- The latest on TR4 resistant banana varieties in Australia.
- Lactobacillus is in fact 25 genera.
- Greenhouse tomatoes pretty diverse after all?
- Digitaria: from weed to forage.
- London’s mulberries.
Brainfood: Red Listing, Name checking, Diversification, New breeding, Seed data, Tea genome, Sampling strategies, Plum diversity, Fruit taste, Enset seeds, Maize & nutrition, Emilian grapes
- Caution Needed When Predicting Species Threat Status for Conservation Prioritization on a Global Scale. Automated rapid preliminary assessments are all well and good, but…
- WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online Taxonomic Backbone data. Automated rapid taxonomic name checking is all well and good, but…
- Diverse approaches to crop diversification in agricultural research. A review. Too diverse.
- Reinventing quantitative genetics for plant breeding: something old, something new, something borrowed, something BLUE. Retire additive variance.
- Nikolaeva et al.’s reference book on seed dormancy and germination. A treasure trove of data comes to light.
- The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants. Three groups, originating in SW China.
- Taxonomic similarity does not predict necessary sample size for ex situ conservation: a comparison among five genera. The old rule-of-thumb of 50 individuals was not all that far off after all.
- Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe. 93 unique accessions out of 104 across 14 partners. Pretty good, no?
- Genome‐wide association of volatiles reveals candidate loci for blueberry flavor. Can predict taste from genetics.
- Germination ecology of wild and domesticated Ensete ventricosum: Evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop. Seeds from domesticated material are not much different from the wild ones, except in germination niche.
- Mining maize diversity and improving its nutritional aspects within agro‐food systems. Biofortification is only the beginning.
- Genetic Characterization of Grapevine Varieties from Emilia-Romagna (Northern Italy) Discloses Unexplored Genetic Resources. About half (62) of the unique accessions (122) in a collection (178) are hardly known.
Brainfood: French Neolithic, African forages, Sorghum inflorescences, Root morphology, Folium, Tillage, Sparing, Food localness, Indian diet diversity, Sourdough, Genomics costs, Breeding strategies
- Early Neolithic (ca. 5850-4500 cal BC) agricultural diffusion in the Western Mediterranean: An update of archaeobotanical data in SW France. Agriculture came to southern France from southern Italy around 5700 BC, initially focusing on hulled wheats, then transitioned to naked cereals as it moved inland.
- Improved feeding and forages at a crossroads: Farming systems approaches for sustainable livestock development in East Africa. Adoption of tropical forages at scale can make a big difference to livelihoods in East Africa, but will need careful consideration of agroecological and socioeconomic settings. My mother-in-law unavailable for comment.
- Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences. Fancy gadgets and maths show that botanical sorghum races overlap more in morphology than genetics.
- Using clear plastic CD cases as low‐cost mini‐rhizotrons to phenotype root traits. Now do roots.
- A 1000-year-old mystery solved: Unlocking the molecular structure for the medieval blue from Chrozophora tinctoria, also known as folium. 6′-hydroxy-4,4′-dimethoxy-1,1′-dimethyl-5′-{[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-[3,3′-bipyridine]-2,2′,5,6(1H,1′H)-tetraone, if you must know.
- Generating a rule-based global gridded tillage dataset. The most amazing thing about this is that there are only 6 types of tillage.
- The global cropland-sparing potential of high-yield farming. We could give up 40% of current farmland if yields of 16 major crops were higher. Unclear what all those farmers would do. Or what kind of tillage they would use.
- Local food crop production can fulfil demand for less than one-third of the population. Still going to need global supply chains.
- Regional differences in agricultural and socioeconomic factors associated with farmer household dietary diversity in India. And national supply chains for that matter.
- Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread. Bakers are part of bread.
- Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants. Down to $22 per sample, if you play your cards right.
- Evolutionary insights into plant breeding. When you’ve played those cards, target selective sweeps for introgression, among other things. Oh, and gene editing. Here, read these tweets from one of the authors.
Brainfood: Parkia rights, African Green Revolution, Fonio genome, Maize double, Soil erosion, Agave fructans, Rice pangenome, Napier evaluation, Flour quality, Diet diversity
- 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.
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.