Category: Wild relatives

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

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.

Posted on

Three into one for new wheat

Scientists at the Australian CSIRO and Sydney University, working with colleagues at CIMMYT in Mexico, have built a chromosome that brings together the disease resistance genes of two wild wheat species into a single genetic package. ((L. Ayala-Navarrete, H. S. Bariana, R. P. Singh, J. M. Gibson, A. A. Mechanicos and P. J. Larkin (2007) Trigenomic chromosomes by recombination of Thinopyrum intermedium and Th. ponticum translocations in wheat. Theoretical and Applied Genetics, 116: 63-75.)) This should make life easier for wheat breeders; while they may be able to find valuable genes in wheat’s wild relatives, those genes are often accompanied by large blocks of other genes that often bring bad qualities. Getting the harmful genes out of the cross is apparently sometimes so difficult that breeders give up.

Thinopyrum intermedium (intermediate wheatgrass) contributed resistance to barley dwarf yellow virus, while Th. ponticum (tall wheatgrass) supplied a couple of rust resistance genes. They are both on the short arm of one of the wheat chromosomes, but without the baggage normally associated with genes from wild relatives. Crosses with bread wheats resulted in fertile offspring with the required resistance. These are being used to study the genes further in search of molecular markers that will help breeders to identify valuable crosses.

According to a press release:

By developing new DNA markers and by careful testing the team has produced a number of the disease resistance packages for wheat breeders, making it faster and easier to include these important disease resistance traits in future wheat varieties.