- Banana germplasm gets around.
- Kenyan urban cows get around. Not local breeds, though…
- Can agriculture deliver both resilience and nutrition? FAO thinks so.
- Yeah, about that: we’re gonna need better data.
- Participatory varietal selection in Nepal. Not as novel as made out here, surely.
- Brazil nut gets it all.
- Today’s beer story comes from India.
- Sorting the sheep from the goats, the molecular way.
Brainfood: Lima been diversity, Cassava diversity, Urban soils, Oil palm seed supply, Ginger ploidy, Certification, Gene flow, Maize & drought, Coffee seed storage, Pathogens on seeds, Wheat breeding, Intensification tradeoffs
- Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: Implications for conservation and the domestication of the species. Three, not just two, genepools.
- Farmer’s Knowledge on Selection and Conservation of Cassava (Manihot esculanta) Genetic Resources in Tanzania. Farmers exchange landraces, some of which are widespread and others more restricted in distribution. Only about 10% are new, but some have been lost.
- Urban cultivation in allotments maintains soil qualities adversely affected by conventional agriculture. You can farm in cities without killing the soil.
- Social institutional dynamics of seed system reliability: the case of oil palm in Benin. Farmers are being increasingly screwed.
- Natural occurrence of mixploid ginger (Zingiber officinale Rosc.) in China and its morphological variations. About a quarter of plants have both diploid and tetraploid cells, and they look different; no plants are wholly tetraploid. Weird.
- Conserving biodiversity through certification of tropical agroforestry crops at local and landscape scales. Certifying the coffee or cacao farm only is usually not enough.
- Is gene flow the most important evolutionary force in plants? May well be, which means that conservationists, among others, need to take it into account. Fortunately, they have the data-rich genomic tools to do so.
- Greater Sensitivity to Drought Accompanies Maize Yield Increase in the U.S. Midwest. It’s agronomy’s fault.
- Desiccation and storage studies on three cultivars of Arabica coffee. Yeah, not orthodox. Didn’t we know that already though?
- Seed-borne fungi on genebank-stored cruciferous seeds from Japan. There’s lots of them. And something needs to be done about it.
- Delivering drought tolerance to those who need it; from genetic resource to cultivar. In making synthetic wheat, you can fiddle with the AB as well as the D genomes, but then you have to phenotype properly under target stress conditions, and have a way of tailoring the resulting global public goods to local needs.
- The Effects of Agricultural Technological Progress on Deforestation: What Do We Really Know? Not as much as we thought we did.
- Large-scale trade-off between agricultural intensification and crop pollination services. Intensification bad for pollinators in France, so bad for agricultural productivity and stability.
- Achieving production and conservation simultaneously in tropical agricultural landscapes. Intensification good for smallholder income in Uganda, bad for birds. If only birds were pollinators.
The future of genebanks unfolds, a bit
The potential benefits of recent developments in DNA sequencing technologies to both collection management and use will also be explored during the course of the project.
That was from an article a couple of days ago on the future of the UK’s vegetables genebank. Well, we learned yesterday that for rice, at least, that brave new world is almost at hand:
…access to 3,000 genomes of rice sequence data will tremendously accelerate the ability of breeding programs to overcome key hurdles mankind faces in the near future.
That would be DNA sequences from 2,466 of the International Rice Genebank Collection’s (IRRI) accessions, plus 534 accessions housed at the CAAS genebank, amounting to 13.4 terabytes of data. This begins the long road to sequencing the whole IRRI collection of about 100,000 accessions, the rationale for which was recently set out:
In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.
Alas, the news came a few days too late for the Pahiyas Festival:
Clearly, rice is the main inspiration of this delightful affair. The rice grains, rice plants and rice seedlings on display may all seem the same, but a closer look will reveal that they are not. Some seeds are longer, some are rounder and some are lighter in color than others, reminding us of just how rich and diverse our rice varieties are.
Maybe next year.
Meanwhile, if you want to celebrate instead by cracking open a nice bottle of wine from the Quinta do Crasto estate in Portugal, well, they’re using high-resolution genotyping there as well to figure out just exactly what clones they have in their fields. What’s that you say? You don’t drink wine? How about a nice bar of quality heirloom chocolate, also thoroughly genotyped, then? Truly the future is upon us.
Nibbles: Wheat database, Livestock maps, Indian apple genebank, UC Davis strawberries, Cheese fungi postdoc, Fruit domestication, Brassica genome, Early hunting dogs, Threatened species numbers, Bolivia conservation
- A Wheat Germplasm Database To Rule Them All. No, not from CGIAR.
- New livestock maps of the world. Yes, from CGIAR.
- Kashmir ponders an apple genebank.
- More from Game of Strawberries.
- Wanna study the population genomics of cheese fungi? Course you do.
- Domesticating local fruit trees good for nutrition, but need secure tenure and good planting material.
- Building better broccoli, the genome way.
- Early domesticated dogs helped in mammoth hunts.
- Current extinction rate about 1000 times higher than background. Databases can help with that, believe it or not.
- Building a national PGRFA system in Bolivia. When will they ratify the ITPGRFA, though?
Brainfood: Yam tissue culture, Barley core, Date genome, Ecosystem services & land use change, Remote sensing and conservation, Okra diversity, Carob diversity, Mexican genebank project, Chicken skin music, Mongolian camel, Coloured rice
- Effect of various growth regulators on growth of yam (Dioscorea trifida L.) in vitro shoot tips. One small step for yam cryopreservation.
- The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies. 5 sub-populations: roughly, Mediterranean, W Europe, E Europe, Asia and Ethiopia. GWAS effective in locating important phenotypes.
- A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. Lots of synteny with oil palm and coconut despite differences in genome size. And we now (probably) know how sex determination works.
- Economic evaluation of ecosystem goods and services under different landscape management scenarios. Agriculture usually wins at the expense of more “ecological” land uses, unless income from C and biodiversity (and timber) go up, or discount rates go down.
- Oil in the Sahara: mapping anthropogenic threats to Saharan biodiversity from space. You can spot biodiversity threats from space. More examples along the same lines.
- Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces. Much phenotypic variation, less AFLP variation, but geographically structured. Germination characteristics vary with ecology.
- Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.). First time carbob has been genotyped using microsatellites. And that seems to be the only reason why this work was done.
- Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Breeds are diverse but geographically distinct, the western ones especially. Unlike sheep, which are moved around a lot more. Some evidence of inbreeding, which can and should be counteracted.
- Diversity Assessment and Development of Sustainable Use of Mexican Genetic Resources: Prospects of a SATREPS Project. That would be Science and Technology Research Partnership for Sustainable Development, between the Japanese and Mexican genebanks. Looks like a lot of genotyping and in vitro conservation research on lesser-known crops.
- Establishing the validity of domestication genes using DNA from ancient chickens. You really need ancient DNA to study domestication.
- Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus). No breeds, no problem.
- Exploring Variability: New Brazilian Varieties SCS119 Rubi and SCS120 Onix for the Specialty Rices Market. Brazilian hipsters now have red and black rice.