of the authors, Dr David Lowry.

https://twitter.com/DavidBLowry/status/1353358445710172161

Now, I know some of you are not going to want to click on the above, so here it is in ThreadReader. And if you just want the bottom line…

November 16, 2020November 16, 2020

Brainfood: Genebank technology, Genebank research, Apple genomes, Napier genome, Wheat genome, Blue maize, FACE, Pigeonpea diversity, Millet domestication, Ancient dogs, Ancient bovids, Domestication syndrome, Date pollen, Commons, Genetic diversity trifecta

New technologies to improve the ex situ conservation of plant genetic resources. Genebanks need to catch up with the latest science even just to maintain their seeds.
Advanced Strategic Research to Promote the Use of Rice Genetic Resources. High-throughput phenotyping and genome sequencing are the latest science that will make the most of those seeds.
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Analysis of genomes of two main wild progenitors plus the crop uncovers genes so far untapped for improvement.
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth. It’s related to pearl millet, apparently. Which may or may not be a good thing. No word on any genes so far untapped for improvement.
Triticum population sequencing provides insights into wheat adaptation. Wide adaptation is largely due to introgression from the wild. No word on any genes so far untapped for improvement.
The Right Tortilla for the Right Occasion: Variation in Consumers’ Willingness to Pay for Blue Maize Tortillas Based on Utilization. Consumers are willing to pay 42% more for blue tortillas, but only when eating out, presumably as part of virtue signalling.
30 years of free‐air carbon dioxide enrichment (FACE): What have we learned about future crop productivity and its potential for adaptation? That enrichment wont save us, that’s what.
Phenotypic Divergence Analysis in Pigeonpea [Cajanus cajan (L.) Millspaugh] Germplasm Accessions. From 81 accessions to 9 promising ones, at least for Malawi.
A model for the domestication of Panicum miliaceum (common, proso or broomcorn millet) in China. Domestication took 3000 years.
Origins and genetic legacy of prehistoric dogs. All dogs are descendants of a now extinct wolf population, and their genetics show both interesting parallels with, and divergences from, that of humans.
Brain Size Does Not Rescue Domestication Syndrome. Not even for humans, I suspect. Kidding apart, this is fascinating. It suggests that, for animals at least, the domestication syndrome is not actually a thing. Or at least has not been properly tested. If there’s interest, I’ll do a full post. Let me know in the comments below.
Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic. The now tropical gaur ranged much further north during the warmer Neolithic, which facilitated the exploration of the Tibetan Plateau.
Optimization of in vitro germination and cryopreservation conditions for preserving date palm pollen in the USDA National Plant Germplasm System. Always good to have another way of storing germplasm.
Beyond the material: knowledge aspects in seed commoning. Comparing global with local seed commons reveals importance of managing knowledge, both scientific and traditional.
Genetics to the rescue: managing forests sustainably in a changing world. To manage forests sustainably, you have to conserve and use their genetic diversity. Interesting that they needed a conference to work that out.
Genetic mixing for population management: from genetic rescue to provenancing. And using that genetic diversity could mean mixing it up.
The importance of genomic variation for biodiversity, ecosystems and people. Maintaining ecosystem services means maintaining genetic diversity. Sounds like these authors went to the same conference.

November 13, 2020November 12, 2020

Nibbles: Avocado development, Marketing seeds, Saving seeds, Lettuce DNA

Avocado value chain gets it together. Hope some money flows back to the genebank.
Indian women fall back on vegetable seeds.
A seed saving network takes root in Kenya.
CGN teams up with BGI to sequence its lettuce collection.

October 26, 2020October 26, 2020

Brainfood: CGIAR genebanks, Sweet potato heat, Rice breeding, CWR gap trifecta, PES, Wild potatoes, Wild olives, Rare olives, Cryo veggies, Broccoli diversity, Crop switching, Cattle diversity, IK

Germplasm Acquisition and Distribution by CGIAR Genebanks. A lot of stuff going in, a lot of stuff coming out, to everyone’s benefit. 35 years of data, with special focus on the last 10.
Intraspecific diversity as a reservoir for heat-stress tolerance in sweet potato. 132 out of 1973 accessions tolerant of heat, though in different ways. A prime example of the above benefits.
Identification and characterization of high‐yielding, short‐duration rice genotypes for tropical Asia. Short-duration varieties will need to be a bit taller and leafier to yield more. Another example of the above benefits.
Modelled distributions and conservation priorities of wild sorghums (Sorghum Moench). More stuff needs to go into the above genebanks, though, for example from N. Australia.
Ex situ and in situ conservation gap analysis of crop wild relative diversity in the Fertile Crescent of the Middle East. Same from the Fertile Crescent.
In situ and ex situ conservation gap analyses of crop wild relatives from Malawi. And not just the above genebanks either.
The Potential of Payment for Ecosystem Services for Crop Wild Relative Conservation. Ok, we have the gaps (see above), and now here we have the method. What’s stopping us?
Assessing under-Estimation of Genetic Diversity within Wild Potato (Solanum) Species Populations. Wild diploid species more diverse than previously thought. So providing more ecosystem services?
Genetic diversity and differentiation of Olea europaea subsp. cuspidata (Wall. & G.Don) Cif. in the Hajar Mountains of Oman. No word on the ecosystem services being provided.
The investigation of minor and rare Tunisian olive cultivars to enrich and diversify the olive genetic resources of the country. Rare + minor doesn’t mean bad. But maybe an influx of Omani genes would help?
Biobanking of vegetable genetic resources by in vitro conservation and cryopreservation. Yes, even for vegetables.
From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection. Four subpopulations: Calabrese broccoli landraces, hybrids, sprouting broccoli, and violet cauliflower. Diversity in modern varieties decreasing with time.
Crop switching reduces agricultural losses from climate change in the United States by half under RCP 8.5. But it will have to be a lot of switching. Hopefully out of broccoli.
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. An influx of zebu genes about a thousand years ago is responsible for the success of African pastoralism.
Protection of traditional agricultural knowledge and rethinking agricultural research from farmers’ perspective: A case from Turkey. Against power imbalances the gods themselves contend in vain.

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.