Agricultural Biodiversity Weblog

Brainfood: Extension, Wheat adoption, Bean ideotypes, Chilli evaluation, Rice domestication, ...

Mon, 30 Nov 2020 07:12:50 GMT

Does it matter who advises farmers? Pest management choices with public and private extension. Yes, at least in Switzerland. Public = prevention, private = cure. Well colour me surprised.
Ethiopia’s transforming wheat landscape: tracking variety use through DNA fingerprinting. Only 28% of farmers correctly named their wheat varieties, many of which were from CGIAR breeding programmes.
Analysis of the Similarity between in Silico Ideotypes and Phenotypic Profiles to Support Cultivar Recommendation—A Case Study on Phaseolus vulgaris L. Italian farmers not great at keeping track of new varieties either, but who needs names when you have fancy maths?
Morphological, Sensorial and Chemical Characterization of Chilli Peppers (Capsicum spp.) from the CATIE Genebank. From 192 accessions to this little beauty from Panama.
Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production. Rice is from Mars, rice is from two Venuses.
Identification of Mung Bean in a Smallholder Farming Setting of Coastal South Asia Using Manned Aircraft Photography and Sentinel-2 Images. From 10-m imagery for pity’s sake! Amazing stuff. Soon we’ll be able to distinguish landraces from modern varieties, right? Right?
Linking biodiversity into national economic accounting. Yikes, biodiversity makes no contribution to agricultural development at all?
High sink strength prevents photosynthetic down-regulation in cassava grown at elevated CO2 concentration. Could result in higher yields, but effect will vary among varieties.
Discovery of beneficial haplotypes for complex traits in maize landraces. Landrace diversity for early plant development, robustness and growth form that could be useful in Europe made accessible.
Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. It’s the dispersion of favorable alleles between parents.
Challenges and Prospects for the Conservation of Crop Genetic Resources in Field Genebanks, in In Vitro Collections and/or in Liquid Nitrogen. Everything that can be in cryo should be in cryo, and some things that currently can’t too.

Nibbles: Climate change vid, Lemongrass, Millets, GHUs, US potatoes

Sat, 28 Nov 2020 11:25:13 GMT

Nice video on Future Climate for Africa.
Indian forest communities diversify with lemongrass to help out with their climate change resilience.
Have they tried millets, though? According to Millet Finder, millet products are taking over the world, so marketing should be no problem.
If they don’t have seeds, they can get them from genebanks, via Germplasm Health Units, of course. The impact pathways of genebanks goes through GHUs.
The Russet Burbank sure has had a big impact.

Nibbles: Seed pod, Lost Thanksgiving, Prairie crops, Wild PNG bananas, Seedkeeper Rowen White, ...

Fri, 27 Nov 2020 09:06:02 GMT

Podcast on saving crop diversity every which way you can.
Because it can be lost.
Yes, lost, but, with some effort, bison permitting, found again.
Wild relatives too, of course.
And maybe then rematriated, even used for a greener agriculture, who knows.
So that eventually it can make it into things like Legume Perspective, the cool journal of the International Legume Society that was inexplicably unknown to me until just now.

The pangenome is the new genome – Part Deux

Thu, 26 Nov 2020 08:08:53 GMT

1) Today's been a hell of a day for plant #pangenomes.
In https://t.co/FSxNthxoG9 Walkowiak et al analyze up to 16 wheat cultivars to report on the global variation pool accessible to modern breeding pic.twitter.com/xPTtIvEZyC

— BContrerasMoreira (@BrunoContrerasM) November 25, 2020

Indeed it was “a hell of a day” (somewhat re-ordered compared to the above tweet thread):

Multiple wheat genomes reveal global variation in modern breeding. Genomes of 10 cultivars from around the world’s breeding programmes and a few other things added to that of Chinese Spring.
A haplotype-led approach to increase the precision of wheat breeding. The above and fancy maths used to spot novel, agronomically significant haplotypes in landrace collections. Here’s a Twitter thread from one of the authors with his insights on why the work is important.
The barley pan-genome reveals the hidden legacy of mutation breeding. Genomes of 20 really diverse barley lines, including a wild relative, used to (among other things) find novel variants in 300 genebank accessions.
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Some transposable elements affect gene expression.
GreenPhylDB v5: a comparative pangenomic database for plant genomes. Pan-pangenomes, kinda.

LATER: Had completely forgotten I had used that title before :) It’s the zeitgeist for sure. And here’s a nice primer on pangenomes.

