Genetic diversity

September 10, 2025September 10, 2025

A breed is a breed is a breed?

I feel maybe yesterday’s Nibble on the definition of a “breed” may have been a bit too laconic, even for me. So let me give a bit more context.

A ram and ewe of the South Down and Norfolk breeds of sheep. Etching, ca 1822. Created 1 June 1822. Cattle. Livestock – Breeding. Domestic animals. Livestock breeds. Rams. Ewes. Work ID: ytvy3rzq.

The link was to a YouTube playlist, which was described thus (link added):

The presentations in this playlist are from the webinar on “Genomic assessment of genetic variation and the future of the breed concept”, originally held on 12.12.2024 under the umbrella of the Food and Agricultural Organization (FAO). This represents the culmination of collaborative work by a diverse group of experts from institutions from all around the world to prepare materials for a sub-chapter in the upcoming 3rd Report on the State of the World’s Animal Genetic Resources for Food and Agriculture.

It amounts to over an hour of talks, but if I had to summarize the point the playlist is making, it is that genomics is redefining a breed as a fluid, porous, genotypically-characterized population rather than a fixed, pedigree-based, phenotypic entity. Thus, it is shifting livestock conservation from saving labels (“Breed A”) to preserving genetic options.

Here’s a handy table I came up with to describe the change:

Interesting to juxtapose this to the post a few days ago on how to value and use Indigenous knowledge to solve today’s problems. Would Indigenous livestock keepers necessarily care about those genetic options more than their traditional breed?

It would be great to hear from people engaged in livestock conservation on this. It’s unfortunately not a community I interact with much.

September 8, 2025September 8, 2025

Brainfood: Core collections of…durum, deulkkae, barnyard millet, durian, sesame, flax, Fendler’s horsenettle, jute mallow, barley

Creation of a core set of durum wheat accessions based on agro-morphological traits with maximum diversity and lower redundancy. From 710 to 13 accessions (2%!) using 32 morphological traits, thanks to Power Core.
Construction of a core collection of Perilla frutescens (L.) Britton Germplasm in the South Korean gene bank using agro-morphological traits. From 1227 to 235 accessions (19%) using 17 morphological traits, thanks to a bunch of different methods.
Comprehensive Phenotyping of 1,807 Indian Barnyard Millet (Echinochloa frumentacea Link) Accessions from Indian National Genebank: Unlocking Diversity for Core Set Development. From 1,807 to 271 accessions (15%) using 23 quantitative traits, thanks to Core Hunter 3.
Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm. From 114 to 26 accessions (23%) using 39 million high-quality SNPs across the genome.
Development of a composite core collection from 5,856 sesame accessions being conserved in the Indian National Genebank. From 5,856 to 1,768 accessions (30%) using SNPs and phenotypic data.
Optimizing core collections for genetic studies: a worldwide flax germplasm case study. From 1,593 to 350 accessions (22%) using phenotypic and genotypic data, times 200, thanks to CoreCollection, corehunter III, TrainSel, and more.
An Optimized Core Sample of the Wild Potato Solanum fendleri in the USA. From 269 accessions, to 38 plants, to 1 accession (0.4%!). Beat that!
Countrywide Corchorus olitorius L. core collection shows an adaptive potential for future climate in Benin. From 305 to 54 accessions (18%) using 1,114 high-quality SNPs, thanks to ShinyCore. Some indication of usefulness.
Multi-environmental evaluation of barley core collection against spot blotch for genetic variability and identification of promising genotypes exhibiting resistance. From a core collection of 678 accessions to 2 genotypes that might actually be useful to breeders. Finally!

September 1, 2025September 1, 2025

Brainfood: Agroecology, Afghan wheat, CWR microbes, Chocolate microbes, Liberica coffee, Wild apples, USDA cotton collection, Parmesan cattle, Sweetpotato genome, Vertical tomatoes

Embracing new practices in plant breeding for agroecological transition: A diversity-driven research agenda. Plant breeding for agroecology will need access to locally-adapted plant diversity, sure, but also the involvement of a diversity of stakeholders and the use of a diversity of co-design strategies.
Conservation and Utilization of Wheat Genetic Resources in Afghanistan Expanded with the Homecoming Wheat Landraces Collected Half a Century Ago. The above could also be said of wheat breeding in Afghanistan. Fingers crossed.
Blueprints for sustainable plant production through the utilization of crop wild relatives and their microbiomes. Oh, wait, breeders (agroecological and otherwise) will also need the diversity of microbiomes associated with crop wild relatives.
A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Oh, wait, we will also need the diversity of the microbes involved in fermentation, at some point.
Genomic data define species delimitation in Liberica coffee with implications for crop development and conservation. It might help if we knew how many species made up a crop in the first place. In the case of Liberica coffee, it turns out to be 3. No word on the microbiomes involved.
Assessment of genetic diversity and population structure of Malus sieversii and Malus niedzwetzkyana from Kazakhstan using high-throughput genotyping. It would also help to know where interesting diversity was concentrated within crop wild relatives. In apples, it’s not necessarily the ancestor.
The National Plant Germplasm System cotton collection—a review of germplasm resources, phenotypic characterization, and genomic variation. Lots of morphological characterization and agronomic evaluation, not so much molecular data, but increasing. No word on the microbes.
Establishing a genomic-driven conservation of a cattle genetic resource: the case of the Parmigiano-Reggiano cheese iconic breed. In contrast, these guys have genotyped practically a whole breed. But yeah, no microbes.
Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato. The contributions of different wild relatives to the sweetpotato genome are to be found intertwined along chromosomes rather than restricted to subgenomes. Unclear what that will mean to agroecologial breeders.
Harnessing Green Revolution genes to optimize tomato production efficiency for vertical farming. Agroecological breeders unavailable for comment.

