Tuesday, 30 June 2009

Rice genetics watch

A few notes on three recent additions to the library of publications of rice genetics.

1. Yamamoto et al (from Tusukuba) have publiished a review "Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?" in DNA Research. This seems to be aimed at breeders and the potential of marker-assisted breeding, but it contains a useful compilation on a good range of QTLs for various domestication-related and post-domestication traits. It includes a schematic map with ~4000 qtls mapped onto the 12 chromosomes of rice, which just goes to show both how much information there is on rice, and how complex it is to understand the history of this crop when there is so much information. It is fair enough to say that most reviews have an inevitably partial view of evidence from the rice genome.

2. Panuad has published a short essay, ostensibly in honour of Darwin, on "The molecular bases of cereal domestication and the history of rice" in the French journal C. R. Biologies.It strikes me as neither particularly insightful nor up-to-date, but it is short and might of interest the less rice-savvy. Its limited reference to archaeology is rather disappointing and odd (a single Chinese article in the minor journal Nongye Kaogu), and the claim that we have less evidence from India as opposed to China because preservation is worse in tropics, is not really a fair assessment. True charred seed densities tend to be lower in India than China, but the main reason is that more Neolithic sites have been excavated in the Yangtze than in the Ganges. And even though flotation was started in India in the 1970s, perhaps 20years ahead of China, it is now being widely practiced in China as a rapid rate, whereas it is the the same 2 two labs doing flotation and analyses in India that started it in the 1970s (plus a couple of us occasional foreign visitors). Indian needs more sampling, and not to be written off as too tropical to work i, but needs more work, more workers, and more critical analysis and debate (e.g. about the nature of Lahuradewa's early rice).

3. The recent genetics paper I have seen that I am most impressed with is the study by Yamane et al (2009, in Rice) of the phylogenegentics of Hd6, one of the genes involved in regulating heading (flowering), and linked to response to photoperiod (daylength). It is clear that non-responsive plants have one of two alternate forms of the responsive (short-day) type, corresponding to two indica vs. japonica domestication pathways. It also suggests that a non-reponsive type found mainly in temperate japonica rices also derives from the wild and is found in some South Chinese wild rices. This story is entirely reminiscent of the case in barley recently brought to light by Huw Jones and colleagues.

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