- Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. Domestication was Lamarckian.
- Global economy interacts with climate change to jeopardize species conservation: the case of the greater flamingo in the Mediterranean and West Africa. Financial crisis leads to closing down of Mediterranean saltpans, which is not good news for flamingo. Climate change doesn’t help. Must be similar examples for plants, Shirley.
- Parallel Evolution Under Domestication and Phenotypic Differentiation of the Cultivated Subspecies of Cucurbita pepo (Cucurbitaceae). C. pepo subsp. pepo and subsp. texana underwent similar genotypic and phenotypic changes during domestication.
- Ecological and human impacts on stand density and distribution of tamarind (Tamarindus indica L.) in Senegal. Climate change will lead to an area of currently low density in the NW being a refugium. Connectivity problems will ensue.
- Biofortification of wheat through inoculation of plant growth promoting rhizobacteria and cyanobacteria. Breeders give up.
- Nutritional ranking of 30 Brazilian genotypes of cowpeas including determination of antioxidant capacity and vitamins. Breeders take heart.
- A short history of Lagenaria siceraria (bottle gourd) in the Roman provinces: morphotypes and archaeogenetics. Out of Asia. And more.
- Functional Properties, Nutritional Value, and Industrial Applications of Niger Oilseeds (Guizotia abyssinica Cass.). It has them, in spades, as this paper summarises.
- Sex at the origin: an Asian population of the rice blast fungus Magnaporthe oryzae reproduces sexually. The Himalayan foothills would seem to be the place where to look for resistance.
- Evolutionary History of Pearl Millet (Pennisetum glaucum [L.] R. Br.) and Selection on Flowering Genes since Its Domestication. Bayesian modelling of 20 random genes supports domestication about 4,800 years ago, with protracted introgression from the wild relative, and selection sweeps suggest flowering related genes unsurprisingly underwent strong selection as the crop spread southward. But a single domestication scenario? Anyway, sounds familiar, doesn’it.
- Genome-Wide Analysis of the World’s Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. Much like, ahem, pearl millet. For flowering genes, read horniness genes. The bit about an initially broad sampling of diversity sounds a bit like the horse. Who out there is going to synthesize all this domestication stuff? Not that I’m looking for a meta-narrative, mind.
- Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Well, sequence the whole thing and be done with it is what I say, why flaff around with ultra-this and super-that?
- The crop yield gap between organic and conventional agriculture. 20%.
- Marcela, a promising medicinal and aromatic plant from Latin America: A review. Achyrocline satureioides, in the Asteraceae. Yeah, I never heard of it either. But these guys say it’ll make you rich and beautiful.
- Comparative genetic structure within single-origin pairs of rice (Oryza sativa L.) landraces from in situ and ex situ conservation programs in Yunnan of China using microsatellite markers. 2-5 times more unique alleles in the in situ version of various landraces compared to the ex situ version, collected in 1980. But same number of common alleles.
- Mutualism breakdown in breadfruit domestication. More recent cultivars have less abundant and less species-rich arbuscular mycorrhizas.
Nibbles: Vavilov conference, Rice rituals, Tomatoes, Agave
- The Tatar Information Agency announces a conference to celebrate NI Vavilov’s 125th birthday, neglects to include date: 25 November 2012?
- Rice and ritual expresses the “intangible cultural heritage of agriculture and food”.
- Canadian scores four new old tomatoes from their genebank.
- The agave fight goes on.
Next-generation sequencing and genebanks: a teaser
We’re of course all holding our breath, are we not, over the imminent appearance of the American Journal of Botany Special Issue on what next-generation sequencing (NGS) technologies mean for the plant sciences. A few teasers are already out on the journal’s website, and it looks like the papers will come out in piecemeal fashion over the next weeks, and months for all I know. The paper that’s most relevant to us here is perhaps that of Susan McCouch and others on NGS and genebanks. I saw an early version of it, but am not allowed to share it, so until it comes out officially, here’s a taster from the introduction to the volume as a whole by Ashley N. Egan, Jessica Schlueter and David M. Spooner. I trust the journal will consider it fair use and not come after us with their lawyers.
A total of 1750 national and international gene banks worldwide preserve ~7 million accessions of advanced cultivars, landraces, and wild species relatives of plants that the world depends on for food, fiber, and fuel (FAO, 2010 ). McCouch et al. (2012) present a vision for the potential of large-scale genotyping to help characterize, use, and manage gene bank collections, from their perspectives as scientists working with large-scale rice collections. Genebanks have many pressing challenges due to the large size of their collections and the need to characterize them properly for a wide variety of users. They also face legal constraints (and opportunities) imposed in today’s climate of ownership of genetic resources. The challenges include the need to correctly identify accessions, track seed lots, varieties, and alleles, identify and eliminate duplicate accessions, justify adding new accessions to the collection, identify a small subset of the collection that represents a majority of the variation in the entire collection (a “core collection”), identify geographic areas holding useful sets of diverse alleles, associate genotypes with phenotypes, and motivate innovative collaborations to place useful materials into the hands of plant breeders. McCouch et al. (2012) outline these challenges and show how NGS can vastly improve genetic characterization efforts in genebanks. Initial NGS projects with the rice collections include identification of SNPs and other polymorphisms (http://www.oryzasnp. org/; http://www.ricediversity.org/; http://www.ricesnp.org/) based on large-scale resequencing and genotyping projects.
Back with a full discussion (and a comparison with the paper on the same subject in a recent Brainfood) when the publication is online.
Nibbles: PGR course, Vegetable seed kits, Maize data, Rice metabolomics, Rewilding, Sheep diversity, Llama economics, Canary flora, Cuba urban ag, Ducks, Cynara, Food sovereignty
- The annual Wageningen agrobiodiversity conservation course is in India this year. Hannes says it’s really good.
- AVRDC’s veggie seed kits are a hit in Orissa.
- CIMMYT swimming in data. Waving, not drowning.
- IRRI not doing badly either. But “quantitative train loci” is a new one on me.
- Australia thinking about introducing elephants. Yeah because that sort of thing has been such a success in the past.
- Well, actually, with sheep, I suppose it has, in a way. And the genetics says breeders have a lot of diversity to play with still.
- Your mama is a llama.
- The Island of Dogs has crop wild relatives. No, not the one in London.
- Cuba goes for new urban crops. And not for the first time, Shirley. But what about the old ones?
- Quick, duck! This piece has been rather a hit for me over on Facebook.
- VII International Symposium on Artichoke, Cardoon and Their Wild Relatives: The (Very Expensive) Book.
- Food sovereignty “started in New England”. Huh? And proponents “want to eat and sell the food they grow free from interference from state and federal regulators”. Huh?
Consolidation in the seed industry
We’ve written before about consolidation in the seed industry making the same tired joke that I want to make again now, that a picture is worth 1000 words. It doesn’t hurt to stay up to date though, which is why I am grateful to Resources Research for finding, and colouring in, the diagram from the USDA report on Research Investments and Market Structure in the Food Processing, Agricultural Input, and Biofuel Industries Worldwide.
The USDA report is not, as far as I can tell, anything to do with the US Department of Justice’s investigation of antitrust practices in the seed industry, announced a couple of years ago. So what has become of that? Anyone know?