Nibbles: Seedscapes, Bee map, Sacred bananas, Sustainable eating, Hazelnuts, Investing

Wed, 25 Nov 2020 07:43:05 GMT

Why do seeds matter?
Where do bumblebees matter?
Where bananas really matter.
How to eat like it matters.
Nutella matters a little too much perhaps.
Biodiversity matters to investors, apparently. Crop diversity unavailable for comment.

Nibbles: Climate ready, Commoners, Beer, Banana collecting, Roman food, Indian corn

Tue, 24 Nov 2020 11:41:52 GMT

Demoing new varieties in Mali.
Old ways of doing things in the New Forest.
Nice roundup of beer in ancient history.
Profile of supercool banana guy Gabriel Sachter-Smith.
Eat like a Roman.
Eat like a (multiracial) Southerner.

Brainfood: Covid, Tropical trees, Tree GR, Brazil nut, Fair research, ICARDA, FIGS, Landraces, ...

Mon, 23 Nov 2020 07:40:24 GMT

From biomedical to politico-economic crisis: the food system in times of Covid-19. How to build back better? Food sovereignty, peasant agriculture, territorial markets and agroecology.
Food for thought: The underutilized potential of tropical tree‐sourced foods for 21st century sustainable food systems. How to realize that potential? Lots of ideas here, including: “Investment in the conservation of tree genetic resources and the development of formal seed delivery systems.”
Priorities, challenges and opportunities for supplying tree genetic resources. Invest in what bits of conservation and seed delivery, though? Read this and find out.
Genetic threats to the Forest Giants of the Amazon: Habitat degradation effects on the socio‐economically important Brazil nut tree (Bertholletia excelsa). After reading the above, maybe apply to this?
From texts to enacting practices: defining fair and equitable research principles for plant genetic resources in West Africa. How to make sure everyone understands words the same way? Theater.
Safeguarding a global seed heritage from Syria to Svalbard. It takes a (global) village.
Focused Identification of Germplasm Strategy (FIGS): Polishing a rough diamond. Natural selection is not enough.
Göte Turesson’s research legacy to Hereditas: from the ecotype concept in plants to the analysis of landraces’ diversity in crops. “Understanding … landrace diversification assists also on breeding new cultivars sustainably since it provides insights regarding crop evolution across stress-prone environments, and for finding genebank accessions and other germplasm whose allelic diversity may be missing in today’s breeding programs.”
Yield, yield stability and farmers’ preferences of evolutionary populations of bread wheat: A dynamic solution to climate change. Maybe the problem is with today’s breeding programs?
What Do We Really Know About Adaptation at Range Edges? Peripherality does not predict degree of adaptation.
The Central Asiatic region of cultivated plants. 800 species, no less.
Biodiversity enhances the multitrophic control of arthropod herbivory. Plants lose less to arthropods in mixtures, as compared to monocultures.
Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia. Not PNG, according to chloroplast DNA.
Abattoirs – A Hidden Centre for Livestock Genetic Resources Loss in Nigeria. Because they slaughter pregnant animals.
More than fish: Policy coherence and benefit sharing as necessary conditions for equitable aquaculture development. Regional policies need to be domesticated.

Nibbles: MSB birthday, Ethiopia impact, Coffee threats, African greens

Thu, 19 Nov 2020 09:45:55 GMT

It’s 20 years of the Millennium Seed Bank. Happy birthday!
CGIAR summarizes 20 years of impact in Ethiopia.
In 20 years, half of Africa’s coffee land could be gone. Well, 30, but I need to keep this streak going.
Must have been about 20 years ago that systematic research on African indigenous vegetables really took off, and now look.

Nibbles: F2F, Jute, IITA, ICARDA, ILRI, Grazing

Wed, 18 Nov 2020 09:01:36 GMT

USDA throws shade on EU’s Farm to Fork strategy. I see trouble in its future.
Turns out jute has a future.
Is CRISPR the banana’s future?
How Svalbard gave ICARDA’s genebank a future.
Ensuring the future of Ethiopia’s livestock through forage seeds.
The future of Europe’s meadows is livestock. No word on forage seed or Farm to Fork.

Diversify your landscapes redux

Tue, 17 Nov 2020 08:15:15 GMT

I originally published this post on 29 July, but then Dr Baudron pointed to two additional papers on Twitter, and then later to another one, so I’m re-upping, for the second time, with a sixth bullet point.

There’s a nice series of papers on the benefits of diverse landscapes in Ethiopia from Frédéric Baudron of CIMMYT and others.

