Category: DNA

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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.

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Can’t stomach golden rice? Get your teeth into golden maize!

ResearchBlogging.orgVitamin A deficiency causes eye disease in 40 million children each year and places another 200 million or thereabouts at risk for other health problems. In sub-Saharan Africa and Latin America, between 17% and 30% of children under the age of 5 suffer vitamin A deficiency. Simple solution: give them more vitamin A. But how?

The poorest regions, which stand to benefit most, often do not have the infrastructure to deliver vitamin supplements, either directly or in fortified foods. Diversifying the diet is dismissed out of hand. ((Full disclosure: I don’t myself buy the reasons given for not doing more to diversify diet, but this is not the place for that argument. This is: Johns, T. & Eyzaguirre, P. B. (2007). Biofortification, biodiversity and diet: A search for complementary applications against poverty and malnutrition. Food Policy, 32(1), 1-24.)) So the technical types turn to plant breeding, and in particular the notion of biofortified foods, whereby staple crops are selected to contain higher levels of micronutrients. It was this approach that gave the world Golden Rice, by shifting one of the enzymes in the carotenoid synthesis pathway from daffodil to rice.

An ungrateful world still has not accepted golden rice as the saviour of blind little children, but the technical types have not stopped working. In the latest Science ((Harjes, C.E., Rocheford, T.R., Bai, L., Brutnell, T.P., Kandianis, C.B., Sowinski, S.G., Stapleton, A.E., Vallabhaneni, R., Williams, M., Wurtzel, E.T., Yan, J., Buckler, E.S. (2008). Natural Genetic Variation in Lycopene Epsilon Cyclase Tapped for Maize Biofortification. Science, 319(5861), 330-333. DOI: 10.1126/science.1150255)) a large team led by Edward Buckler at Cornell University, reports on a different approach to biofortification.
Harjes2Hr

So what other staples are there, preferably ones that might already contain the genes to make vitamin A precursors? Step forward maize, some varieties of which have yellow and even golden orange kernels. It is not enough, however, simply to look at the maize kernels and score them on some scale from pale yellow to deep orange. The reason is that not all carotenoids are created equal. Beta carotene is the precursor of choice, because it contains two of the necessary chemical rings to make vitamin A. Shade of yellow correlates very poorly with total beta-carotene. But all this is detail above and beyond the call of duty. The point is that maize varieties display enormous variability both in total carotenes and in the proportion of beta carotene.

Maize varieties are also hugely genetically diverse. In fact, the differences between two maize varieties is considerably greater than the difference between humans and chimpanzees. Buckler’s group took the known variability in maize kernel colour and asked whether genetic differences were associated with the carotene profile of the variety. They were. The gene for one particular enzyme — lycopene epsilon cyclase — has a large effect on the provitamin A carotenoids.

There’s more in the full paper (which requires a subscription), but one reason that this could be an important result is that it is reasonably easy for others to make use of it. Genetic markers for the favourable versions of the crucial gene make it possible for breeders to look for the potential in any varieties they have that are already adapted to the conditions for which they are breeding. The favourable type is reasonably widespread, so finding parents for crosses should be reasonably easy. Analyzing carotenoid compounds is expensive and difficult, but scoring the target gene is not only about 1000 times cheaper, it is also well within the capabilities of those developing countries that need more vitamin A.

The contrast with Golden Rice couldn’t be greater. That is a proprietary technology that has graciously been made available to those who have the expertise to make use of it. This approach to a nutritionally-improved maize should be much simpler to put to work. Information needed for the DNA analysis is being made freely available, as are inbred maize lines that could make it easier for breeders worldwide. So things look good for biofortified maize, at least technically.

There’s just one remaining little problem — will people eat yellow maize, even if they know it is good for them? Changing human feeding behaviour can be so much harder than changing the food they eat.

Stop press: Prefer wheat to maize or rice? Golden wheat comes a step closer too, with a paper in Euphytica. Italian and Spanish wheat breeders transferred nuclei from wheat into cells from wild barley and from wild wheat relatives. Wheat wild relatives increased the amount of lutein, another carotenoid.