Category: DNA

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A second helping of rice

More today to satisfy your hunger for rice information, hot on the heels of the recent paper trying to explain the pattern of genetic variation across and within two subspecies of cultivated rice, discussed by Jeremy a couple of days ago.

First there’s a paper ((Global Dissemination of a Single Mutation Conferring White Pericarp in Rice. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, et al. PLoS Genetics Vol. 3, No. 8.)) looking at how the red pericarp of wild rice became the white pericarp of cultivated rice. The answer is that a mutation arose in the japonica subspecies, crossed to the indica and became fixed in both under very strong selection pressure by ancient rice farmers. They must have really liked those funny mutant white grains when they first noticed them! Oh to have been a fly on the wall — or a brown plant hopper on the rice stalk — when the white pericarp mutation was first noticed in some ancient paddy…

Then comes news that the three CGIAR centres with an interest in rice — IRRI, WARDA and CIAT — are to boost their collaboration to solve the pressing production problems of Africa. There’s talk of forming a consortium. More flags being prepared.

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Diversity in rice varieties: what caused it?

Larry Moran has a very good article on the genetic diversity found in the DNA of rice varieties. I won’t try to summarize what he has to say, because he says it so well. But I will emphasize something that he doesn’t. The biologists who looked at rice wanted to know what caused the pattern of diversity they see across rice vareties. One possibility is selection. The other is the founder effect, where a very small subset of a larger population gives rise to a new species (or variety) so that the new species contains less diversity than the ancestor population from which it sprang. In rice, neither explanation on its own is sufficient.

An agricultural scientist might not care one bit, or might simply assume that it was all due to selection by farmers. But the truth is that it needed a combination of the founder effect and positive selection to create modern rice diversity. The founder effect relates to the fact that Oryza sativa indica and Oryza sativa japonica were both domesticated independently from the wild Oryza rufipogon, maybe a few times. The results of those early events set up the foundation genes for rice. Then selection was brought to bear and created the diversity we now see. Luck and hard work, every time.

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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

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More on cowpea breeding

Hot on the heels of a recent nibble on breeding cowpeas for Striga resistance comes a paper in GRACE on the diversity being exploited by cowpea breeding programmes in the US and Africa. It turns out that these programmes are using non-overlapping sets of genetic material and that therefore

US and Asian breeding programs could increase genetic variability in their programs substantially by incorporating germplasm from West Africa, while national programs in West Africa should consider introgression of Asian germplasm and germplasm from other parts of Africa into their programs to ensure long-term gains from selection.

That’s what we mean when we talk about global interdependence in plant genetic resources, I guess. And that’s why the International Treaty was negotiated: to facilitate the exchanges of germplasm necessary to broaden plant breeding programmes worldwide.