rice genetics watch: structure in Chinese rices but not domestication genes?

• In the Oct. 2009 issue of Theoretical and Applied Genetics, a large Chinese research group (Zhang et al.) looked Genetics structure among Chinese rice landraces, with over 3000 Chinese rice populations. They find clear population structure, not just between indica and japonica as expected, but also within each of these. Interesting they report that the structure in indica seems to relate to flowering time (early, middle or late flowering varieties), which suggests that early differentiation after indica originated may be focused on seasonality (and constraints of seasonal land and water availability). In the case of japonica (primarily temperate japonica one presumes), seasonality is pretty much always restricted to the warm wet summer, as China has dry, cool winters that are not conducive to rice. Instead structure seems to divide Chinese japonica landraces on the ground of soil and water adaptations, and whether they are best grown ion paddies or on upland rainfall. Indeed, as predicted from the archaeology the earliest ecological efforts in rice domestication in China are likely to have focused on water manipulation (see Fuller & Qin in World Archaeology), while early dispersal must have also seen diversification in rainfed and less labour intensive systems of cultivation. On the whole an interesting approach that one would like see extended beyond China.
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• Another paper also with Zhang et al. authorship (but a different Zhang), that came out at the end of the summer in New Phytologist looked in more detail at the phylogeny of sh4 and qsh1 non-shattering (domestication) genes, and provides a coallescent model of their origin in terms of fixation time. Their estimate this trait should have been fixed in ~100 years seems a throwback to the kind results that models produced a decade ago, now at odds with the archaeobotanical evidence on domestication rates. The authors are at odds to explain this by positing thhat the now universal(?) sh4 domestication gene evolved after initial domestication and then diffused throughout rice (and replaced some earlier domestication genes). Not a particular elegant, nor historically/archaeologically compelling model. I am forced to assume that something is amiss in the math or the assumptions of the model. Can an apparent rapid bottleneck be artefact of another process in the way the apparent monophyly can (as per Allaby et al 2008). I also note that the phylogeny that relate domesticated sh4 to wild populations the same or a close gene, on the surface suggests an origin of sh4 from a Lao rufipogon or an Indian nivara-- but surely these wild taxa, and the indica and japonica types deriving from them should not group together in a population phylogeny when they have different chloroplast genomes (with a common ancestor in excess of 70,000 years ago!). Of course a Neighbourjoining tree, however much bolster by bootstraps and Montecarlo methods is still just a cluster analysis that is not a particularly logical or robust way to look for phylogenetic relationships within a species that hybridizes. Thus the method employed here denies the reticulate evolution which is so clearly a part of evolutionary story of rice, as so elegantly argued in earlier papers by Sang & Ge or more robustly in the recent papers of Kovach et al or McNally et al. I am therefore provisionally not at all sure what this sh4 data is actually telling us.

Rice genetics watch: many sweet-smelling genes

Although it is now a couple of months old, the paper by Kovach et al. (2009) in PNAS in August on the "Origin and Evolution of Fragrance in Rice" is an important contribution on the cultural history of rice. It is a clear example of selection by cultural preferences for rice that cooks a certain way, in this case with sweet or 'jasmine' aroma. Clearly many people from many cultural traditions have preferred their aromatic rices, whether Indian Basmati or Thai Jasmine rice, and this trait has been selected just as surely as ecological or domestication traits . But equally some people prefer otherwise, for their rice to smell of rice, which is true through Central China and much of east Asia.

While the responsible gene, BADH2, has been known for a while what is of interest here is that mutations in the sequence that produce fragrant rice have been distinguished and these have been tested over a very large diverse geographical sample. A single mutation is most widespread throughout regions with fragrant rice. It is clear that this originally from an early japonica lineage, presumably East Asian. And my inclination would be to see this evolving en route as Neolithic rice dispersed from S. China to SE Asia, (although it could be a later wave). But there are 9 additional more minor alternative mutations to the same gene to the same effect. They show clear geographical patterning, and the implication of that is this geographically separate groups have recurrently developed a preference for and selected for aromatic rices. It remains to be determined. Whether some of these were developed truly independently, with local fragrant mutations being kept or pushed to low frequency as the dominant BADH2 came in, or else these local aromatic variants were selected to mimick a preference developed after fragrant rice arrives. Of course the story may be different in different cases...

Au Revoir Levi-Strauss

This blog returns, with a start, at the news that Claude Levi-Strauss died today. Startling because I hadn't even realized he was still alive! Although he probably hasn't influenced too many archaeobotanists, he certainly changed the way we think anthropologically about food, what is classed as edible, defined as cooked or rotten and how we refract much of what we mean to be cultural through a lens of cooking. In a general way, his brand linking cooking traditions to cultural cosmologies does run through the recently published (preliminary) study I wrote with Mike Rowlands on a "Macrogeography of Substances: Food & Sacrifice Traditions in East, West and South Asia" [pdf]. Levi-Strauss also plays the role of one of the characters (alongside the late Mary Douglas who lived and wrote to the ripe age of 86, less than Levi-Strauss' 100) interpreting archaeological feasts and human food sociality in Martin Jones' book Feast. As my tribute to Levi-Strauss I can think only to quote from one the myths he recounts on the origins of agriculture according to the Brazilian Munduruku:

In former times, game and cultivated plants were unknown to the Mundurucu.

They fed on wild tubers and tree fungi.

It was then that Karuebak, the mother of manoic, arrived and taught men the art of preparing it.

One day, she ordered her nephew to clear an area of forest, and she announced that soon bananas,

cotton, caras (Dioscorea), maize, the three varieties of manioc, watermelons, tobacco and cane

sugar would grow there. She ordered a ditch to be dug in the newly cleared area,

and asked to be buried in it. Care should be taken not to walk over her.

A few days later, Karuebak's nephew found that the plants listed by his aunt were growing on

the place where she lay; however, he inadvertantly walked on the hallowed ground, and

the plants at once stopped growing. This determined the size to which they have grown ever since.

A sorcerer, displeased at not having been informed of the miracle, caused the old woman to perish

in the hole where she lay. Since she was no longer there to advise them, the Indians

ate manikuera [manoic] raw, not knowing that this particular variety of manioc is poisonous

and emetic in that form. They all died, and next morning went up into the sky where they

became stars. Other Indians, who had eaten manikuera first raw and then cooked,

were transformed to honey flies. And those who licked the remains of the cooked manikuera

became the kind of bees which produce bitter, emetic honey..."

-- From Honey to Ashes, p. 56 (Levi-Strauss 1966)