Genetic diversity

August 6, 2020August 7, 2020

Switched on switchgrass

Do you live in Kentucky, Tennessee, Alabama, Mississippi, eastern Indiana, western Ohio, eastern Iowa, western North Dakota, eastern Montana, northern Wisconsin, northern Michigan, or the southern Appalachian mountains? Basically the gappy areas below.

Ok, now, do you have any switchgrass (Panicum virgatum) around where you are? Might look something like this.

By Warren Gretz, DOE/NREL – National Renewable Energy Laboratory (NREL), Public Domain.

If so, Dr David Lowry at Michigan State University would like to hear from you.

NOTE: In the interest of full disclosure, I had to change the photo because I uploaded the wrong species having dowloaded a number of different ones from Wikipedia. Thanks to Dave Wood for pointing that out. I originally did it in a hurry and wasn’t paying close enough attention. Sorry.

August 3, 2020August 24, 2020

Brainfood: Perennial favourites, Feral grapevines, Silky cat, Damaged yams, Maize vs sorghum, Sunflower ecotypes, Fungal diversity, Pacific voyaging, Vitamin seeds, Biogeoinformatics, Natural language, Evaluation, Aquaculture

Perennial vegetables: A neglected resource for biodiversity, carbon sequestration, and nutrition. Over 600 perennial veggies on 6% of global vegetable cropland.
Genomic Evidences Support an Independent History of Grapevine Domestication in the Levant. Separate from what happened in the Caucasus, that is.
Distribution, prevalence and severity of damages caused by nematodes on yam (Dioscorea rotundata) in Nigeria. A quarter of tubers and half of heaps showed nematode symptoms.
Maize long-term genetic progress explains current dominance over sorghum in Argentina. Follow the money.
Phenotypic and physiological responses to salt exposure in Sorghum reveal diversity among domesticated landraces. Salinity tolerance was acquired early but then lost in some geographic regions where it wasn’t needed. See what happens when you invest in a crop?
Massive haplotypes underlie ecotypic differentiation in sunflowers. It’s the recombination-suppressing inversions, stupid.
GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Cool. Do landraces of a crop next.
The earliest domestic cat on the Silk Road. Coincided with rapid urbanization in the 9th century.
Native American gene flow into Polynesia predating Easter Island settlement. Yeah, but did Americans go west of their own accord or in Polynesian boats? And did they have sweetpotatoes with them? And cats?
Genetic markers associated with seed longevity and vitamin E in diverse Aus rice varieties. 5 markers on 4 chromosomes.
Biogeoinformatics for the management of Farm Animal Genetic Resources (FAnGR). Software for monitoring erosion and detecting locally adapted genotypes. Plus preserve traditional practices.
Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement. Casually talk about a plant in the field –> fancy math –> the plant’s genotype.
Data synthesis for crop variety evaluation. A review. Focus on ranking. Oh, to mash it up with the above.
Scenarios for Global Aquaculture and Its Role in Human Nutrition. For aquaculture to contribute to nutrition it needs enabling trade and economic policies. Well I never.

July 30, 2020July 30, 2020

Trying tricot

Interested in participatory variety evaluation? Wanna try triadic comparisons of technologies (tricot)? This little thing might help…

https://twitter.com/RManners3/status/1288731146377932800

More background in this paper and others.

Watch out for downloadable copies in multiple languages on the ClimMob website.

July 27, 2020July 14, 2020

Brainfood: Bacterial contamination, Yam diversity, Multi-parent pops, Small millets breeding, Plural valuation, Seed conservation, Transition, Wild spuds, Enset conservation, Cassava viruses, Maize stemborer, Rice roots

Identification and Control of Latent Bacteria in in vitro Cultures of Sweetpotato [Ipomoea batatas (L.) Lam]. 10% of about 2400 in vitro plantlets had a total of about 20 types of bacteria, some of which might be beneficial for all we know, but all of which could be removed.
Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.). Asian and Pacific genepools, thence to India, then Africa, then the Caribbean.
Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Like MAGIC.
Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions. Here’s all the promising material, now go crazy with the MAGIC.
Plural valuation of nature for equity and sustainability: Insights from the Global South. The road to decolonizing conservation.
Long-Term Storage and Longevity of Orthodox Seeds: A Systematic Review. Treat your seeds right.
Changes in food access by mestizo communities associated with deforestation and agrobiodiversity loss in Ucayali, Peruvian Amazon. Less diversified diets, loss of forest cover and reduced agricultural biodiversity go together, somehow.
Evaluation of Wild Potato Germplasm for Tuber Starch Content and Nitrogen Utilization Efficiency. Wild species are better on both counts.
Conservation protocols for Ensete glaucum, a crop wild relative of banana, using plant tissue culture and cryopreservation techniques on seeds and zygotic embryos. 2 accessions thus conserved at NBPGR.
Computational models to improve surveillance for cassava brown streak disease and minimize yield loss. Fancy maths shows that planting clean material helps a lot.
Genome wide association analysis of a stemborer egg induced “call-for-help” defence trait in maize. “…egg-induced parasitoid attraction trait was more common in landraces than in improved inbred lines and hybrids.”
Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice. That would be root growth under drought and Al stress conditions. Every accession has a different set of low frequency causal alleles.

July 20, 2020January 18, 2021

Brainfood: SDGs, Ancient sustainability, Phenomics, Wheat phenotyping, Public breeding, Almond breeding, Ethiopian sorghum, Methane mitigation, Reindeer games, Raised fields, #ArtGenetics

Living Links Connecting the United Nations Sustainable Development Goals: Small-Scale Farmers and Agricultural Biodiversity. Want to address a whole bunch of SDGs at once? Here’s a tip…
Archaeology for Sustainable Agriculture. Sustainability is not forever.
A Congo Basin ethnographic analogue of pre-Columbian Amazonian raised fields shows the ephemeral legacy of organic matter management. Another example of the above?
Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. A lot of useful phenotyping can be done fast and cheap, and genebanks should do it.
LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens. This might help with the above.
Affordable Phenotyping of Winter Wheat under Field and Controlled Conditions for Drought Tolerance. This certainly could. Basically a supermarket cart with a drone mounted on top of it.
Plant Breeding Capacity in U.S. Public Institutions. It’s in trouble.
Redomesticating Almond to Meet Emerging Food Safety Needs. Turning to peach, wild and cultivated, to reduce immunoreactivity and control aflatoxin and Salmonella. Somebody say public breeding is in trouble?
Genetic variability among Ethiopian sorghum landrace accessions for major agro-morphological traits and anthracnose resistance. From 360 accessions to 10. Let’s hope at least the public sector can get hold of them.
Review: Genetic and genomic selection as a methane mitigation strategy in dairy cattle. Gotta measure emissions on individual animals.
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Two domestications, affecting at least a dozen genes. No word on methane.
Genomes on Canvas: Artist’s Perspective on Evolution of Plant-Based Foods. Crowdsourcing historical images to trace crop evolution.