Just in case this tweet disappears, or whatever, here are the links:

Wheat yields and zinc content are higher closer to forests because of elevated organic matter in the soil.
Diets are also more diverse nearer forests.
Livestock (but not crop) productivity is higher nearer forests, and smallholder systems generally more sustainable.
Bird diversity benefits from tree cover too, and that provides important ecosystem services to smallholders.
Even limited reforestation in the surrounding landscape is associated with higher wheat yields in simulations, and you can potentially measure it from space.
“More people, more trees.”

Domesticating the podcast

Tue, 17 Nov 2020 07:20:49 GMT

Want to review the state of knowledge on domestication of chickens, sheep and cattle in less than half an hour? Yes? Well then, Jeremy has a podcast for you. It’s an interview with Olivier Hanotte, who teaches livestock genetics at the University of Nottingham.

The beautiful chicken pic is from a book by photographers Moreno Monti and Matteo Tranchellini.

There’s also a stunning book on the diversity of African cattle from ILRI, where Dr Hanotte also has a position.

Featured comment: Community seed drying

Mon, 16 Nov 2020 11:25:03 GMT

Denise Costich, who has just retired as head of the CIMMYT genebank, gives us a bit of the back story to a paper we included in a recent Brainfood:

Thanks for the mention of our Dry Chain work… the first time I heard about drying beads was at my very first AGM in Rome in 2012. That was a key introduction to this technology for me. It was there in my “knowledge base” when we first began to tackle the problem of seed storage in remote locations without electricity – the community seed reserves and farmers’ corn cribs of the Western Highlands of Guatemala.

AGM stands for Annual Genebank Meeting. The managers of the CGIAR genebanks have been organizing them since 2012.

Brainfood: Genebank technology, Genebank research, Apple genomes, Napier genome, Wheat genome, ...

Mon, 16 Nov 2020 08:25:32 GMT

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.

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

Fri, 13 Nov 2020 11:33:52 GMT

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.

A little R&R for ecosystems

Thu, 12 Nov 2020 08:51:59 GMT

It seems we missed, back in August, a huge report on CGIAR’s work on ecosystem restoration. After a thorough stocktaking, the report suggests the following are critical for successful restoration:

secure tenure and use rights
access to markets (for inputs and outputs) and services
access to information, knowledge and know-how associated with sustainable and locally adapted land use and land management practices
awareness of the status of local ecosystem services, often used as a baseline to assess the level of degradation
high potential for restoration to contribute to global ecosystem services and attract international donors

Which seems sensible. At least if “practices” in 3 and “services” in 4 and 5 include some consideration of genetic diversity. And on that note, it’s also about time we linked to the Royal Botanic Gardens Sydney’s page on Restore & Renew (R&R).

It only covers New South Wales and Victoria, but the R&R Webtool could be something for CGIAR to run with globally. You pick a spot you want to restore, and, for a selection of trees, it tells you where best to source germplasm from. That’s based on current climate, future climate and, crucially, genetic similarity1 (if data are available).

Of course, this is just the start. Scaling up the supply of tree seeds for landscape restoration remains a major challenge. A recent review, also involving CGIAR scientists, makes quite a few useful recommendations. But in the end, I suspect, it will come down to this:

put in place incentives and enabling policies to support smallholders in producing, trading and using high-quality genetically diverse reproductive materials

But see this for a different view.

Nibbles: HarvestPlus, Peppers, Dreaming, Botanical rescue, Feed database, Pigs in E Germany, ...

Thu, 12 Nov 2020 07:58:14 GMT

Genebanks for nutrition. Indeed they are.
Hot peppers may be good for you. Genebanks alerted.
For Aboriginal Australians, knowledge is held by the living landscape, and humans get together to animate it. Fascinating.
Humans getting together to rescue near-extinct plants from wounded landscapes of North America.
There’s a database of animal feeds for sub-Saharan Africa. Could do with being mashed up with genebank databases, no?
Agriculture under communism wasn’t all that communist. At least in E. Germany. I wonder what they were fed.
A 4000-year-old apple core found in Vienna. Any DNA though?

When landraces are elite

Wed, 11 Nov 2020 11:30:15 GMT

Have you ever found a genebank accessions that performed better straight out of the box than a modern variety, under a particular set of conditions? If so, let me know below. I’d like to compile a list, because why not?

Some examples already up on Twitter.

We have many examples in corn.
PT = Palomero Toluqueño (CIMMYTMA 2233) pic.twitter.com/3pi7Kxpvdx

— Rubén Rellán-Álvarez (@rellanalvarez) November 10, 2020

Yes, we have lots of banana news

Wed, 11 Nov 2020 07:09:31 GMT

There’s recently been some interesting banana germplasm collecting in Papua New Guinea.1

The results are summarized in two articles, one in Plants evaluating methods to ensure the viability of collected seeds, and the other in Crop Science summarizing the characterization of diverse phenotypes.

