Genetic diversity

May 11, 2017May 11, 2017

Citrus in a nutshell

Look, I suppose I could try and explain that recent Citrus phylogeny paper in Annals of Botany. But am I really likely to do better than this graphic?

I didn’t think so.

Important to know what’s what. But if all that’s just too much for you, wind down by listening to Helena Attlee on Eat this Podcast on citrus in Italy.

May 8, 2017May 8, 2017

Brainfood: Cannabis roundup, Citrus genomes, Mapping Africa, Maize diversity, Qat diversity, Language diversity, Apple taste, Coconut diversity, Napier grass review, Rangeland management, Chinese goats, Arabica evaluation, Bangladeshi chickens, Seed endophytes

Cannabis Domestication, Breeding History, Present-day Genetic Diversity, and Future Prospects. The weed is in trouble, man. Just one of the papers in a very special issue of Critical Reviews in Plant Sciences. And for a historical perspective…
Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Apomixis is down to a “miniature inverted-repeat transposable element insertion in the promoter region of CitRWP.”
Automated cropland mapping of continental Africa using Google Earth Engine cloud computing. Croplands increased by 1 Mha/yr between 2003 and 2014.
Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. Three groups: Mexico + southern S. America, lowland Mesoamerica + Caribbean, Andes.
Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation. Centres of origin in Kenya and Ethiopia, with limited movement between the two, but some hybrids in N. Kenya; the Yemeni stuff came from Ethiopia.
Process-based modelling shows how climate and demography shape language diversity. If you assume human groups split after reaching a certain population size, and rainfall limits population density, you can predict language diversity in Australia.
Volatile Compound Profiles of Malus baccata and Malus prunifolia Wild Apple Fruit. Look at the esters.
Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers. I can’t see much new here. Please, coconut experts, tell me what I’m missing.
Opportunities for Napier Grass (Pennisetum purpureum) Improvement Using Molecular Genetics. Could do better.
Heterogeneity as the Basis for Rangeland Management. Gotta mix it up.
Analysis of genetic diversity of Chinese dairy goats via microsatellite markers. The locally developed breeds are all derived from a single European breed.
Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.). You can’t use morphology to predict taste.
Breeding for the improvement of indigenous chickens of Bangladesh: evaluation of performance of first generation of indigenous chicken. I don’t understand this much, but I liked the names of the genotypes: Naked Neck, Hilly and Non-descript Desi.
Persistence of endophytic fungi in cultivars of Lolium perenne grown from seeds stored for 22 years. It’s a record!

May 2, 2017May 2, 2017

Nibbles: Aeroponic yams, Ancient crops, Kumara, Informal food vendors, Foxy, Salumi, Corn whiskey, Doomed cassava

Yams up in the air, but in a good way.
Yet another couple of things on how “ancient crops” will save us all. All crops are ancient. Well, except the kiwi.
Lovely little film on a lovely sweet-potato-growing New Zealand couple to make up for that uncalled-for dig at the kiwi. Made my day.
Engage with kiosk holders, don’t hassle them.
Review of a book on the quixotic attempt to resynthesize the dog. Why bother?
More Italian salami than you can shake a stick at.
Might go well with some artisanal Mexican corn whiskey.
Cassava is “pointed in the direction of extinction.” Thank goodness for genebanks, eh?

May 2, 2017May 2, 2017

It didn’t take long for my prediction to come true that the Mexican maize dataset I blogged about a couple of weeks back would get some more attention. The lead author of that previous paper, Hugo Perales, has teamed up with Quetzalcóatl Orozco-Ramírez and our old friend Robert Hijmans to do a deep dive into the database of 18,176 georeferenced observations of about 60 maize races. Some key findings:

Both at national and state level, there are a few very common races, and many races with very few observations.
10% of the races account for 54% of the records.
Over half of the races account for 10% of the records.
The maximum distance between two records of the same race was just over 1000 km on average, the maximum about 2600 km, and lower than 200 km for 7 races.
There was a positive association between the number of observations and the number of races in both 50 km and 100 km square cell.

I particularly liked the new map of “maize communities,” that is, regions where more or less similar assemblages of races are found.

Although the previous paper had a similar map of “biogeographic regions,” this is more detailed and robust. Intriguingly, the hotspots of highest diversity tend to occur where distinct maize communities meet.

I’ll see if I can get Robert so say a few words about this work here.

May 1, 2017April 30, 2017

Brainfood: Dope diversity, Potato chips, Conservation costing, Island breeding systems, Indus civilization cereals, Drone phenotyping, Wild rice in Asia, Wild rice & Native Americans, Pearl millet temperature, Climate change & fruit/veg

Cannabis Domestication, Breeding History, Present-day Genetic Diversity, and Future Prospects. The traditional landraces are being contaminated and need urgent collection and evaluation by dedicated professionals.
Cold sweetening diversity in Andean potato germplasm from Argentina. 5 out of 48 Andigena landraces make good chips.
Considering cost alongside the effectiveness of management in evidence-based conservation: A systematic reporting protocol. Here comes the metadata. No excuse now.
Self-compatibility is over-represented on islands. 66% vs 41% in Asteraceae, Brassicaceae and Solanaceae. Any crop wild relatives in the list?
Cereals, calories and change: exploring approaches to quantification in Indus archaeobotany. Millet may not have been as important as is generally thought.
High-Throughput Phenotyping of Sorghum Plant Height Using an Unmanned Aerial Vehicle and Its Application to Genomic Prediction Modeling. A near-infrared, green and blue (NIR-GB) camera on a drone gives pretty good results compared to a person with a tape measure, and is much more fun.
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. No such thing as completely wild Asian rice.
The dispute over wild rice: an investigation of treaty agreements and Ojibwe food sovereignty. Not wild rice at all, but what’s been happening to it might be a violation of the White Pine Treaty with the Ojibwe.
Quantifying pearl millet response to high temperature stress: thresholds, sensitive stages, genetic variability and relative sensitivity of pollen and pistil. The problem is the pistils.
Effect of environmental change on yield and quality of fruits and vegetables: two systematic reviews and projections of possible health effects. Bad for yield, good for nutritional quality.

Category: Genetic diversity

Citrus in a nutshell

Brainfood: Cannabis roundup, Citrus genomes, Mapping Africa, Maize diversity, Qat diversity, Language diversity, Apple taste, Coconut diversity, Napier grass review, Rangeland management, Chinese goats, Arabica evaluation, Bangladeshi chickens, Seed endophytes

Nibbles: Aeroponic yams, Ancient crops, Kumara, Informal food vendors, Foxy, Salumi, Corn whiskey, Doomed cassava

More Mexican maize mayhem

Brainfood: Dope diversity, Potato chips, Conservation costing, Island breeding systems, Indus civilization cereals, Drone phenotyping, Wild rice in Asia, Wild rice & Native Americans, Pearl millet temperature, Climate change & fruit/veg