Agricultural Biodiversity Weblog

Brainfood: Bending the curve edition

Mon, 21 Sep 2020 06:16:13 GMT

Bending the curve of terrestrial biodiversity needs an integrated strategy. Meaning: (i) sustainable agricultural intensification, (ii) trade, (iii) less food waste, (iv) more plant-based human diets, and (v) more and better protected areas.
The carbon opportunity cost of animal-sourced food production on land. See (iv) above.
Just ten percent of the global terrestrial protected area network is structurally connected via intact land. See (v) above.
Cropland expansion in the United States produces marginal yields at high costs to wildlife. See (i) above.
A cultivated planet in 2010 – Part 1: The global synergy cropland map. Gotta know where the cropland is before you can do (i) above.
Advances in plant phenomics: From data and algorithms to biological insights. Fancy maths can really help with (i) above.
Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields. Different fancy maths shows that CIMMYT’s Obregon wheat testing site can really help with (i) above.
Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Here’s some stuff that wheat breeders can use to develop new materials to test at Obregon using phenomics, genomics and fancy maths.
First report on cryopreservation of mature shoot tips of two avocado (Persea americana Mill.) rootstocks. This should help with (iv) above. Eventually, work with me here.
Bread and porridge at Early Neolithic Göbekli Tepe: A new method to recognize products of cereal processing using quantitative functional analyses on grinding stones. Ahem. Well… No, sorry, I got nothing.

Nibbles: Artocarpus, Malus, Citrullus, spp, Asimina, Daucus

Sat, 19 Sep 2020 07:35:29 GMT

The colonial history of the jackfruit in Sri Lanka.
“…some of the best cider you can drink is as funky and wild as a 1970s Berlin bathhouse.” Ok, you twisted my arm.
The world in a Philadelphia watermelon stand.
Bee Wilson’s review of wheat book Amber Waves by Catherine Zabinski.
The Canadian genebank at 50.
Oh shoot I missed National Pawpaw Day.
Podcast on carrot breeding using crop wild relatives.

Brainfood: Special citizen science edition

Fri, 18 Sep 2020 06:13:13 GMT

Something for the weekend. I hope you enjoy this special edition of Brainfood focusing on citizen science, Indigenous knowledge and participatory research. Do you like themed Brainfood editions like this? There will be another one on Monday, as it happens. They’re more tricky to produce, but if there’s significant interest I may make the extra effort. Let me know, and suggest topics.

The value of climate-resilient seeds for smallholder adaptation in sub-Saharan Africa. Up to USD 2 billion in Malawi and Tanzania over the next 30 years.
Agricultural productivity and deforestation: Evidence from input subsidies and ethnic favoritism in Malawi. Cheaper fertilizers increased yields and decreased deforestation. Better seeds would help too, no doubt (see above).
Channels used to deliver agricultural information and knowledge to smallholder farmers. Farmer groups and demonstration plots work well to spread the news about fertilizers and seeds.
Integrating Conventional and Participatory Crop Improvement for Smallholder Agriculture Using the Seeds for Needs Approach: A Review. Combine high-tech centralized and participatory decentralized germplasm evaluation and breeding approaches to get those better seeds to farmer groups and their demonstration plots.
Citizen science breathes new life into participatory agricultural research. A review. Why do the participatory, decentralized bit? Here’s why. Fortunately, there’s an app for it…
A global resource for exploring and exploiting genetic variation in sorghum crop wild relatives. If those seeds include sorghum, you could start with this lot.
Gendered differences in crop diversity choices: A case study from Papua New Guinea. And don’t forget gender as you do all this participatory, decentralized stuff. For example, in PNG, the women are into marketing, the men into tradition.
Crowd breeding of Danish apple cultivars. No word on gender differences, alas.
Modelling illustrates that genomic selection provides new opportunities for intercrop breeding. Here’s the high-tech, centralized bit, or at least a model of it, ripe for mashing up with citizen science.
Dissection of the domestication‐shaped genetic architecture of lettuce primary metabolism. More high-tech, centralized stuff, the real thing this time. Which can now be used to breed a better lettuce, hopefully by lots of citizens growing the stuff in their gardens and providing salad tasting results through a nifty app.
Indigenous and Local Knowledge Practices and Innovations for Enhancing Food Security Under Climate Change: Examples from Mijikenda Communities in Coastal Kenya. Maybe farmers should run participatory programmes, with scientists as the citizens.
Micronutrient composition and microbial community analysis across diverse landraces of the Ethiopian orphan crop enset. Don’t know how you’d do citizen science on this, but I bet somebody does.
Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii. Someone mention traditional fermentation practices?
The Milpa Game: a Field Experiment Investigating the Social and Ecological Dynamics of Q’eqchi’ Maya Swidden Agriculture. Citizen science is not a game. No, wait…
The Ancient Tree Inventory: a summary of the results of a 15 year citizen science project recording ancient, veteran and notable trees across the UK. Not a game indeed: very serious, but fun, definitely fun.

