Genetic diversity

November 24, 2012November 23, 2012

It’s germplasm evaluation, Jim, but not as we know it

Next generation sequencing (NGS) holds the promise for a more efficient approach to germplasm evaluation whereby a carefully selected subset of accessions can be sequenced and phenotyped in detail; associations discovered between genotypes and phenotypes in this subset could be used to predict the phenotype of other accessions based on sequence data alone.

Ah, “the promise.” Always the promise. But actually, in this document, “Technical appraisal of strategic approaches to large-scale germplasm evaluation,” some of the practicalities are spelled out, and in quite a lot of detail. You be the judge of whether the vision outlined in that opening quote is of a far-away, Star Trek world, or something that’s really just around the next corner. You can comment on the document itself, or here if you prefer.

November 21, 2012May 2, 2014

Nibbles: Vegetables, UK funding, Oz funding, Oz genebank, Jefferson, Hawaiian food, Markets, Tree seeds, NUS journal, Geographic targeting, ITPGRFA, Arabica and climate, Protected areas, European farmland biodiversity, Sustainable use, Ethiopian seed video

Palestinian rooftop gardens. Including crucifers, no doubt.
Brits support work with rice and wheat wild relatives. Among other things. They’ll probably use some of these genomics things.
Aussies support sweet potatoes. HarvestPlus rejoices.
That new Australian genebank. Will it have any sweet potatoes?
The agricultural legacy of Thomas Jefferson. It doesn’t say here, but I bet he was into sweet potato.
Hawaiian menus. What, no sweet potato?
Forget biotech, the road to sexy agriculture is via the supermarket. Where you can buy sweet potato. Maybe even of the organic persuasion.
Or maybe better tree seeds. Even in the Nordic countries. Or the US. Is cacao a tree?
Plans for special edition of Sustainability on neglected crops. Like amaranth?
Geographic targeting reaches roots/tubers. Using this newfangled atlas? Or no?
Treaty and Consortium love-in filmed. Thanks for sharing. It’s all part of this CGIAR perestroika thing, no doubt.
What that Kew coffee extinction paper really said.
Protected areas need work. Especially for coffee (see above).
Yeah but protected areas is not the only way to go, and Europe now has a bunch of biodiversity indicators for farmland. I guess it’s all part of some big plan.
Policy brief on sustainable use of PGR. Or, as we used to call it, on farm conservation.
Which you can kind of see happening here.

November 20, 2012December 20, 2012

Nibbles: Chicken diversity, Pig genome, Genome size

Breeders like chicken diversity. Blogger refrains from cock and chick jokes.
Breeders will like the pig genome. Blogger refrains from sausage jokes.
Size matters. In genomes, that is. Blogger quits while he’s ahead.

November 19, 2012November 19, 2012

Brainfood: Spanish terraces, Flower patches, Population ecology, Maize germplasm use, Seed info system, Maize and CC, Medicago predation, Species richness prediction, Rice salt-tolerance

The genesis of irrigated terraces in al-Andalus. A geoarchaeological perspective on intensive agriculture in semi-arid environments (Ricote, Murcia, Spain). They were built very early on, on a specific soil type, by first burning the vegetation and then essentially inverting the soil profile.
Creating patches of native flowers facilitates crop pollination in large agricultural fields: mango as a case study. Sweet.
The ecology of plant populations: their dynamics, interactions and evolution. A whole special issue. Most intriguing is perhaps review of plant-pollinator interactions on the Galapagos. All very important for in situ conservation of crop wild relatives.
Diversity in global maize germplasm: Characterization and utilization. Three priorities: phenotyping, phenotyping, phenotyping.
Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids. They could have used GRIN-Global, but I guess that doesn’t track plasmids.
Increasing influence of heat stress on French maize yields from the 1960s to the 2030s. Any day with maximum temperature above 32°C is bad, and their recent increase has led to yield stagnation. They are going to increase further, which means that the French are going to have to find a 12% increase in base yields by 2035 or eat less maize. Do they in fact eat any maize now? What countries are now like what France will be like in 2035?
Combined impact of multiple exotic herbivores on different life stages of an endangered plant endemism, Medicago citrina. IUCN says it’s endangered. Rabbits, mice and rats are important parts of the problem.
Estimating species richness: still a long way off!. Bummer.
New allelic variants found in key rice salt-tolerance genes: an association study. A couple possibly interesting mutations identified by EcoTILLING bunch of IRRI accessions. We shall see if anything comes of them. Actually, how will we find out if something does? I hope the info will go back into the IRRI genebank documentation system.

November 13, 2012November 9, 2012

Brainfood: Sierra Leone rice, Bean breeding, Cacao geographic diversity, Red fleshed apples, Species richness & productivity, African maize diversity, Human expansion, Barley gaps, Wild coffee and CC, Acacia and CC, Genetic erosion

Analysis of genetic diversity in farmers’ rice varieties in Sierra Leone using morphological and AFLP markers. Still a lot of diversity in traditional rice after the war, both among and within landraces, mostly among, organized regionally, and recognized by local names.
Simultaneous selection for resistance to five bacterial, fungal, and viral diseases in three Andean × Middle American inter-gene pool common bean populations. Thanks goodness for multiple independent domestication events. And genebanks.
Present Spatial Diversity Patterns of Theobroma cacao L. in the Neotropics Reflect Genetic Differentiation in Pleistocene Refugia Followed by Human-Influenced Dispersal. So need to collect in areas at the margins or just outside the refugia if you want high diversity. But of course that may already be ex situ. But wait, didn’t you just do the analysis based on the provenance of ex situ holdings?
An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. The whole genome got duplicated during evolution of the apple and the red flesh phenotype is controlled by loci in both copies, but in different ways.
What is the form of the productivity–animal-species-richness relationship? A critical review and meta-analysis. Positive.
Spatial Structure and Climatic Adaptation in African Maize Revealed by Surveying SNP Diversity in Relation to Global Breeding and Landrace Panels. Distinct Sahelian, Western and Eastern clusters. Some SNPs associated with high temperatures.
MtDNA analysis of global populations support that major population expansions began before Neolithic Time. Humans needed good weather to thrive, not agriculture.
Genetic gap analysis of wild Hordeum taxa. Argentina?
The Impact of Climate Change on Indigenous Arabica Coffee (Coffea arabica): Predicting Future Trends and Identifying Priorities. Generally very bad to disastrous, but some “core localities” will be ok, and therefore could be used for in situ conservation. Interestingly, genebank accession locality data not used.
The genus Acacia (Fabaceae) in East Africa: distribution, diversity and the protected area network. No such luck for Acacia, I’m afraid.
Monocropping Cultures into Ruin: The Loss of Food Varieties and Cultural Diversity. Are you sure you want to know what a sociologist and a political scientist have to say on the matter?