August 28, 2025September 1, 2025

How to revive your landraces

How can you get humble heirloom varieties of the humble potato back into cultivation? Well, fortunately, Potato News Today ¹ has a handy step-by-step guide, which I reproduce verbatim below:

Start with a story you can legally sell. In Europe/UK, use the conservation-variety route; in North America, lean on certified seed suppliers and Indigenous stewardship agreements.
Source clean, traceable stock. CIP and the U.S. Potato Genebank maintain indexed, disease-tested material; combine with reputable local seed houses.
Pilot with chefs and specialty retail. Early-season launches with menu credit and a farm feature move the needle.
Package the provenance. PDO/PGI examples like Jersey Royal and Papas Antiguas de Canarias show how origin, agronomy, and micro-harvest rituals create value.
Engineer storage for shape and use. Follow the curing/holding guidance above.
Ride the calendar. Tie launches and media to the International Day of Potato (30 May) or to local potato festivals.

Sounds pretty sensible, and applicable to other crops as well, I suspect, with a little tweak here and there.

The article also has a list of case studies. This doesn’t include any examples from Italy, but coincidentally a recent paper describes just such a thing. Which maybe points to something that is missing from the Potato News Today playbook, to whit having lots of interesting characterization and other data on your heirloom landraces handy to help get them ready for prime time.

August 18, 2025August 18, 2025

Brainfood: Agroforestry, Afro-descendant conservation, Opportunity crops, Off-farm income, Phureja conservation, European taro, Argania products, Honeybee intensification, Mycorrhizal hotspots

Effects of tree cover and crop diversity on biodiversity and food security in tropical agricultural landscapes. In tropical agricultural landscapes, modest tree cover in diverse cropping systems supports higher biodiversity and higher crop yields, demonstrating that agroforestry can deliver win-win synergy between conservation and food production.
Afro-descendant lands in South America contribute to biodiversity conservation and climate change mitigation. I guess biodiverse landscapes managed according to traditional knowledge deliver superior environmental outcomes not just in farms with trees but also in forested territories under community management.
Science for Africa’s future food security: reimagining the histories and futures of underutilised crops. Reviving indigenous, underutilised crops in sub-Saharan Africa by restoring their historical and cultural significance can enhance nutritional diversity, climate resilience and food security, paralleling the evidence above that culturally rooted, biodiversity-rich systems are good for both the environment and communities.
Off-farm income and dietary diversity in subsistence farming in Burundi. Across rural and urban settings, from farms to forests to cities, culture-informed, biodiversity-rich food systems offer interlocking benefits: ecological resilience, climate mitigation, improved nutrition, and community empowerment. Or am I stretching a point here?
Cultivar loss and conservation of genetic resources of the phureja potato (Solanum phureja L., Phureja Group) in Peru. Traditional Andean farming communities are witnessing the disappearance of this culturally significant diploid potato group, which has rich genetic diversity and interesting adaptations, highlighting an urgent need for in situ conservation to preserve it. Oh wow, look, locally rooted, biodiversity-rich farming systems, anchored in cultural heritage, are key to sustaining ecosystem services, safeguarding genetic diversity, and building climate-resilient, equitable food futures. Again.
Taro (Colocasia esculenta) in Europe: a journey through fields, botanical gardens, ditches and city markets. This culturally important root crop was introduced in Europe in antiquity and now survives in fields, markets, and even city waterways as both ornament and food, but despite its genetic and cultural richness, it remains under-researched and requires both ex situ and in situ conservation to safeguard its long-term use. So yep, even this one says that conserving crop diversity through culturally embedded, multi-dimensional stewardship is essential for strengthening food security and preserving heritage in a changing climate.
Innovation of argan (Argania spinosa (L.) Skeels) products and byproducts for sustainable development of rural communities in Morocco. A systematic literature review. Innovative uses of argan tree products and by-products in Morocco, from bioplastics and biochar to livestock feed and natural repellents, offer promising pathways for conservation, cultural preservation, and rural economic development, provided local communities are actively engaged in participatory management. Where have I heard that before?
Negative ecological impacts of honeybees begin at densities below recommended levels for crop pollination. Too many honeybee hives can reduce wild bee abundance, species richness, and fruit yield on farms, even when wildflower strips are present, suggesting that ecological balance is disrupted when managed pollinators outcompete native species. Which can probably be cleverly connected with all of the above with a little more time than I have at the moment.
Global hotspots of mycorrhizal fungal richness are poorly protected. What can I tell you, we need in situ conservation for mycorrhiza too. And machine learning can help us figure out where best to do it. For all of the above, and more, naturally.