Genetic diversity

January 14, 2019

PAGXXVII in the air

The self-styled “Largest Ag-Genomics Meeting in the World” is on again. It’s not really my thing, but I don’t mind following the proceedings at a distance: the hashtag is #PAGXXVII. I particularly recommend Zoë Migicovsky’s live-tweeting, but there are others who are doing a fine job too.

Top #PAGXXVII Tweeters:
1 @pop_gen_JED 155
2 @zoemig 113
3 @JChrisPires 109
4 @Campbell_JD_PhD 68
5 @So_it_flows 49
6 @khanmather 48
7 @isugif 43
8 @mossMatters 42
9 @TroyNRowan 40
10 @JasonWilliamsNY 38

— Jared Decker (@pop_gen_JED) January 14, 2019

January 14, 2019January 12, 2019

Brainfood: Coca phylogeny, Potato taste & nutrition & resistance, CC & nutrition, Light & nutrition, Remote poverty, Spicy toms, Input subsidies, Broilerocene, European livestock then & now, Bean domestication, Peach domestication, Machine conservation, Habitat fragmentation, Conservation planning, Taxidermy, Wheat diversity, Livestock GS

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species). Morphology is not enough.
Improving Flavor to Increase Consumption. Yield is not enough.
The Nutritional Contribution of Potato Varietal Diversity in Andean Food Systems: a Case Study. Yield is not enough.
Stacking three late blight resistance genes from wild species directly into African highland potato varieties confers complete field resistance to local blight races. One resistance gene is not enough.
Income growth and climate change effects on global nutrition security to mid-century. Calories will not be enough.
Urbanization and Child Nutritional Outcomes. Urbanization is enough.
Socioecologically informed use of remote sensing data to predict rural household poverty. Night light is not enough.
Capsaicinoids: Pungency beyond Capsicum. Peppers and tomatoes are not enough.
The impact of agricultural input subsidies on food and nutrition security: a systematic review. The data are not enough.
The broiler chicken as a signal of a human reconfigured biosphere. The broiler is enough.
Pre-Roman improvements to agricultural production: Evidence from livestock husbandry in late prehistoric Italy. The Romans were not enough.
Optimizing ex situ genetic resource collections for European livestock conservation. One genebank is not enough.
Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? One genome is enough.
Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Human selection was not enough.
Predicting plant conservation priorities on a global scale. This black box is enough.
Is habitat fragmentation bad for biodiversity? Small patches may be enough.
Synergies between the key biodiversity area and systematic conservation planning approaches. One conservation approach is not enough.
Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland. Stuffed goats are enough.
Decline in climate resilience of European wheat. The current varieties are not enough.
Harnessing genomic information for livestock improvement. Genomic selection was going to be enough.

January 12, 2019January 17, 2019

Nibbles: Magic beans et al., Avocado etymology, Honey please, Pig maps, Banana pics, Commons, Diet footprint, Sparing/sharing, Old caviar, Old whiskey, Potato wild relatives, Cassava breeding, Apple double, Ancient potatoes, Ancient grapes, African cooking, Native American craft beer, Agricultural heritage site, Aboriginal biodiversity, Svalbard 10th, Alpaca calendar.

Telegraph op-ed on agricultural biodiversity. Yeah, you read that right.
No, avocado does not come from the Aztec’s word for testicles. It’s the other way around.
Why honey is a keeper.
Mapping the hell out of pigs.
Photo database to help tell bananas apart.
Deconstructing the Tragedy of the Commons.
The C footprint of your diet.
“We can spare 50 percent and share the rest.”
Cave man caviar.
Whiskey with that?
Potato wild relatives and food security.
Cassava and food security. No word on its wild relatives.
Wales finds a new apple.
Maybe someone will take a cool picture of it.
Potatoes were always for the masses. Ok, but not sure anyone ever thought otherwise, though.
Grapes, on the other hand…
The cuisines of Africa get their shot.
Some of those will go well with craft beer.
Agricultural heritage list gets saffron and argan. Bet they go together well.
Maybe wild kiang tea will get there too someday.
Or the Aboriginal Australians. Not really agriculturalists, but still.
Is this alpaca exploitation? Maybe you can take the promotion of agricultural biodiversity too far.
Will the Svalbard Global Seed Vault qualify one day? Ten years on, still going strong. And return to top.

