Category: Genetic diversity

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Food composition

The new issue of the Journal of Food Composition and Analysis has reviews of food composition activities in both Latin America and Oceania. I only have access to the abstracts, but I know that in the Pacific a lot of attention is being paid to differences in nutrient composition among varieties of crops like banana, pandanus and giant swamp taro. This is something that might be of interest to the authors of a third paper in the same issue of the journal. They look at differences in micronutrient composition within different cereal species in Mali but fail to mention this varietal dimension. They ascribe the differences to climate and ecology — at least in the abstract. Important, of course, but surely not the whole story. I’m going to try to get hold of the paper.

LATER: So it looks like what they did is collect various different samples of fonio, say, in each of several distinct eco-geographic zones and pool the samples collected in each zone for analysis. Nothing in the paper about trying to collect material with similar varietal names or anything like that. So any differences due to environment will be confounded with genetic variation. Seems to me like an opportunity missed, at best.

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Fido decoded

An article by Elaine Ostrander in the latest American Scientist summarizes recent advances in canine genomics, which have been considerable:

The dog genome has been mapped and sequenced. A host of disease loci have been mapped, and in many cases the underlying mutations identified. Our understanding of how dog breeds relate to one another is beginning to develop, and we have a fundamental understanding of the organization of the canine genome. The issue of complex traits is no longer off-limits. We have begun to understand the genetic portfolio that leads to variation in body size and shape, and even some performance-associated behaviors.

Some snippets:

  1. Between-breed genetic variation is about 27.5% of the total, compared to about 5% between human populations.
  2. Dog breeds fall into 4 main groups: Asian and African dogs, plus grey wolves; mastiffs; herding dogs and sight hounds; and modern huntings dogs.
  3. 75% of the 19,000 genes that have been identified in the dog genome show close similarities with their human counterparts.
  4. Variation in a single gene (IGF1) explains a lot of the size differences among and within breeds.

What to do with all this information?

It is certainly hoped that the disease-gene mapping will lead to the production of genetic tests and more thoughtful breeding programs associated with healthier, more long-lived dogs. It will be easier to select for particular physical traits such as body size or coat color… Finally, canine geneticists will have a chance to develop an understanding of the genes that cause breed-specific behaviors (why do pointers point and herders herd?).

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Genotyping Support Service

The CGIAR’s Generation Challenge Programme‘s mission is

To use advanced genomics science and plant genetic diversity to overcome complex agricultural bottlenecks that condemn millions of the world’s neediest people to a future of poverty and hunger

They’ve just announced a new service: the Genotyping Support Service. What will GSS do?

Here’s a sample of what our latest service offers: assessing proposals, hiring genotyping services from the best providers, taking care of the administrative hassles, ensuring the generation of high-quality data and training participating researchers to interpret and work with the data to optimise outputs. In this way, researchers get to use the technology right away, while also learning how to get the greatest mileage out of the technology, thus creating local capacity. As such, GSS contributes to GCP’s effort to support and motivate plant breeding ‘champions’ in developing regions.

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Seed sleuth

There’s a glowing portrait of Ken Street, a plant hunter, in the Sydney Morning Herald. Street works with ICARDA, the International Centre for Agricultural Research in the Dry Areas, based in Aleppo, Syria and spends much his time in the wilds of central Asia, searching out crop diversity. The piece is a bit gushy for my taste, and I’m not sure I agree with everything Street is quoted as saying. “We have been eating genetically modified organisms for 10,000 years” turns the phrase “genetically modified organisms” into meaningless guff. But he does make some good points about the amount of diversity that survives — for now — in places like Armenia and Tajikistan. If you want a glimpse into the life of a man they call “an agricultural Indiana Jones,” that’s what you’ll get.

Luigi unavailable for comment.

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Watermelon: Out of Africa

Summer here in Rome tastes of watermelon. So, as the temperature outside hit the upper 30s today, it was great to sit in air-conditioned splendour in the office this lunchtime, eat a slice of cocomero and read a paper on the origin of the crop in the latest GRACE, which has just come out. Fenny Dane and Jiarong Liu at Auburn have looked in detail at chloroplast DNA from material collected all over Africa in an effort to reconstruct the history of both the familiar fruit (Citrullus lanatus var. lanatus) and the related tsanna or citron melon, which is a different botanical variety (var. citroides) of the same species. It turns out that the split of var. lanatus and var. citroides from a common ancestor (C. ecirrhosus, maybe) is ancient. The citron melon split off independently in the area of Swaziland and South Africa, while the wild precursor of the cultivated watermelon has its roots, as it were, on the other side of the continent, in Namibia. The picture below (courtesy of GBIF) shows why watermelon does ok in the Italian summer heat. Its natural habitat is pretty much desert (the record is for an accession in the US National Plant Germplasm System).

melon.jpg