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.

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.

Rice is among the world’s most important and ancient domesticated crops. However, the spatial and temporal pattern of the early rice domestication process remains unclear due to the lack of systematic study of wild/domesticated rice remains and corresponding dates during the early Holocene. Here, we collected 248 samples from five typical Shangshan cultural sites in the lower Yangtze region where is the most likely origin place of rice for phytolith analysis. The results showed the following. (1) Rice bulliform phytoliths from the five sites all present domestication traits, suggesting that the rice domestication process had begun across the region by the early stage of the Holocene. (2) The relative domestication rates reflected by the rice bulliform phytoliths were different between sites, the sites with higher domestication rates were distributed closer to the mainstream river. (3) The rice domestication process revealed by bulliform phytoliths can be divided into three periods during the early Holocene: from 10 to 9 ka, rice domestication began and stayed at a low level under 35%; from 9 to 8.5 ka, rice domestication level increased to 50%; and from 8.5 to 8 ka, rice domestication level was in a fluctuating state. (4) By 9 ka BP, rice double-peaked phytoliths from glume cells are present in most of the studied sites, which imply the presence of crop dehusking processing. This study reconstructed the spatial and temporal patterns of rice domestication during the early Holocene, which will improve our knowledge of early crop domestication and enhance our understanding of changes in rice status.

Located in the transitional region between northern and southern China, the middle Han River valley is of pivotal significance for current debates on rice domestication and the formation of mixed farming in early China. Based on phytoliths and macro-plant remains from 10 sites, along with radiocarbon dating, this study has narrowed the 2000-year gap in early rice utilization by 700 years in the middle Han River valley, and demonstrated the continuous development of rice agriculture in this region. This new evidence also reveals that as early as 7000 cal. BP, mixed farming emerged in this region and facilitated the further southward dispersal of foxtail millet and broomcorn millet into southern China and beyond. In addition, a sample-by-sample comparison of our results with phytoliths and macro-plant remains highlighted the potential biases inherent in these methods. This work emphasized the importance of multi-index archaeobotanical analysis to reconstruct ancient crop assemblages.

Neolithic rice remains were recovered from a mixed rice–millet farming area in China outside the original centers of rice farming. Whether the rice remains were the result of local cultivation or obtained through trade remains unclear. Rice paddy fields are direct evidence of local cultivation. In this study, phytolith samples from the Zhangwangzhuang site were analyzed. The discriminant function distinguished 17 of 30 samples in the suspected paddy field area as rice paddy fields with an average probability of 74%; The proportion of rice bulliform phytoliths with ≥9 scales indicated that rice (Oryza sativa) was still being domesticated and, moreover, six η-type phytoliths from broomcorn millet (Panicum miliaceum) were identified. These results suggested that the suspected paddy field at Zhangwangzhuang might be the earliest rice paddy field (ca. 6000 cal. BP) in northern China and that mixed farming was practiced here since the early Yangshao period. This study adopted discriminant analysis methods to discover ancient rice paddy fields, observed rice paddy fields outside the core rice origin area, and provided the earliest evidence regarding the development of mixed rice–millet farming in the upper Huai River region.