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Abstract To understand rice types that were utilized during postdomestication and in the modern age and the potential of genetic research in aged rice materials, archaeogenetic analysis was conducted for two populations of archaic rice grains from the Mojiaoshan site during the Liangzhu Period in China (2940 to 2840 BC). Sequencing after the PCR amplification of three regions of the chloroplast genome and one region of the nuclear genome showed recovery rates that were comparable to those in previous studies except for one chloroplast genome region, suggesting that the materials used in this work were appropriate for recovering genetic information related to domestication traits by using advanced technology. Classification after sequencing in these regions proved the existence of Japonica and Indica chloroplasts in archaic grains from the west trench, which were subsequently classified into eight plastid groups (type I–VIII), and indicated that these rice grains derived from different maternal lineages were stored together in storage houses at the Mojiaohsan site. Among these plastid groups, type V exhibited the same sequences as two modern Indica accessions that are utilized in basic studies and rice breeding. It was inferred that part of the chloroplast genome of archaic rice has been preserved in modern genetic resources in these two modern Indica accessions, and the results indicated that rice related to their maternal ancestor was present at the Mojiaoshan site during the Liangzhu Period in China. The usefulness of archaeogenetic analysis can be demonstrated by our research data as well as previous studies, providing encouragement for the possibility that archaeogenetic analysis can be applied to older rice materials that were utilized in the rice-domesticated period. Graphical abstract

Rice was introduced to northern Japan in the prehistoric era, when the local climate was relatively cool for rice cultivation. Ancient strains of rice could potentially be productive in unfavorable conditions for cultivation; modern strains sharing genetic traits with ancient rice may contribute useful genetic diversity. To understand the variation in Japanese rice, a comparison of seed sizes and chloroplast and nuclear DNA sequences was conducted, on modern rice accessions from diverse geographical areas, and eleven populations with seven reference populations of rice seed remains from 800 BC to 1500 AD. The populations of rice seed remains shared short grain shape and a specific chloroplast genotype with modern Japanese and worldwide rice accessions. This morphology and genotype may have been introduced to Japan along with farming techniques. Variability of seed shape and diversity of the nuclear genome both reduced through time, indicating genetic erosion in Japanese rice. Greater diversity in the populations of rice seed remains, taken together with archaeological and historical evidence, suggests that older rice populations had genetic traits that could adapt to unfavorable conditions of cultivation, such as flooding and low temperatures. Modern landraces share a genome structure with rice seed remains populations, which suggests that the modern landraces may have useful breeding traits such as tolerance of flooding and low temperatures.

To identify and study the Neolithic rice paddy in Shandong, eastern China, is not only an important issue in the development of Chinese rice agriculture, but also a key part of the study on rice spread in East Asia. Due to the limitation of archaeological materials and the research methods, there have been no discoveries about the Neolithic rice paddy in Shandong Province for a long time. Based on the identification of possible rice paddy by archaeological excavation, phytolith analysis of soil samples from this “paddy” has been systematically carried out and the results have shown a 4600–4300 years old rice paddy preserved at the Zhaojiazhuang site. This is the first examination and study of the rice paddy in North China by systematic phytolith analysis, which is very important for the Neolithic archaeological research and the study of the eastward spread of rice agricultural techniques in East Asia.

The presence of phytoliths derived from motor cells of rice (Oryza sativa L.) in archaeological sites could provide strong evidence for cultivation of rice in ancient times. The shape of phytoliths is now considered an effective criterion for determining subspecies of ancient rice. To understand the molecular genetic basis of determining subspecies of ancient rice based on the shape of phytoliths, and to analyze the quantitative trait loci (QTLs) controlling the shape of the silica body, which is the predecessor of phytoliths, we used 68 recombination inbred lines (RIL) from progeny of a combination of a cross between japonica variety, Asominori and indica variety, IR24. Knowledge of the positions of QTLs for the shape of the silica body would contribute to the study on the differentiation and evolution of rice at the molecular level. A total of 16 QTLs associated with the shape of the silica body were detected. Of these, five QTLs for vertical length of the silica body were mapped to chromosome 2, 3, 4, 8 (two QTLs) and accounted for 7.1–10.7% of the total phenotypic variation. Six QTLs for the horizontal length were detected on chromosome 1, 2, 3, 4 (two QTLS), 8 and accounted for 8.1–10.7% of the total phenotypic variation. Five QTLs controlling the lateral length on chromosome 1 (two QTLs), 2, 11 (two QTLs) were detected and explained 7.3–8.6% of the phenotypic variation. The genetic linkage relationships between QTLs for the shape of the silica body and taxonomic traits for classifying subspecies of rice showed feasibility of classifying subspecies of rice based on the shape of phytoliths in archaeological sites.

