My discussion of rice domestication may have been a bit behind the times. Duncan Vaughan, of the National Institute of Agrobiological Sciences in Tsukuba, Japan, was kind enough to send two recent papers on the subject. [1] The “old” view, based on molecular clock studies that showed a divergence long before the start of domestication, was that indica and japonica types of rice were domesticated independently. Vaughan and his colleagues, Bao-Rong Lu and Norihiko Tomooka, point out that the mutation most prominent in domestication is identical in indica and japonica types. This is the mutation to sh4, the gene that controls shattering, the tendency of ripe seeds to shatter or split from the flower stalk. Without it, the grain falls to the ground and is hard to harvest. There are other factors too, all of which Vaughan says point to a single origin for rice. This was, in fact, the prevailing view from Vavilov onwards, until molecular studies starting 30 years ago or so started to discover deep genetic divisions among current rice varieties.
Vavilov, as we have seen, thought that centres of diversity were essentially centres of origin, but later researchers pointed out that crosses with wild relatives are often a major source of diversity, and these crosses may take place distant from the site of domestication. Vaughan et al. point out that “[t]he earliest archaeological sites that have domesticated rice remains are well outside the region where highest traditional varietal diversity was found in the last century, Yunnan province, China and surrounding areas.”
The distinction between cultivated and domesticated is important: domesticated plants depend on people for their survival. People may cultivate plants without those plants ever becoming domesticated. But once certain key mutations have occurred — foremost among them a change to non-shattering, which means that seeds do not easily disperse without human help — the plants are domesticated.
Despite the evidence of changes to the genome that long predate domestication, Vaughan points out that among wild perennial rice one can find indica types and japonica types growing in the same region. And the domesticated types are not restricted to specific areas either, even in places more or less untouched by modern varieties. In China, in the early part of the 20th century, japonica rice grew mainly in the colder north and indica in the warmer, moister south, but there were places where the two grew side by side.
The traditional areas where indica and japonica varieties were grown in the mid-twentieth century, from Vaughan et al. (2008) rice 1:16-24.
Vaughan asks, somewhat rhetorically, “Is it coincidental that this is close to where the first evidence of rice domestication has been reported?
There is no archaeological evidence of rice domestication in India, although there is evidence for other crops. Furthermore, and this would have swayed Vavilov, in the area of the Yangtze delta that has the earliest evidence of domesticated rice, there were three distinct linguistic groups of people, and this “human diversity may have hastened the early diversification of rice”.
There’s more than this, of course, including detailed analyses of the degree to which wild rice populations lean towards either indica or japonica tendencies. But the crucial piece of evidence, the one that really requires explanation, is that the non-shattering mutation to sh4 is the same in all indica and japonica varieties tested to date. Ockham’s Razor suggests a single event, but then how to explain the tendency of wild rice to be either indica or japonica?
Vaughan’s view is that the molecular evidence is saying that at various stages after the mutation to sh4, populations that were in the process of being domesticated shared genes with populations that were still wild, and the flow went in both directions. Much of the data on gene flow from farmed rice to wild and weedy relatives we have thanks to the need to monitor possible escapes from genetically-modified varieties. Among these are studies showing transfer frequencies between O. sativa and O. rufipogon of up to 18% in a single generation. Introgressed genes often persist in wild populations, and even much lower rates would support considerable exchange from cultivated varieties back through weedy types into the wild “ancestral” species. Indeed, some “famous” wild varieties, like IRRI accession 101508, the celebrated specimen of O. nivara that conferred resistance to grassy stunt virus on modern varieties has a straw-coloured hull, like cultivated and unlike wild rice.
Vaughan and his colleagues make a good case for a single domestication event. Is it the last word? Almost certainly not.
Notes:- Duncan A. Vaughan, Bao-Rong Lu, Norihiko Tomooka (2008). Was Asian Rice (Oryza sativa) Domesticated More Than Once? Rice, 1 (1), 16-24 DOI: 10.1007/s12284-008-9000-0
D VAUGHAN, B LU, N TOMOOKA (2008). The evolving story of rice evolution Plant Science DOI: 10.1016/j.plantsci.2008.01.016 [↩]
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