DNA – Page 9 – Agricultural Biodiversity Weblog

August 13, 2021August 13, 2021

Boffins unravel mandarins

I was just going to include the paper Diversification of mandarin citrus by hybrid speciation and apomixis in a forthcoming Brainfood, but the very different approaches taken in the two articles on the paper that I have seen convinced me to give it a bit more space.

The piece in The Packer has very much the industry take, and highlights the contribution of the University of Florida authors: this new information will make breeding easier, including to fight citrus greening.

On the other hand, the press release from the Okinawa Institute of Science and Technology makes much more of how the paper unravels the origin of shiikuwasha and tachibana, which are culturally important citrus fruits in Japan, though not very significant economically.

Something for everyone.

August 2, 2021August 11, 2021

Brainfood: Bambara groundnut, Germination prion, Future foods, Hotspots, Soybean expansion, Remote sensing, Micronutrients, Madagascar food security, Aromatic maize, Sunflower oil, Grasspea, ICARDA lentils, Australian wild rice

Bambara Groundnut (Vigna subterranea [L.] Verdc.) Production, Utilisation and Genetic Improvement in Sub-Saharan Africa. Needs breeding for better yield and nutritional value, and there’s plenty of diversity to work with.
A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. And variation may be linked to ecological adaptation, and so could be used in breeding for drought tolerance. Possibly even in Bambara groundnut?
Future foods for risk-resilient diets. Yeah, microalgae, mycoprotein and mealworm, what could possibly go wrong? I almost prefer the prion.
Hotspots of land-use change in global biodiversity hotspots. Agricultural expansion is the main threat in the Global South, urbanization in the North. Bring on the microalgae.
Massive soybean expansion in South America since 2000 and implications for conservation. A lot of it happens on pastures, but not all, and those cows have to go somewhere.
Remote sensing of biodiversity: what to measure and monitor from space to species? How the above was done. Still waiting for my landrace erosion early warning system.
Priority micronutrient density in foods. Organs, small fish, dark green leafy vegetables, shellfish, beef, goat, eggs, milk, cheese, and canned fish with bones. What, no microalgae?
Food insecurity related to agricultural practices and household characteristics in rural communities of northeast Madagascar. Diversification is needed. Have they thought of microalgae?
Creation of aromatic maize by CRISPR/Cas. Because it’s there? Since you’re at it, why not aromatic microalgae?
Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. Analysis of lots of Russian material identifies interesting genomic regions. Hold the microalgae.
Study of Knowledge, Attitude, and Practice in Participants with Regular Intake of Lathyrus, But No Spastic Paraparesis. Neurolathyrism is not a problem even where grasspea is a major crop.
Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection. Who needs grasspea, though, eh, when you have lentils?
Starch structure-property relations in Australian wild rices compared to domesticated rices. Good, and good for you. Keep your microalgae.

July 26, 2021July 26, 2021

Brainfood: Genetic diversity, Germplasm exchange, Genomic selection, New varieties, Maya agriculture, AnGR, Diverse planted forests, Vermont seeds, Wine appellation, Roots & tubers, Late blight, Nordic barley landraces

The long-standing significance of genetic diversity in conservation. I suppose it does need to be repeated.
Germplasm exchange is critical to conservation of biodiversity and global food security. Yes, indeed it does look like it needs to be repeated.
From gene banks to farmer’s fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms. A prime example of why it should not need to be repeated.
Large potential for crop production adaptation depends on available future varieties. 39% of global cropland could require new crop varieties to avoid yield loss from climate change by the end of the century? You don’t say. Bears repeating.
More than Maize, Bananas, and Coffee: The Inter– and Intraspecific Diversity of Edible Plants of the Huastec Mayan Landscape Mosaics in Mexico. Looks like we don’t need to repeat it to the Maya.
Monitoring and Progress in the Implementation of the Global Plan of Action on Animal Genetic Resources. Significant progress, but correlated with per capita GDP. So some people are listening to the endless repetition; but not enough.
For the sake of resilience and multifunctionality, let’s diversify planted forests! Yes, it needs to be repeated for forests too.
Motivations for maintaining crop diversity: Evidence from Vermont’s seed systems. Yes, repeat by all means, but with variation.
How big is the “lemons” problem? Historical evidence from French wines. Quality certification schemes can support the market value of products. And of course they can be good for genetic diversity too.
Crop resistance and household resilience – The case of cassava and sweetpotato during super-typhoon Ompong in the Philippines. Root and tuber crops are good for household resilience in typhoon-affected areas. Not exactly genetic diversity, but still bears repeating.
Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents. Why genetic diversity is necessary for root and tuber crops too. As if it needed repeating.
Genetic Diversity in 19th Century Barley (Hordeum vulgare) Reflects Differing Agricultural Practices and Seed Trade in Jämtland, Sweden. What causes all that genetic diversity we’ve been repeating endlessly about.

