- Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance. Fancy genotyping and phenotyping picks out landrace whose name in Sinhalese means “drought rice.”
- The relationship between agricultural biodiversity, dietary diversity, household food security, and stunting of children in rural Kenya. Increasing dietary diversity could increase household food security.
- Biodiversity and origin of the microbial populations isolated from Masske, a traditional Iranian dairy product made from fermented Ewe’s milk. Streptococcus thermophilus doesn’t sound like a safe thing to be drinking, but I still want to try it.
- Well, what can I tell ya, that’s all that caught my eye last week. Send me your favourite paper that I missed, and I’ll summarize it in a sentence by next Monday.
Nibbles: Botanical gardens, Glass flowers, Remarkable trees, Rhubarb history, Expensive pumpkin, Back to the future, Quinoa glut, Citrus greening biocontrol
- All of BGCI’s ex situ surveys on one cool page. Have they re-modelled their website?
- Harvard’s glass flowers are totally cool.
- The world’s coolest trees.
- Rhubarb is cooler than you think.
- I’m not sure paying over a thousand pounds for a pumpkin seed is all that cool.
- Conventional breeding is cooler than genetic engineering. Cool quote of the week: “I tell my students they should drop acid before they go to the field, and just look at the plants and let them tell you what they are doing.”
- Is the coolness over for quinoa? Jeremy unavailable for comment.
- Cool Pakistani bug may help with citrus greening in the US. But don’t stop looking for resistance, y’all.
Brainfood: Banana GWAS, Yeast genebanks, Hybrid sorghum, How to intensify ecologically, Med pastures, Food services, Neolithic transition, Ploughing the savanna
- A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. One strong candidate gene, from 6 possible regions. And here’s the light version.
- Yeast culture collections in the twenty-first century: New opportunities and challenges. Pretty much the same as plant genebanks.
- Genetic variation in sorghum as revealed by phenotypic and SSR markers: implications for combining ability and heterosis for grain yield. Possible parents for hybrids identified.
- Actionable knowledge for ecological intensification of agriculture. Look at the landscape, articulate trade-offs and don’t forget the social dynamics.
- Taxonomic and functional diversity in Mediterranean pastures: Insights on the biodiversity–productivity trade-off. Somebody mention trade-offs?
- Are the major imperatives of food security missing in ecosystem services research? Pretty much.
- Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion. Agriculture got you laid, but then killed you.
- High carbon and biodiversity costs from converting Africa’s wet savannahs to cropland. Bad idea all round.
Blasting away at wheat blast
You may have seen the press reports about the disease wheat blast, previously restricted to South America, reaching Bangladesh. The more technical news pieces in the likes of Nature make the point that the source was Brazil, but do not always make it as clear as they might what a veritable tour-de-force of international collaboration in pathogenomics it was to get to that conclusion.
It’s of course all thanks to the Open Blast Initiative, an effort to get sequence data on the causal fungus into the public domain as quickly as possible. Their website helpfully provides a handy timeline, which I reproduce with some slight editing below:
- March 1. First news report of wheat blast in Bangladesh.
- March 8. Tofazzal Islam and Sophien Kamoun discuss applying field pathogenomics to the wheat blast outbreak.
- March 16. Tofazzal’s students collect samples from multiple locations in Bangladesh and store them in RNALater.
- March 23. Field samples are delivered to The Sainsbury Lab in Norwich.
- March 24-31. RNA extractions and library preparations in the Laboratory of Diane Saunders at TGAC and JIC.
- April 8. Sequencing completed at TGAC. Thanks to Dan Swan and team for fast-tracking the samples.
- April 14. Magnaporthe (Pyricularia) oryzae sequences confirmed based on analyses by Antoine Persoons and Joe Win. Similarity to Br32 wheat blast strain noted.
- April 18. Open Wheat Blast goes live! All sequence data is freely available to use without any restrictions. Nick Talbot’s group at Exeter simultaneously releases the genome sequences of 14 Brazilian wheat blast isolates.
- April 27. Daniel Croll and Bruce McDonald, ETH Zurich, post in Github an analysis on the origin of wheat blast in Bangladesh. They conclude that the pathogen was most likely introduced from South America.
So, less than two months from the first reports of the disease in Bangladesh to the discovery of where the little blighter came from. Impressive. And we now also have a pre-print out on the taxonomy of the organism involved, which suggests that multiple species are to blame. And that’s started quite a online discussion. A great advertisement for open data, not to mention a more flexible approach to publication and peer review.
The next step, of course, is to look for resistance to the different strains of the pathogen in the world’s wheat genebanks and breeding programmes.
…plant pathologists say that finding one variant is not enough: wheat strains must be bred with multiple genes for resistance, to stop M. oryzae quickly overcoming their defences… “What I would hope for out of this sorry situation … is that there will be a bigger international effort to identify resistance genes.”
Let’s see if the breeders are as fast and open with their international collaboration as the pathologists. Stay tuned.
Brainfood: Sesame diversity, Teff & drought, Semen bank, Forest genomic monitoring, Sahiwal cattle status, Genomic prediction, Ecuadorian homegardens, Spinach association mapping, ICRISAT pigeonpea & pearl millet, Women & milpa, African rice at AfricaRice, Bacteria helping wheat
- Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation. Strong geographic structure, and more diversity in Asia than Africa.
- Performance of Tef [Eragrostis tef (Zucc.) Trotter] Genotypes for Yield and Yield Components Under Drought-Stressed and Non-Stressed Conditions. Out of 144 genotypes, 15 were good in ideal conditions, 8 under stress, and none, alas, in both cases.
- Genome resource banks pay conservation dividends. Banked semen from “genetically valuable” individuals used to slightly raise diversity in captive populations. Of black-footed ferrets.
- Conservation and Monitoring of Tree Genetic Resources in Temperate Forests. Theory.
- Logging by selective extraction of best trees: Does it change patterns of genetic diversity? The case of Nothofagus pumilio. Praxis: maybe.
- Population structure and demographic trends of the registered Sahiwal cattle in Kenya. It’s losing diversity, so Something Must Be Done.
- Genomic Prediction of Gene Bank Wheat Landraces. It’s not perfect, but not bad either.
- Plant diversity and ecosystem services in Amazonian homegardens of Ecuador. Ethnicity is the stongest determinant of floristic composition.
- Association mapping of leaf traits in spinach (Spinacia oleracea L.). “Five, seven and 14 SNPs were identified to be associated with surface texture, edge shape and petiole colour, respectively.”
- Pre-breeding to expand primary genepool through introgression of genes from wild Cajanus species for pigeonpea improvement. Even the tertiary genepool is interesting.
- Characterization and genetic potential of African pearl millet named landraces conserved at the ICRISAT genebank. 5 agronomic clusters, each with good stuff, but different good stuff.
- The participation of farm women in the milpa system of the Yucatán, Mexico. …is minimal.
- Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity. 3 out of 2000!
- Alleviation of salt stress by halotolerant and halophilic plant growth-promoting bacteria in wheat (Triticum aestivum). Not by a huge amount. For one wheat variety. In hydroponics.