- Delayed luminescence of seeds: are shining seeds viable? Maybe, but more research needed.
- Explaining the spatial scale of campesino agriculture in Mexico: Implications for the supply and conservation of native maize. Maize is not just for subsistence; never has been.
- Impact of Xylella fastidiosa subspecies pauca in European olives. Fancy maths says olives are doomed. But we knew that, right?
- Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement. Amazingly, still more collecting is needed.
- The projected timing of abrupt ecological disruption from climate change. And this is why.
- The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium. Its range may expand in some places, shrink in others. so it’s not like all bad news then? At least you know where to collect it from.
- Early Holocene crop cultivation and landscape modification in Amazonia. REALLY early agriculture in the Llanos de Moxos. Any collecting there, I wonder?
- Exploring the genetic base of the soybean germplasm from Africa, America and Asia as well as mining of beneficial allele for flowering and seed weight. The African material is not very diverse, but is very different
- Novel Source of Biotic Stress Resistance Identified from Brassica Species and its Wild Relatives. From 3000 to about 10 “useful” accessions.
- Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Thinopyrum elongatum got head blight resistance from the fungus Epichloë. GMOs unimpressed.
- A Wild Cajanus scarabaeoides (L.), Thouars, IBS 3471, for Improved Insect-Resistance in Cultivated Pigeonpea. It has multiple disease resistance mechanisms against pod borer. And here it is.
- A Planetary Health Perspective on Agroforestry in Sub-Saharan Africa. Trees on farms are good for you. Here come the data.
- Dietary diversity and fish consumption of mothers and their children in fisher households in Komodo District, eastern Indonesia. Infants and young children are not getting enough of all the fish.
- Agriculture and the Disruption of Plant–Microbial Symbiosis. Agronomy, ecology and breeding can screw up microbial symbioses in cultivated plants, and that’s not good. But it is expected.
- Animal domestication in the era of ancient genomics. “By documenting how livestock populations endured both past epidemics and environmental change, ancient genomics can provide invaluable information that can be used to address current and future societal challenges.” Can.
The pan-genome is the new genome
Our friend Ruaraidh Sackville Hamilton has kindly taken a break during his retirement to answer a burning question. Thanks, Ruaraidh, you can get back to your G&Ts now.
“What earthly use is this?” asked a well-known mutual friend in response to the recent publication of a “platinum standard pan-genome resource” for rice.
I assume he wasn’t questioning the value of reference genomes. After all, everyone knows that the Nipponbare reference genome has enabled rice scientists to do things that are still a dream for other crops. So I assume “this” refers to sequencing 12 more reference genomes for Oryza sativa, to make a total of 16.
Where to start? Suppose you’re a pathologist studying a variety with a disease resistance gene that’s completely absent from Nipponbare. What earthly use is the Nipponbare reference genome to you? None.
Or suppose you’re a diversity scientist trying to quantify diversity in the genepool of Oryza sativa by comparison against Nipponbare. You find that the more different a variety is from Nipponbare, the more missing data you have, and the less you can tell about its genome. How useless is that?
Large indels and long-range structural variation in the genome present insurmountable problems when aligning short-read sequences to a single reference genome. To get some indication of the magnitude of the problem, look at an earlier paper “Genomic variation in 3,010 diverse accessions of Asian cultivated rice.” Coverage of 453 of these genomes was sufficiently good to enable some sort of de novo assembly and thus overcome the problem of a single reference. The “core genome” (the part of the genome that is present in all varieties tested) contains little more than half the gene families that are present in at least one accession (figure 4c). And, on average, pairing a japonica variety with an indica variety you get 2,878 genes that are present in only one (figure 4e). That’s an awful lot of uselessness in a single reference.
And look where Nipponbare sits in the phylogenetic tree shown in figure 1 of the new paper. It’s way off at one end, highly unrepresentative of the species.
And look at the genome sizes in Table 3. Genomes of the japonica group (which includes Nipponbare) are on average around 12 million base pairs shorter than those of the indica group (which is the more important group in tropical agriculture). That converts to a lot of missing genes.
So, rather than ask “What earthly use is this?”, I’d turn it around and say “Why has it taken so long to get here?”. As long as we are constrained to short reads for low-cost high-throughput sequencing, we need multiple reference genomes for every crop, so that we can build a pan-genome per crop.
Nibbles: Native American seeds, Peasant’s Struggle, IWYP, Taxonomy booklet, Phylogenetics booklet, Lost apples, Yak threat, Online mapping, Sampling strategy
- Native Americans are coping with a coronavirus-caused food shortage by seed saving. Among other things.
- On the International Day of Peasant’s Struggle, even.
- IWYP science brief on using wheat wild relatives in breeding.
- Really nice Meise Botanic Garden publication on botanical nomenclature.
- And to complement the above: Phylogenetics in the Genomic Era.
- More old apples found. I’m beginning to think the whole lost apples thing is a scam.
- But losing yaks is a definite possibility.
- Nature Map Explorer is online. Rejoice.
- Sean Hoban on calculating how much to collect and conserve. Without using the above.
Nibbles: Joy of seeds, CC risk map, Community seed banks, Genebanks
- Yes, what does make seeds so incredible?
- Biodiversity risk from climate change: the interactive online map.
- Community seed banks for farmers’ rights. And not only.
- Genebanks in a time of coronavirus.
- SPC genebank is trying to deal with COVID-19.
- The USDA genebank at Ft Collins soldiers on.
Brainfood: PFM, Endemic diversity, VAM, Food systems, Forages, Ganja taxonomy, Maize phenomics, Yield maps, Cassava breeding, Diversification, Distributions
- The illusion of participatory forest management success in nature conservation. Success is in the eye of the beholder.
- Back to the future of a rare plant species of the Chihuahuan desert: tracing distribution patterns across time and genetic diversity as a basis for conservation actions. A combination of genetic analysis and niche modelling shows that population structure is due to habitat, not geography.
- High‐throughput phenotyping reveals growth of Medicago truncatula is positively affected by arbuscular mycorrhizal fungi even at high soil phosphorus availability. And affected differently during the course of plant growth.
- Global drivers of food system (un)sustainability: A multi-country correlation analysis. Most drivers are driving sustainability in the wrong direction.
- Progress and Challenges in Ex Situ Conservation of Forage Germplasm: Grasses, Herbaceous Legumes and Fodder Trees. Highly palatable leguminous woody species tick a lot of boxes. We know what to do. Let’s do it.
- A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives. One subspecies, 4 botanical varieties? Well, that’s like your opinion, man.
- Phenomic selection and prediction of maize grain yield from near‐infrared reflectance spectroscopy of kernels. Yeah, but can you do it in the field?
- Global dataset of historical yields v1.2 and v1.3 aligned version. For maize, rice, wheat and soybean, for the period 1981-2016. No NIRS in sight.
- Cassava breeding and agronomy in Asia: 50 years of history and future directions. 50% yield increase in 20 years. Is that good?
- Decision-Making to Diversify Farm Systems for Climate Change Adaptation. Define goals, assess enabling & disabling factors, quantify risks, look for gaps in functional diversity, pick some interventions, evaluate & learn.
- Connecting species’ geographical distributions to environmental variables: range maps versus observed points of occurrence. Points are better than polygons.