- Intersecting and dynamic gender rights to néré, a food tree species in Burkina Faso. Women are not a homogeneous group.
- A bitter pill: smallholder responses to the new green revolution prescriptions in northern Ghana. Not a revolution, and not very green. More context here.
- Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Not very domesticated: probably needs a green revolution, eh?
- The relevance of gene flow with wild relatives in understanding the domestication process. Maize domestication took a long time, involved introgression with 2 different wild relatives, and did not take place where it was previously thought.
- Diversity of Maize Landraces in Germplasm Collections from South America. And not a genome in sight.
- Global vulnerability of soil ecosystems to erosion. Soil erosion is increasing, and impacting areas of high soil biodiversity.
- The Sweet Taste of Adapting to the Desert: Fructan Metabolism in Agave Species. Not enough is know to fully exploit this remarkable adaptation.
- A platinum standard pan-genome resource that represents the population structure of Asian rice. Because Nipponbare was the wrong thing to sequence initially. Fonio next?
- Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement. Some of the 45 genotypes introduced by ILRI from EMBRAPA, Brazil do well in Ethiopia, and it’s not necessarily the elite material.
- Historical changes in the contents and compositions of fibre components and polar metabolites in white wheat flour. Some went up, some went down.
- Correlation between Agricultural Biodiversity, Dietary Diversity, Household Food Security and Associated Factors of Wasting among 6-59 Months old Children in Ambassel Woreda, North East Ethiopia. Mother’s education and dietary diversity are associated with better children’s health.
Agrobiodiversity everywhere
If that looks familiar, you can help…
Brainfood: Shiny seeds, Mexican maize, Olive plague, Pulse CWR, Climate change & biodiversity, Soybean diversity, Wild tomato, Brassica evaluation, Horizontal gene transfer, Wild Cajanus, Agroforestry benefits, Fishy diets, Symbiosis, Ancient Amazonia, Animal domestication
- 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.
CGIAR genebanks keeping on keeping on
Just a quick Twitter thread illustrating how the international genebanks managed by the CGIAR centres are trying to maintain basic operations in the midst of the coronavirus pandemic.