A Chinese chilli mystery

Thu, 17 Sep 2020 14:59:48 GMT

If you listened to my podcast How the chilli pepper conquered China, you may be wondering, if you care about these things as I do, why there is a chilli species called Capsicum chinense.

The chilli didn’t reach China until the 1570s or thereabouts, and capsicums in the wild are restricted to the Americas, yet C. chinense is a perfectly valid species name. Indeed, many of the hottest peppers in the world have the distinction of belonging to that species, which also includes the more familiar Habanero and Scotch Bonnet varieties.

Start searching, and you learn that the species was described and named by Nikolaus Joseph von Jacquin in 1776. He was a Dutch scientist who ended up working for the Austrian crown and undertook an impressive early collecting trip in the Caribbean. Von Jacquin’s family was highly regarded in Vienna, where Mozart taught his daughter piano and wrote songs for his son. He was also one of the earliest promoters of the Linnean system of binomial nomenclature, and enjoyed a long friendship and correspondence with Linnaeus.

A most difficult taxonomic morass

There are five domesticated species of Capsicum (and some hybrids) and three of them — C. annuum (by far the most common), C. frutescens (Tabasco, and not a lot else) and C. chinense — are not easy to tell apart. Most descriptions focus on the number of flowers that grow from the base of each leaf, 2–5 in chinense as opposed to only a single flower in annuum. The three interbreed to varying extents and back in 1993 one expert said their classification “has been and continues to be a most difficult taxonomic morass”.[1] Modern molecular methods back that up; the three arise from a single ancestor and are one another’s closest relatives.

Von Jacquin’s description[2] does not say why he thought it was from China. It does say, roughly, “I saw [them] cultivated on the island of Martinique, and seeds used in cooking.”

Von Jacquin seems to have described a cultivated variety growing the gardens of Schönbrunn Palace outside Vienna. Almost 200 years later, the species was identified in the wild

Paul Smith and Charles B. Heiser Jr did an exhaustive study of wild and weedy capsicums from all over, in the course of which they found that some plants from Central and South America did not fit into any of the species they had previously recognised.[3] Though it apparently piqued them to admit it, these plants clearly belonged to what they called Capsicum sinense.

Smith and Heiser offered an “emended” description that places special emphasis on the 3–5 flowers at each node and a marked constriction at the base of the calyx. They then say:

It is unfortunate that the earliest name for this American plant appears to be Jacques’ [sic] C. sinense (as “chinense”). The plant shown in his plate, although showing only two pedicels at the nodes is almost identical to some of our collections. Our Ac. 751 (P.I. 157,062) from Lanchow, China, is a fairly close match and it in turn is almost indistinguishable from a line (Ac. 910) from Costa Rica.

I see only one pedicel at the nodes in von Jacquin’s plate, above. Maybe Smith and Heiser were looking at a different one. In any case, I quite like the fact that von Jacquin, who worked to promote Linnean binomials, gets the last laugh because he got the first name. Did the plants he described come from China? He must have thought so.

