New genetics work on rice from a Japanese team indicates that the mutations SD-EQ1, which makes rice plants shorter, was strongly selected early on in the process of rice domestication, at least within the japonica sub-species, which is presumed to be that domesticated in the Neolithic Yangtze. This article bu Matsuoka et al, published in PNAS, has been highlighted in Science magazine's on-line news. A transcript of my full comments and initial thoughts, are provided here.
This study by Asano et al on the SD1 gene, which shows strong selection for shorter rice plants in domesticated japonica, adds to a growing list of genetic evidence for the different origins of indica and japonica rices and for the differing cultural ecologies in which these crops were first cultivated. Subsequent hybridizations transferred some domestication-selected genes, but selectively from japonica to indica, probably around 3800-4000 years ago (see, e.g. Fuller & al. 2010, Archaeological & Anthropological Sciences). Deductions from the modern ecology of wild rice varieties and archaeobotanical evidence (e.g. Fuller & Qin 2009; p. 147 in Fuller & Qin 2010) points to a important role for human manipulation of the water conditions of early japonica rice cultivated in China with necessary adaptations in the growth habit of rice and shift towards a more annual seasonal pattern as opposed to the wild-type perennial pattern. Wild O. rufipogon is a perennial, which prefers growing in more less permanent water or areas that only dry up for short periods. It can produce extremely tall, long culms in order to grow in deeper water, While deeper water reduced competition from other plants it also reduced productivity since growth is focused on vegetation tissues (leaves and culms), and as long as water conditions are fairly staple plants with reproduce vegetatively and produce few seeds. Early cultivation of rice in the Yangtze region of China clearly focused on wetlands margins (for example at Kuahuqiao, 6000-5400 BC, or Tianluoshan, 5000-4300 BC) in Zhejiang. The pollen and microcharcoal data from Kuahuqiao, published already by Zong et al 2007 (for further details see this 2009 paper) already indicated the manipulation of wetland margin environments by 5700-5400 BC. While these sites, especially the evidence from Tianluoshan (which we published in Science in 2009) indicates selection for non-shattering rices over this period, it also suggests a change in the ecology in which the rice was growing. Accompanying weed seeds indicate a shift away from a predominance of perennial, and taller, sedges (Cyperaceae) towards a wider diversity of shorter annual grasses and dicot weeds (summarized inFuller & Qin 2010, but only published in detail in Chinese this past month in a Tianluoshan monograph; English papers still to come!). This suggests that there were also developments for how (and where) rice was grown. This would have involved manipulating the soils and water depth in which rice was grown. One reason for this is that in order to promote annuality and higher seed production the rice plants need to water-starved, i.e. subjected to drought like conditions, when they are starting flowering: the drought conditions lead to increased grain output, a strategy that would be suitable for true drought but also would increase yields for early farmers. Thus more productive early rice required humans to create seasonal drought like conditions; genetic adaptations to these conditions would then be selected for.
Subsequent to Tianluoshan, at around 4200-3800 BC, other sites in the Lower Yangtze regions, such as Caoxieshan and Chuodun (see discussion in Fuller and Qin 2009), show increased human efforts at managing water levels in very small paddy fields some with adjacent channels and water 'storage pits', which would allow these small fields to be drained. Such systems would have strongly selected for changed in rice plant architecture towards less spreading grow habits (based on the gene Prog1, published in by Tan et al in Nature Genetics 2008; some discussion for the selection of this which is parallels in other cereals is provided in Fuller, Allaby and Stevens "Entanglements...", in World Archaeology). Shorter rice plants might also have been favoured here, if not already at the early wetland margin cultivation of Tianluoshan, since human manipulation of water would remove the need for taller plants, which would be prone to falling over (i.e. lodging) and would produce fewer grains (since metobolism was being invested in more culm rather than more seeds). An interesting question would be to know whether shorter plants (SD1) or less branching (Prog1) was selected first.
Once japonica was introdouced into areas with proto-indica, selection for these traits would be well-finished, and shorter growth habits may have been unnecessary and unattractive to South Asian cultivators. Thus in early India there was a selection process of crossing japonica to indica to acquire some, but not all, domestication related traits.