January 7, 2019December 14, 2018

Brainfood: Distribution modelling, New mycorrhiza, Bean diversity, Collecting, Intensification, Wildish rice, Wild tomato genome, Conservation prioritization, Horizon scanning, Maize domestication, Livestock sustainability, Asexual rice

Incorporating knowledge uncertainty into species distribution modelling. Not sure about this.
A mycorrhizal revolution. “Fine root endophytes are arbuscule-forming fungi unexpectedly placed in Mucoromycotina.” Wow. I think.
Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Snap beans came from dry beans, but maybe more than once and from both Andean and Mesoamerican genepools, and now they make up 8 genepools.
Two decades of evolutionary changes in Brassica rapa in response to fluctuations in precipitation and severe drought. It matters when you collect germplasm.
Agricultural intensification, dietary diversity, and markets in the global food security narrative. What if it’s intensification through diversification, though? Didn’t think of that, did you?
Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China: implications for neo-domestication as a grain crop. Crop wild relative that is also a crop might be a good candidate to become another crop.
The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. It’s all in the inositol pathway.
Not all data are equal: Influence of data type and amount in spatial conservation prioritisation. Follow the money. Ok, to unpack that, read this.
A Horizon Scan of Emerging Issues for Global Conservation in 2019. Biotechnological advances in crop breeding may impact insects and land use.
Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Linguistics, archaeology and genetics say maize left Mexico semi-domesticated, was finished off and diversified in Amazonia.
Assessing the Role of Cattle in Sustainable Food Systems. They still have one.
A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Clonal propagation of hybrids. What could possibly go wrong?

December 31, 2018December 4, 2018

Brainfood: Stressful crops, Quinoa, Ganja genome, Medicinal vetch, CWR in PAs, CWR in Zambian farms, African viral chickens, Naked barley, Farmer trials, Cotton genomes, Tuscan toms, Land sharing, Nigerian goats, Walnut diversity, Bean breeders, Sweet rice

Developing naturally stress-resistant crops for a sustainable agriculture. Can’t help thinking there will be a trade-off.
Quinoa Abiotic Stress Responses: A Review. Case in point?
A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the 2 THC/CBD acid synthase locus. At last, the prospect of better weed.
In vitro anthelmintic effect of Vicia pannonica var. purpurascens on trichostrongylosis in sheep. From Turkish folk medicine to the big time?
Should plant breeders be denied of genetic resources from protected areas? Not if you put it that way. Maybe they should be valued? There’s a way to do that…
Estimating in situ conservation costs of Zambian crop wild relatives under alternative conservation goals. Put it out to tender.
The genetic diversity of local african chickens: A potential for selection of chickens resistant to viral infections. No word on their monetary value, though.
Agro-morphological diversity of Nepalese naked barley landraces. Lots of diversity, little used as yet by breeders.
Generating Farm-Validated Variety Recommendations for Climate Adaptation. One word: tricot.
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. 13 QTLs for better fibre quality.
Ancient Tomato (Solanum lycopersicum L.) Varieties of Tuscany Have High Contents of Bioactive Compounds. Better than commercial varieties, apparently.
Biodiversity and yield under different land-use types in orchard/vineyard landscapes: A meta-analysis. Land sharing works.
Small Ruminants as a Source of Financial Security Among Women in Rural Southwest Nigeria. Better with education, extension and cooperation.
Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers. W Europe/N America vs E Europe/Asia.
David Bond and Jean Picard: Two pivotal breeders of faba bean in the 20th century. Bond and Picard?
Status and factors influencing on-farm conservation of Kam Sweet Rice (Oryza sativa L.) genetic resources in southeast Guizhou Province, China. In the end of women and the old.