Wikipedia’s view is that von Jacquin "believed they originated in China due to their prevalence in Chinese cuisine after their introduction by European explorers,”[4] and it cites a chapter by Paul Bosland in support. Chastened by the whole spinach thing, I checked.

Bosland says “the French taxonomist who named this species in 1776 got his seed from China”. Leave aside that von Jacquin was born in The Netherlands and working in Austria at the time; what is Bosland’s source? None other than Smith and Heiser (1957).

And they say absolutely nothing about the source of von Jacquin’s seeds.

The mystery, then, abides. Maybe someone with access to the archives at Schönbrunn Palace or the University of Vienna botanical gardens could take a quick poke around and see if there is any indication of the geographical origin of the plants that von Jacquin named Capsicum chinense.

Eshbaugh, W.H. 1993. History and exploitation of a serendipitous new crop discovery. p. 132–139. In: J. Janick and J.E. Simon (eds.), New crops. Wiley, New York. ↩
Images from von Jacquin’s Hortus Botanicus Vindobonensis at the Biblioteca Digital del Real Jardin Botanico de Madrid. ↩
Smith, P.G. and C.B. Heiser. 1957. Taxonomy of Capsicum sinense Jacq. and the geographic distribution of the cultivated Capsicum species. Bul. Torrey Bot. Club 84:413–420. ↩
Untrue, as they were almost certainly introduced by crew members on ships, probably Chinese, and certainly not “explorers”. ↩

Nibbles: Vavilov podcast, Pomological book, Wine press, Banana data

Wed, 16 Sep 2020 11:26:21 GMT

Audio drama on Vavilov. You heard me.
Proceedings from the First Annual Wild & Seedling Pomological Exhibition. First of many, I hope.
A really old Phoenician wine press.
Update on banana genebank data.

Lay up your dates on earth

Tue, 15 Sep 2020 08:50:11 GMT

I see Jeremy had some fun in his latest newsletter. Want more of the same, every week: subscribe.

Previously, in the Methuselah date story: around 50 years ago archaeologists excavating Masada in Israel dug up a small pile of date seeds. In 2008, to most people’s surprise, one of those seeds — roughly 2000 years old — germinated and was named the Methuselah date. Like its namesake, it proved to be male. Date male and female flowers grow on separate plants, so wails and lamentations accompanied far-fetched plans to tinker with Methuselah.

And it came to pass that in recent years another 32 well-preserved date seeds were set to germinate. And lo, six of them did germinate, and their names were given as Boaz, Eve, Jeremiah, Jonah, Judah and Uriel, and they too were of ancient lineage. And when they came of maturity and revealed unto others their gender, Eve became Adam, and Jeremiah became Hannah and Judah in her turn became Judith.

And Hannah brought forth flowers in their beauty, and the researchers carried the male seed from Methuselah unto Hannah’s flowers and the flowers swelled and were ripened. Then the researchers plucked of the fruits and tasted, and said: “The honey-blonde, semi-dry flesh had a fibrous, chewy texture and a subtle sweetness.”

The New York Times has the story, and there is a bunch of really interesting science behind some of the conjectures.

Nibbles: Cahokia book, Grape stats, Tides of History, Medieval Arabic cookbooks, Bangladesh ...

Tue, 15 Sep 2020 07:02:30 GMT

Prof. Gayle J. Fritz gets 2020 Mary W. Klinger Book Award for “Feeding Cahokia.” Beyond maize and priests.
The ups and downs of grape varieties. Airén relinquishes the top spot! So much data: who will calculate diversity stats?
Nice, long podcast on the beginning of farming in the Fertile Crescent. More coming up.
“Treasure Trove of Benefits and Variety at the Table” is the sort of cookbook we all need.
What is it about floating gardens? Quite a lot, really. But they are not easily transplanted, as it were.

