- I’ve long thought that getting rid of the Aswan High Dam would be the best way Egypt could improve its food security.
- New video from Biofortified, how to pollinate carrots and beets.
- Hey Lawyers; time to study the commons! Including genetic resources? h/t capri.
- Today’s gene banks will save the world story is about cashews.
- Today’s rich world saving heritage varieties story is from Quebec.
- Today’s old stories given new legs story is about paying farmers for ecosystem services.
- Wired magazine discovers pastured poultry. Can the rest of the world be far behind?
- Proposal for a conference session on prehistoric globalisation of food. I’d be there if I could.
- And more from the Archaeobotanist, another journal special issue on Near Eastern domestication.
- CCAFS highlights (and links to) ICRAF report on climate change options for Southeast Asian Farmers
- Danforth Center depicts evolution of plant science, devaluing the word inforgraphic [sic] beyond repair.
- Viking beer. Sköl, or something.
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: Musa taxonomy kerfuffle, Vouchers, Foodies, Aroid roundup, MAS is ok, Sierra Leone conservation
- Banana boffins at each others’ throats over alleged new species. Great spectator sport.
- What does a Musa voucher specimen look like, I wonder.
- Fancy shmanzy Bangkok restaurant links up with heirloom seedbank.
- Aroid network working really hard.
- Marker-assisted selection: a biotechnology we can all get behind. Can’t we?
- Conservation in Sierra Leone. No agrobiodiversity, natch.
Cotton doyen passes away
Sad to hear that Dr Ed Percival, a world expert on cotton and its genetic resources, passed away last month. He collected wild and cultivated germplasm widely, and he was formerly curator of the USDA cotton germplasm collection at College Station, Texas, one of the more important in the world. ((Incidentally, College Station was hit by a tornado recently. There was some damage to the research station. The collections, which include trees such as pecan, were not affected, but this does serve to remind us all of the need for proper safety duplication of germplasm and associated data.))
Brainfood: Falcons, Wild soybean squared, Horse domestication
- Effects of Introducing Threatened Falcons into Vineyards on Abundance of Passeriformes and Bird Damage to Grapes. Potential savings of US$234/ha for Sauvignon Blanc, more for Pinot Noir.
- Genetic characterization and gene flow in different geographical-distance neighbouring natural populations of wild soybean (Glycine soja Sieb. & Zucc.) and implications for protection from GM soybeans. There is a small amount of outcrossing, which decreases with distance. GM crops should be grown far from wild populations, certainly more than 1.5km. And we can work out better ways to collect for ex situ conservation.
- Phylogenetic relationships, interspecific hybridization and origin of some rare characters of wild soybean in the subgenus Glycine soja in China. Intermediate forms are closer to the wild than the cultivated species.
- Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. A diversity of maternal lines were domesticated about 150,000 years ago, leading to about 18 modern haplogroups. One of them is only found in the only remaining wild horse, E. przewalskii.