The purpose of this study was to discuss the practical usefulness of the discrimination of indica and japonica cultivar groups based on the morphology of silica bodies from motor cells in rice (Oryza sativa L.) . The effects of nitrogen levels on the morphology of silica bodies from the flag leaf were investigated. Two indica varieties, "T-153" and "T-160" and a japonica variety, "T-708" were used and cultivated in pot scale (1 / 5000a). Nitrogen treatment was divided into three levels of 20 gm-2, 10 gm-2, and 5 gm-2 and they were applied when the rice plants had 1.5-2.0 in remaining plant age in number of leaves (corresponding to 15 to 20 days before heading). The result showed little effect of nitrogen level on the morphology of silica bodies. No effect of nitrogen level was observed on the discrimination of indica and japonica cultivar groups based on the morphological characters of silica bodies, although the discriminating scores were slightly changed.

Genetic analysis of the morphology of silica bodies from motor cells in rice (Oryza sativa L.) was conducted by examining an F2 population and a set of 3×5 NCII diallel crosses. Segregation for the four morphological characters-vertical length, horizontal length, Iateral length and shape coefficient (b/a)-of silica bodies in the F2 population showed a countinous and a wide distribution exceeding the ranges of the two parents (Fig.2), suggesting that the morphological characters of silica bodies were quantitative and controlled by several genes. In the NCII diallel analysls, the heterogenelty of W'r+1/2Vr between arrays was not significant for all the morphological characters but b/a, and the heterogeneity of W'r-1/2Vr was not observed for all the characters tested (Table 4). The regression coefficients of W'r on Vr were nearly 0.5 but significantly different from zero (Table 5), indicating that the shape of the silica bodies was controlled by an additive-dominance genetic system. The heritabilities in a broad sense for the four characters were in the range of 0.43-0.73 and those in a narrow sense in the range of 0.29-0.54 (Table 6).

A joint research project has been carried out between Japan and China on the origin and spread of rice in the Middle and Lower Changiiang River Valley of China by plant opal analysis since 1992. The excavation of ancient paddy fields near the Caoxieshan site in Wu County, Jiangsu Province was conducted. Ten accumulated soil layers with each cultural period property were confirmed, and the layers from the fifth layer to the tenth layer were identified as belonging to the Middle Majia-bang period (B.P.5900-6200). And the existence of paddy fields in soil layers of Chunqiu, Songze and Majiabang period were identified by plant opal analysis. Moreover, more than forty paddy field sites were excavated under the ninth or tenth layer. This paper reports on the results of quantitative and morphological analysis of plant opals on soil samples collected from nineteen paddy filed sites and ten soil layers at the Caoxieshan site in 1994 and 1995, and discusses the cultivar group and its historical change of ancient rice cultivated near the Caoxieshan site. The quantitative analysis of plant opals detected large amounts of rice plant opals from motor cell silica bodies in all the samples, suggesting that the rice cultivation near the Caoxieshan site began from the middle Majiabang period and continued up to the present. Moreover, the rapid increase of rice leaf weight inferred from plant opals in soil layers of middle Majiabang period suggested that rice cultivation had been prevalently practised during this period. The morphological analysis of plant opals suggested that the plant opals from the soil layers of middle Majiabang period were derived from japonica rice. Compared to the motor cell silica bodies from Chinese native Keng (correspond to japonica) rice, the plant opals had a larger value in b/a as well as in vertical length and lateral length, and the discriminant scores were more like those from typical japonica rice. A comparison of the discriminant scores of plant opals from the ten soil layers showed a slowly decreasing trend from the lower layers to the upper ones. And the scores were especially small for the soil layers above the third one (the Song period), suggesting that it is highly possible that the indica rice would be probably cultivated from Song period near the Caoxieshan site.

Methods of discrimination of indica and japonica rice based on the shape of silica body from motor cells in the leaf blade and on morphological and physiological characters of grain were compared, and their relationship was investigated. Fifty Chinese native and im-proved rice varieties (25 Hsien and 25 Keng) were used. Four morphological characters of silica body from the motor cells (vertical length, VL; horizontal length, HL; Iateral length, LL and shape coefficient b/a) (Fig. 1), grain shape (length, L; width, W and their ratio L/W), apiculus hair length (AH), phenol reaction of the hull (PR) and potassium chlorate (KCI03) resist-ance of seedlings (KC) based on injury scores (O to 3) were analysed. Based on the above characters of indica and japonica cultivars defined by Sato's discriminant function (Z (SD) =PR+1.313KC-0.82AH-1.251)