Agricultural Biodiversity Weblog

March 22, 2023

Dams, damn dams, and accessions

Every once in a while a new dam dataset crops up. Dam, not damn. Well, maybe damn as well. Anyway, when that happens, I feel compelled to mash it up with accession locality data. Because if I don’t do it, who will?

The new dataset is the Global Dam Tracker, and you can download it and everything of course. It’s pretty easy to then upload it to Google Earth and play around with it. Including combining it with data on wild Oryza accessions from Genesys, for example.

On this map, the dams are shown in blue and wild rice accessions in red.

You can zoom in if you’re worried about the long-term in situ future of any given population.

Not for the first time, I wonder about the feasibility of one day automatically and in real time combining data from multiple such potential stressors to predict the risk of genetic erosion around the world. Something that AI should be able to do, surely?

March 21, 2023

Spring forward!

Pieter Breughel the Younger, CC BY-SA 4.0, via Wikimedia Commons

March 20, 2023March 20, 2023

Brainfood: Seed imaging, Disease imaging, Seed traits, Irvingia shape, Mexican tomatoes, Fine cacao, Wine tourism, Wild peas

Implication of high variance in germplasm characteristics. Last week’s Brainfood focused on genomic variation. This week, in contrast, we look at phenotyping. But not old school phenotyping, oh no. This paper, for example, uses fancy-ish, but not especially expensive, imaging.
High-throughput imaging of powdery mildew resistance of the winter wheat collection hosted at the German Federal ex situ Genebank for Agricultural and Horticultural Crops. This paper uses somewhat fancier, and possibly more costly, imaging. Vorsprung durch Technik.
Low availability of functional seed trait data from the tropics could negatively affect global macroecological studies, predictive models and plant conservation. Even embryos in seeds can be phenotyped.
Agroforestry Trees’ Architecture as Evidence of Domestication: Case of African Mango Tree in the Dahomey Gap, West Africa. I wonder if one could describe the shape of tree crowns from space? I hope not, this work sounded like fun…
Diversidad biocultural de tomate nativo en Oaxaca, México. Phenotype is socially constructed in tomato too.
Who Defines Fine Chocolate? The Construction of Global Cocoa Quality Standards from Latin America. Can you standardise a social construct such as the flavour of chocolate, and would it help farmers? Maybe.
Douro wine-tourism engaging consumers in nature conservation stewardship: An immersive biodiversity experience. How to make money out of a socially constructed phenotype.
Natural range, habitats and populations of wild peas (Pisum L.). We should get out of our labs and look for wild peas in the oases of the Sahara Desert, the subalpine communities of Georgia, and the Asir Mts of Yemen. But will we know them when we see them?

March 17, 2023

What have micronutrients ever done for us?

Over on Twitter, Ty Beal of GAIN has a thread on micronutrients. It’s based on a recent lecture and it has useful data and nice slides. Here’s the money quote:

In lower income countries micronutrient deficiencies are due in part to people not having access to diverse diets. They want healthy, nutrient dense foods but can’t afford them or access them in markets.

March 13, 2023March 15, 2023

Brainfood: Genomics for conservation and use edition

How genomics can help biodiversity conservation. Let’s find out, but let’s broaden it to use as well, shall we? On the assumption that what’s good for conservation is good for use, and vice versa.
Genetic and genomic interventions in crop biofortification: Examples in millets. Genomics can help you get more nutritious millets, and also use millets to improve the nutritive content of other cereals too.
Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Genomics can help you figure out ways to decrease the toxicity of grasspea.
Extensive crop–wild hybridization during Brassica evolution and selection during the domestication and diversification of Brassica crops. Genomics can help you figure out the evolutionary history of crops…
Molecular characterization of Brassica genebank germplasm confirms taxonomic identity and reveals low levels and source of taxonomic errors. …assuming you have you accessions labelled correctly that is.
Dual domestications and origin of traits in grapevine evolution. Genomics can help you figure out the evolutionary history of crops. No, wait, we already had that one…
Balancing grain yield trade-offs in ‘Miracle-Wheat’. Genomics can help you figure out the best phenotype in wheat.
Focusing the GWAS Lens on days to flower using latent variable phenotypes derived from global multienvironment trials. Genomics can help you figure out the best phenotype in lentils too.
Awned versus awnless wheat spikes: does it matter? Although actually you don’t necessarily need genomics to help you figure out the best phenotype in wheat. But let’s get back on track.
SNP Diversity and Genetic Structure of “Rogosija”, an Old Western Balkan Durum Wheat Collection. That’s better. Genomics can help you figure out that a wheat collection can consist of distinct ecogeographic groupings.
Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion. Genomics can help you figure out what’s behind local adaptation in crop wild relatives.
Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers. Genomics can help you figure out the evolutionary history of crop wild relatives. Where have I heard that before?
A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Genomics can help you figure out the evolutionary history of plant pathogens too. Here’s a Twitter thread from one of the authors with lots of maps to prove it.
Honey bee populations of the USA display restrictions in their mtDNA haplotype diversity. Yeah, you guessed it, pollinators too.
Mezcal worm in a bottle: DNA evidence suggests a single moth species. I rest my case.