Biotechnology

April 4, 2023April 5, 2023

The cost of tomatoes

I don’t know whether the article in The Media Line ((Strap line: Trusted Mideast News.)) a few days ago entitled “Israeli Scientists Develop Drought-Resistant Tomatoes in Response to Climate Change” was based on a press release. But if it wasn’t, it’s a pretty good catch, given the paper on which it is based is called “Epistatic QTLs for yield heterosis in tomato.” ((It’s part of the PNAS Special Feature: Harnessing Crop Diversity.))

Anyway, what the authors of the paper did was cross a wild tomato with a cultivated one, which conjured up about 1,500 different progenies, each with a different bit of wild genome. They then figured out which of those bits of genome were good at allowing their possessor to grow well with less water than normal.

According to our Trusted Mideast News source:

The study found that two specific areas in the plant’s genome lead to a 20%-50% increase in the overall yield in both regular and dry conditions. The overall size of the plant also was improved.

According to the researchers, the findings demonstrate the effectiveness of using wild species to enhance agricultural output. They could also prove to be widely applicable to other plants in the future.

Which got me thinking. Effective, sure. But how long did it take? Digging a little deeper revealed that the work relied on a genome of the wild tomato Solanum pennellii that was published in 2017. But that’s not where it all started:

…we sequenced and assembled the accession LA5240 (LYC1722) of the wild tomato species Solanum pennellii, an accession that was identified spuriously. Unlike the Solanum pennellii accession LA0716, for which we have previously generated a high quality draft genome, the accession LA5240 does not appear to exhibit any dwarfed, necrotic leaf phenotype when introgressed into modern tomato cultivars.

And that LA0716 was sequenced in 2014.

So our new climate-change-proof tomato was almost 10 years in the making and relied on a “spuriously” identified accession. Well done and all, but gosh, I hope the next one is easier.

Oh, and here’s a nice detail to close. The LA in LA5204? It stands for “Lost Accession.” What’s the story there, I wonder?

April 3, 2023March 30, 2023

Brainfood: Traits & environment, Acacia growth, Local extinction risk, Lebanese CWR priorities, Malawi CWR payments, Bread wheat origins, Wild lettuce, Ethiopian forages, Editing forages

Why can’t we predict traits from the environment? Because plants are not collections of independent, isolated traits. All the more reason to study, understand and protect wild plants of economic importance, as the following papers show.
Differential climatic conditions drive growth of Acacia tortilis tree in its range edges in Africa and Asia. Case in point of the above. Makes germplasm evaluation really hard.
Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology. Modelling based on the genomic offset (GO) method and the mutations–area relationship (MAR) can help better predict the risk of extinction of different populations.
Crop wild relatives in Lebanon: mapping the distribution of Poaceae and Fabaceae priority taxa for conservation planning. Bekaa and Baalbak have the highest diversity and the SW the most gaps.
Community-Level Incentive Mechanisms for the Conservation of Crop Wild Relatives: A Malawi Case Study. Paying communities to conserve crop wild relatives could work and be relatively cheap. Waiting to see this being applied in the Bekaa.
Population genomics unravels the Holocene history of bread wheat and its relatives. Yeah but crop wild relatives really held back bread wheat domestication. So maybe the Bekaa owes everyone else.
New insights gained from collections of wild Lactuca relatives in the gene bank of the Institute of Evolution, University of Haifa. Maybe they can gain an insight into how to make lettuce taste of something. And I wonder what environmental variable that will be associated with.
Climate change and land-use change impacts on future availability of forage grass species for Ethiopian dairy systems. Two forages will do better under climate change, one worse. Assuming a lot of stuff.
Application of CRISPR/Cas9 technology in forages. But plants are not collections of independent, isolated traits, right?

March 21, 2023March 24, 2023

Nibbles: Food system transformation, Global food crisis, Rewilding, Genomics, Data management

According to WWF, Solving the Great Food Puzzle involves, inter alia, nutritious indigenous crops, agrobiodiverse cropping systems, and traditional food cultures. Those are just 3 of 20 levers for food system transformation. Is it me or are levers and accelerators the current flavours of the month?
Even the Gates Foundation agrees on that indigenous crop thing, kinda sorta, if you squint. In this piece, for example, Enock Chikava, Interim Director, Agricultural Development, waxes lyrical about teff.
Meanwhile, in the middle of its tomato shortage, and not much interested in teff, the UK is betting on re-establishing prehistoric landscapes full of wild pigs and bison. Bold move.
But who needs bison protein when you have the genome of the faba bean? Which after all is a nutritious indigenous crop, part of agrobiodiverse cropping systems, and a component of traditional food cultures.
Ah, but you need to manage all that data on indigenous crops, and Clemson University is there to help. WWF take note.

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.

March 6, 2023March 3, 2023

Brainfood: Food biodiversity, Diversification, New crops, GMO maize, African livestock, Greek innovation clusters, Amazonian native cacao

Food Biodiversity as an Opportunity to Address the Challenge of Improving Human Diets and Food Security. Biodiversity and food security can be mutually supportive, but you need education, research and inclusion, say educators and researchers.
Achieving win-win outcomes for biodiversity and yield through diversified farming. Biodiversity and yield both win in only about a quarter of cases. But humanity does not live by yield alone, right?
Accelerated Domestication of New Crops: Yield is Key. Ooops, looks like humanity does live by yield alone after all.
Genetically Modified Maize: Less Drudgery for Her, More Maize for Him? Evidence from Smallholder Maize Farmers in South Africa. No, wait, man lives by yield alone, but not woman.
Climate Change’s Impact on Agriculture and Food Security: An Opportunity to Showcase African Animal Genetic Resources. Forget GMO maize, Africa needs to develop its own agrobiodiversity…
Friend or Foe? The Role of Animal-Source Foods in Healthy and Environmentally Sustainable Diets. …and it need not be bad for either health or the environment.
AgriDiverCluster: An Innovative Cluster for the Utilization of Greek Biodiversity and Plant Genetic Resources. Maybe the Greeks have a way to make it not bad for either health or the environment. By vertical integration, it looks like.
Socio-ecological benefits of fine-flavor cacao in its center of origin. Amazonian cacao farmers also seem to have a way to vertically integrate.