Phytolith remains of rice (Oryza sativa L.) recovered from the Shangshan site in the Lower Yangtze of China have previously been recognized as the earliest examples of rice cultivation. However, because of the poor preservation of macroplant fossils, many radiocarbon dates were derived from undifferentiated organic materials in pottery sherds. These materials remain a source of debate because of potential contamination by old carbon. Direct dating of the rice remains might serve to clarify their age. Here, we first validate the reliability of phytolith dating in the study region through a comparison with dates obtained from other material from the same layer or context. Our phytolith data indicate that rice remains retrieved from early stages of the Shangshan and Hehuashan sites have ages of approximately 9,400 and 9,000 calibrated years before the present, respectively. The morphology of rice bulliform phytoliths indicates they are closer to modern domesticated species than to wild species, suggesting that rice domestication may have begun at Shangshan during the beginning of the Holocene.

Rice ( Oryza sativa ) serves as a staple food for more than one-third of the global population. However, its journey from a wild gathered food to domestication remains enigmatic, sparking ongoing debates in the biological and anthropological fields. Here, we present evidence of rice phytoliths sampled from two archaeological sites in China, Shangshan and Hehuashan, near the lower reaches of the Yangtze River. We demonstrate the growth of wild rice at least 100,000 years before present, its initial exploitation as a gathered resource at about 24,000 years before present, its predomestication cultivation at about 13,000 years before present, and eventually its domestication at about 11,000 years before present. These developmental stages illuminate a protracted process of rice domestication in East Asia and extend the continuous records of cereal evolution beyond the Fertile Crescent.

Phytoliths are noncrystalline minerals that form inside cells and cell walls of different parts of plants. Organic carbon in living cells can be occluded in phytoliths during plant growth. It has been documented that the occluded carbon within phytoliths is an important long-term terrestrial carbon reservoir that has a major role in the global carbon cycle. Common millet and foxtail millet have become typical dry-farming crops in China since the Neolithic Age. The study of carbon conservation within phytoliths in these crops could provide insights into anthropogenic influences on the carbon cycle. In this study, we analyzed the carbon content in phytoliths of common millet and foxtail millet. The results indicated that (1) common millet and foxtail millet contained 0.136% ± 0.070% and 0.129%± 0.085% phytolith-occluded carbon (PhytOC) on a dry mass basis, respectively; (2) based on the mean annual production of common millet and foxtail millet in the last 10 years, the phytolith occluded carbon accumulation rate of common millet and foxtail millet was approximately 0.023 ± 0.015 and 0.020± 0.010 t CO₂ ha⁻¹ a⁻¹, respectively; (3) assuming a similar phytolith occluded carbon accumulation rate as for common millet (the highest accumulation rate was 0.038 t CO₂ ha⁻¹ a⁻¹), this could result in the sequestration of 2.37 × 10⁶ t CO₂ per year for the 62.4 × 10⁶ ha dry-farming crops in China. Although there was a decline in the annual production rate and planting area of foxtail millet during 1949 to 2008, the total phytolith carbon sequestration rate was 7×10⁶ t CO₂ within the 60-year period. However, phytolith occluded carbon has not yet been fully considered as a global carbon sink. Also, this carbon fraction is probably one of the best candidates for the missing carbon sink.

Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process.

Mixed millet and rice agriculture is a unique agricultural style of China, and is distributed in a broad band between the Yangtze and Yellow River basin. However, the development of this style during the Neolithic-Bronze Age has not been comprehensively clarified, owing to limited archaeobotanical data and imprecise chronology for most of the regions. Here, the Central Plain, a location where mixed agriculture may have first appeared, was selected as the area for research. Phytolith and macrofossil analyses from the Zhuzhai site, together with the accelerator mass spectrometer (AMS) radiocarbon dating of samples, reveal information about the temporal changes of mixed agriculture as well as the domestication and cultivation of crops in this region. The results indicate that mixed millet and rice agriculture formed in the Central Plain about 8000 years ago. Common millet was the principal crop in the Peiligang and Yangshao periods, with the domestication process beginning in the Peiligang period and continuing up to the Shang period, at which time it was replaced by foxtail millet. Foxtail millet may have gone through a significant degree of domestication by ca. 6000 cal. BC, but its domestication process was still unclear. Rice had appeared since the Peiligang period, but its proportions were always low. Rice assigned to the Peiligang and Yangshao Cultures was the domesticated japonica, and its cultivation was always performed in dry field systems through the Neolithic-Bronze time. Within the subsistence economy, mixed agriculture was a minor component during the Peiligang period, but has been dominant since the Yangshao period.