Farmers’ Rights webinar coming up fast

Mon, 14 Sep 2020 06:27:35 GMT

I realize another webinar is probably the last thing you want to know about right now. I see you, I really do. But this is important, and it’s a great lineup.

“Farmers’ Rights in the International Legal Architecture for Food and Agriculture Article 9, the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) recognizes the enormous contribution that the local and indigenous communities and farmers of all regions of the world, particularly those in the centers of origin and crop diversity, have made and will continue to make to the conservation and development of plant genetic resources which constitute the basis of food and agriculture production throughout the world. This webinar will examine the links between Farmers’ Rights (as established in the ITPGRFA) and related international treaties alongside the right to food and gender perspectives on Farmers’ Rights.”

Date: 16 September 2020. Time: 3.00 pm to 5.00 pm (Rome).

Moderator: Ms Titilayo Adebola (School of Law, University of Aberdeen)

Panelists

Ms Regine Andersen: Research Director for Biodiversity and Natural Resources, Fridtjof Nansen Institute (FNI), Norway
Mr Michael Fakhri: The United Nations Special Rapporteur on the Right to Food
Ms Susannah Chapman: Research Fellow, the University of Queensland
Ms Yolanda Huerta: Legal Counsel, International Union for the Protection of New Varieties of Plants
Ms Isabel Lopez Noriega: Alliance of Bioversity International and the International Center for Tropical Agriculture
Mr James Gathii: Wing Tat-Lee Chair of International Law and Professor of Law, Loyola University of Chicago.

Brainfood: CGIAR, Genebank data, AI & diseases, Mentha CWR, Tree crops, Carrot diversity, ...

Mon, 14 Sep 2020 06:17:11 GMT

The development of the international center model for agricultural research: A prehistory of the CGIAR. The model didn’t start with those canonical US foundations, and owes more than a little to colonialism. Further integration is needed.
Document or Lose It—On the Importance of Information Management for Genetic Resources Conservation in Genebanks. Standardization, openness and interoperability. Easier said than done, but if you’re looking for further integration…
AI-powered banana diseases and pest detection. But can it tell bananas from plantains? Nice to link it up with the above.
Crop Wild Relatives as Germplasm Resource for Cultivar Improvement in Mint (Mentha L.). 450 clones representing 34 taxa maintained by USDA. The next 2 are USDA things too.
Germplasm Development of Underutilized Temperate U.S. Tree Crops. Sure, introduce species from abroad, but if they have local wild relatives you have another route to adaptation. Take the hazelnut, for example…
Subspecies Variation of Daucus carota Coastal (“Gummifer”) Morphotypes (Apiaceae) Using Genotyping-by-Sequencing. One morphology and niche, 5 genetic groups.
Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Some differences in results among sampling methods, but not huge.
Combining ability analysis on rhizomatousness via incomplete diallel crosses between perennial wild relative of rice and Asian cultivated rice. If you want perennial cultivated(ish) rice, you have to pick your parents carefully.
Something old, something new: Evolution of Colombian weedy rice (Oryza spp.) through de novo de‐domestication, exotic gene flow, and hybridization. Weedy rice is just local domesticated rice gone bad, at least in Colombia. Gosh I hope that perennial rice doesn’t get de-domesticated.
It’s not just poverty: unregulated global market and bad governance explain unceasing deforestation in Western Madagascar. Stop blaming subsistence slash-and-burn.
Climate change enforces to look beyond the plant – the example of pollinators. Create nice conditions for pollinators on farms, it’ll be worth it.
Paternal Origins and Migratory Episodes of Domestic Sheep. 4 parental lineages, one with primitive features and another with fat tails.
Women and Fish-for-Sex: Transactional Sex, HIV/AIDS and Gender in African Fisheries. Teach a man to fish, FFS.
Use of Untargeted Liquid Chromatography–Mass Spectrometry Metabolome To Discriminate Italian Monovarietal Red Wines, Produced in Their Different Terroirs. A little wine with your fish? Ah no, wait, these are all reds. But at least you can tell them apart now.