July 19, 2021July 6, 2021

Brainfood: Plant services, Ornamental conservation, Cinnamon, Avocado, Apricot double, Apple, Date palm, Bambara groundnut, Amaranth, On farm research, Fertilizer subsidies

A global database of plant services for humankind. 13% of over 13,000 plant genera have been recorded as human food. But twice as many are described as “ornamentals.”
Horticultural plant use as a so-far neglected pillar of ex situ conservation. Something we can do about those ornamentals. But not only ornamentals, surely.
“Ceylon cinnamon”: Much more than just a spice. But not, alas, an ornamental.
Exploring genetic diversity of lowland avocado (Persea americana Mill.) as a genetic reservoir for breeding. Plus it’s a handsome tree.
Population genomics of apricots unravels domestication history and adaptive events. Separate Chinese and European genepools, deriving from independent domestications from distinct populations. No word on which is more ornamental.
Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation. Get farmers to grow varietal mixtures for maximum ornamental value — and conservation.
Unraveling a genetic roadmap for improved taste in the domesticated apple. No evidence of selection for increased sugar content. And ornamental value?
Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Ancient hybrid origin for the coincidentally ornamentally and otherwise valuable food crop, followed by introgression from both wild close congeneric relatives.
Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers. 3 groups: W Africa, Central Africa, E + S Africa. No word on which would make the most attractive ornamentals.
A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop. Yeah, but where are the genes that make it ornamental too?
How accurate are yield estimates from crop cuts? Evidence from smallholder maize farms in Ethiopia. More accurate than estimates of horticultural attractiveness, I suspect.
The unintended consequences of the fertilizer subsidy program on crop species diversity in Mali. Spoiler alert: they’re bad. Fortunately, ornamentals don’t attract subsidies.

June 7, 2021June 7, 2021

Brainfood: Agroecology, Bioinformatics, Brazilian cassava, Cypriot wine, Swiss poppies, Pollinators, Groundnut breeding, Sorghum pangenome, Crop origins, Sparing vs sharing, Language diversity, Watermelon origins

Crop origins explain variation in global agricultural relevance. What explains which crops are most important globally? For seeds, an origin in seasonally dry regions. For root, leaf and herbaceous fruit crops, an origin in the aseasonal tropics. But if you account for all that, basically age.
Linguistic diversity and conservation opportunities at UNESCO World Heritage Sites in Africa. There’s a correlation between linguistic and biological diversity. Has anyone done crop diversity and languages?
Sparing or sharing land? Views from agricultural scientists. If you look at synergies between nature and nurture (as it were), and beyond crop yield, you realize it’s the wrong question.
Can agroecology improve food security and nutrition? A review. Yes, in 78% of 55 cases. But will it scale? And does it need to? Anyway, at least it’s looking beyond yield.
Global effects of land-use intensity on local pollinator biodiversity. Intensification is bad for pollinator biodiversity for most land uses, but cropland intensification is only bad in the tropics. Can’t help thinking this needs to be mashed up with the above.
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. In particular, integrating the phenomics and genomics of landraces and wild relatives at the extremes of habitable ranges. Well, there’s a lot more to it than that, but this is what stuck with me.
Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. 54% duplicates out of 3354 clones, the remaining 1536 arranged in 5 ecoregional ancestral groups.
A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Not from southern Africa after all. Nice bit of work.
Preliminary investigation of potent thiols in Cypriot wines made from indigenous grape varieties Xynisteri, Maratheftiko and Giannoudhi. Cypriot grapes are more drought tolerant than varieties grown in Australia, but produce the tastes Aussie wine drinkers really like.
A morphometric approach to track opium poppy domestication. Fancy math says Swiss Neolithic farmers were involved in the domestication of the opium poppy. Enough to drive one to drink.
Registration of GA-BatSten1 and GA-MagSten1, two induced allotetraploids derived from peanut wild relatives with superior resistance to leaf spots, rust, and root-knot nematode. Sequencing paying off.
Extensive variation within the pan-genome of cultivated and wild sorghum. Sorghum next?