We’ve included both the papers in question in past Brainfoods, but this press release, from which the above quote is taken, does a really nice job of bringing them together. It might also have added an additional recent paper on the work of the International Musa Germplasm Transit Centre (ITC), but anyway.

There’s a whole bunch of summary statistics on the ITC, and lots of useful links, on the Genebank Platform webpage. And of course Genesys has a selection of accession-level data. But the place for all your banana information needs is ProMusa.

No, I don’t mean the Bougainville expedition, do keep up.

China’s path to new crops

Tue, 10 Nov 2020 06:41:11 GMT

Jeremy’s latest newsletter includes this nice write-up of a recent paper on the origins of Chinese food, under the title I’ve stolen above.

Path dependence is the idea that the choices available today are constrained by choices that were made some time back. A new research paper in PLOS One looks at the way existing cooking techniques affected new crops as they made their way into China.

Wheat and barley arrived in China about 4000 years ago. But while the people of western China adopted the new plants quite quickly (you can tell by looking closely at their bones) those in central China were apparently not as keen.

The reason, according to the researchers, reflects north-south differences in cuisine that can be detected 8000 years ago. Northeners had millet as their staple grain, while southerners ate nuts, tubers, fruits and rice. Overlaid on this, central China is part of the northern complex, where millet was prepared by boiling or steaming the whole grain. Western China’s approach to wheat and barley was to mirror their neighbours to the west, grinding the grains to make flour that was baked into breads.

It took much longer for cooking methods in the east to adapt to the new cereals, not least because it takes far longer to boil wheat than millet, and the taste is quite different. There is some evidence, too, that in the course of this adaptation, wheat itself was selected to be more amenable to boiling and steaming.

This east-west vs north-south story adds detail to the [Eat This Podcast] episode with Martin Jones on Prehistoric food globalisation.

Here’s the rest of the newsletter. We blogged here about the paper Jeremy discusses in the podcast episode mentioned at the end.

Brainfood: Diversification, Annona, Banana genebank, Sustainable livestock, One Health, ...

Mon, 09 Nov 2020 07:13:41 GMT

Agricultural diversification promotes multiple ecosystem services without compromising yield. Meta-meta-analysis shows diversification is good for biodiversity, pollination, pest control, nutrient cycling, soil fertility, and water regulation and not bad for crop yields either.
Holocene land and sea‐trade routes explain complex patterns of pre‐Columbian crop dispersion. Cherimoya reached the Andes by boat.
Safeguarding and using global banana diversity: a holistic approach. 1617 banana accessions from 38 countries maintained in an in vitro collection, backed-up in cryo; over 18,000 samples distributed to researchers and farmers in 113 countries in 35 years. And that’s just the basics.
Designing sustainable pathways for the livestock sector: the example of Atsbi, Ethiopia and Bama, Burkina Faso. It’s not just a straight choice between intensive or extensive production, stop with the dichotomies.
Moving health to the heart of agri-food policies; mitigating risk from our food systems. It’s difficult to separate food from health; and yet…
Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. Agriculture depends on polyploidy.
Genetic diversity is indispensable for plant breeding to improve crops. Plant breeding from an industry perspective, using the Brassicaceae as a case study.
Yield, yield stability and farmers’ preferences of evolutionary populations of bread wheat: A dynamic solution to climate change. A totally different perspective to the above, using a totally different crop. Compare and contrast.
Enhancing seed conservation in rural communities of Guatemala by implementing the dry chain concept. Cool way for farmers to save their seeds so they can do the above.
Landrace hotspots identification in Europe. Where to implement the above.
Innovation and the commons: lessons from the governance of genetic resources in potato breeding. This is a tricky one. Near as I can figure it, the authors are trying to say that it’s difficult to govern genetic resources apart from the tools needed to develop and use them. But hey, you have a go.
Conservation of Native Wild Ivory-White Olives from the MEDES Islands Natural Reserve to Maintain Virgin Olive Oil Diversity. I did not have an endemic insular wild albino olive on my bingo card.
Agri-nutrition research: Revisiting the contribution of maize and wheat to human nutrition and health. Staple cereals are more nutritious than often thought.
On the origin and dispersal of cultivated spinach (Spinacia oleracea L.). Spinach originated more eastward than often thought.
What plant is that? Tests of automated image recognition apps for plant identification on plants from the British flora. Botanists shouldn’t give up their day jobs.