Category: Domestication

Posted on

Probing the peanut’s past

ResearchBlogging.orgMany readers in developed countries probably regard Arachis hypogaea — if they regard it at all — as a salty snack, maybe a source of clarty peanut butter. The peanut or groundnut, however, is a major staple crop in many parts of the world, a valuable source of protein and energy. So of course scientists are interested in its ancestry, not least to help them breed better varieties. A recent paper by Guillermo Seijo and his colleagues confirms what many have long suspected; that the cultivated peanut is a hybrid between A. duranensis and A. ipaensis. ((Seijo, G., Lavia, G.I., Fernàndez, A., Krapovickas, A., Ducasse, D.A., Bertioli, D.J., Moscone, E.A. (2007). Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. American Journal of Botany, 94(12), 1963-1971.))

The thing is, like many domesticated plants, peanuts have a complicated genome. Peanut has 40 chromosomes. But it is an amphidiploid, an allotetraploid, meaning that it has two sets of chromosomes from two different ancestors, each of which almost certainly had 20 chromosomes. The genome is described as AABB. But which species did the As and Bs come from? Many attempts have been made to find out, most of them involving attempting to cross existing modern species. Based on all that, the most recent monograph on Arachis ((Krapovickas, A., Gregory, W.C. Translated by David E. Williams and Charles E. Simpson (2007). Taxonomy of the genus Arachis (Leguminosae). Bonplandia, 16(Supplement), 1-205.)) names A. duranensis, A. ipaensis and A. Batizocoi as the wild species that grow where cultivated peanuts have the most characters considered primitive. This kind of evidence is generally taken as indicating the site of domestication.

As in many cases, however, there is a powerful belief abroad that if it is in the DNA it is somehow truer. One of the techniques that addresses the DNA directly, and that is especially useful when chromosomes are believed to come from different species, is called genomic in situ hybridization, or GISH. ((Raina, S.N., Rani, V. (2001). Methods in Cell Science, 23(1/3), 83-104. DOI: 10.1023/A:1013197705523)) In essence, this technique allows researchers to see which parts of which chromosomes match a particular target. Seijo and his colleagues used it to see how seven wild peanut species with 20 chromosomes paired up with the chromosomes of the cultivated peanut. Cut to the chase: “Of all the genomic DNA probe combinations assayed, A. duranensis (A genome) and A. ipaensis (B genome) appeared to be the best candidates for the genome donors.”

That rather vindicates the original conclusion. But it raises a couple of rather interesting questions. One will have to wait for another time. But the other is worth posing now. Why has it proven so difficult — impossible, in fact, so far — to reproduce the original cross that gave rise to the domesticated peanut? Synthetic wheat, made by combining three, not two, genomes, has been a huge boon to breeders, giving them access to a whole range of genetic diversity that they couldn’t readily find in existing wheats. Synthetic peanuts might be expected to do the same. But as yet no new domesticated peanuts have been synthesized by crossing the wild relatives. Why not?

Posted on

An archaeodentist’s take on domestication

Jason at Hominim Dental Anthropology (a bit of a mouthful; hahahaha) has been taking a look at some recent papers on domestication. The papers are, by his own admission, nothing new. We’ve covered some of them ourselves here. What I thought was interesting was the stress on the timing and duration of domestication and Jason’s views of what constitutes “nature” and “natural”. He seems, to me, to be a bit confused as to whether Homo sapiens (just another unique species, as Rob Foley puts it) is a part of nature, or apart from nature and yet with its (our?) own nature.

Posted on

Pussy Galore

A paper appeared in Science last year which used mitochondrial DNA and microsatellites to determine the geographic origin of the domesticated cat. We blogged about it back in June, albeit briefly. The major conclusion was that the cat was domesticated once, in the Fertile Crescent, about 9000 years ago, at about the time that agriculture started to take off. A paper just out in Genomics now takes the story on from there, by looking in more detail at the relationship among pure breeds and random-bred local populations from all over the world. ((Monika J. Lipinski, Lutz Froenicke, Kathleen C. Baysac, Nicholas C. Billings, Christian M. Leutenegger, Alon M. Levy, Maria Longeri, Tirri Niini, Haydar Ozpinar, Margaret R. Slater, Niels C. Pedersen and Leslie A. Lyons. (2008) The ascent of cat breeds: Genetic evaluations of breeds and worldwide random-bred populations. Genomics 91:12-21. doi:10.1016/j.ygeno.2007.10.009))

Using microsatellites, which are best suited to resolving more recent changes in genetic diversity, the authors of this latest study tried to reconstruct what happened when domestic cats left their Middle Eastern cradle and spread all over the world, presumably with the first agriculturalists and then with merchants and other travellers. It turns out that the diversity of the genepool has not decreased much overall during the past several thousand years. But it has fragmented. So now you have quite genetically differentiated groupings among the world’s cats: in the Mediterranean, Western Europe (+ the Americas), Asia and East Africa. The Asian group is particularly interesting, being the most distinct and the one with the most internal patterning. This shows that cats went to Asia early, and became relatively isolated there, from the rest of the world and from each other. ((Don’t I remember something similar for wheat? Must look it up. Later: ok, it was barley.))

There’s interesting stuff in the paper on the relationship among pure-bred breeds. They’re apparently mostly relatively young (less that 150 years old), and there’s not really that many of them (41 are recognized by cat enthusiasts), certainly compared to dogs and livestock like cattle and sheep. And it seems they’re all derived from 16 so-called “foundation” breeds, such as the Persian, for example. These in turn mostly — there are some exceptions — originated from random-bred cats from their region of origin, i.e. Persia, in the case of the Persian. Unsurprisingly, the development of pure-bred breeds from local common-or-garden cats has been associated with a narrowing of genetic diversity. And with the accumulation of deleterious mutations. It’s only in pure-bred cats that genetic disorders have been spotted. This study should lead to better plans for breed management, that could avoid such problems, the authors hope.

Posted on

Animal Genetic Resources on the ground in Uganda

A dying breed. Huge article in the New York Times magazine that looks at the general issue of disappearing livestock diversity through the particular lens of cattle in Uganda, where the local Ankhole cattle are threatened by high-yielding but fragile Holsteins. All the arguments and counter-arguments are there in a well-written piece that pulls no punches and yet, in the end, left me wondering what the solution is. Farmers who do use Holsteins profit thereby, setting off an arms race among fellow farmers, whose primary victim is the local livestock breeds. But when trouble strikes, in the form of drought or civil strife, it is the local breeds that gallop back to the rescue. As long as they remain alive …