Process Of Rice Domestication Research Articles

Rice's trajectory from wild to domesticated in East Asia.

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.

Spatial and temporal pattern of rice domestication during the early Holocene in the lower Yangtze region, China

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.

The Probable Critical Role of Early Holocene Monsoon Activity in Siting the Origins of Rice Agriculture in China

The long process of rice domestication likely started 10,000–8,000 years ago in China, and the pre-existing hunter-gatherer communities gradually adopted more sedentary lifestyles with the dependence of rice agricultural economies. The archeological evidence builds a strong case for the first domestication of rice to Oryza sativa centered in the Middle-Lower Yangtze Valley during the early Holocene. The genetic evidence identifies the main ancestor of O. sativa was O. rufipogon, however, this now occurs naturally south of the Yangtze where its distribution is limited by summer temperatures and mean annual temperature. The mismatch between occurrence of ancestors and presumed sites of early cultivation leads to a number of hypotheses. These include that first domestication actually took place further south, such as in the Pearl River valley but archeological evidence is currently lacking for this. Or domestication took place, when O. rufipogon had a more extensive natural range in the past. Early to mid-Holocene palaeoclimate reconstructions show that the East Asian Summer Monsoon was more active in the early Holocene and estimates show that the temperature requirements for O. rufipogon were met for a substantial area of northeast China at the time. This would mean that earliest known domestication sites and presumed ancestor distribution coincided for several millennia. Thus early records of rice farming in Henan and Shandong were easily accommodated by early to mid Holocene climates.

Comparative analysis of the transcriptomes of two rice subspecies during domestication

Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

Process of rice domestication in relation to Holocene environmental changes in the Ningshao Plain, lower Yangtze

Understanding the process of domestication and its relationship with environmental changes is fundamental to rice domestication research. The lower Yangtze region in China, with varied coastal environments and a flourishing Neolithic culture, was one of the major rice domestication centers in Asia. Here we present the results of 348 phytolith and 87 diatom samples from a 43.88-m-long core HMD1401 in the Ningshao Plain, southern part of the lower Yangtze. The results show that the study site was in a marine condition during the interval of ~10,000–7000 cal. yr BP. Marine regressed after ~7000 cal. yr BP, with occasional influences by sea water and flood. Rice was being domesticated in the Ningshao Plain at ~9600 cal. yr BP, and rice domestication experienced a protracted process that lasted for over 3500 years. The influence of marine condition might contribute to the prolonging of rice domestication. Relatively stable terrestrial condition and intensive human activities promoted rice domestication in the Ningshao Plain. The results provide an improved understanding of the interrelations between early rice domestication and Holocene environmental changes in East Asia.

Genetic evaluation of domestication-related traits in rice: implications for the archaeobotany of rice origins

Domestication is the process in which preferred genetic changes in wild plants and animals have been selected by humans. In other words, domesticated plants have become adapted to being part of human-managed ecosystems. Asian cultivated rice, Oryza sativa L., is one of the most important crops in the world and is known to have been domesticated from its wild ancestor, O. rufipogon. Many morphological changes in cultivated rice have been beneficial to humans in terms of increased efficiency of cultivation and yield that supported the development of human civilisations. The genetic mechanisms of these changes have been extensively studied since rice genome sequences were determined, and based on genome analyses, the origin of rice has been widely discussed. Most of the domestication-related traits and genes are, however, often evaluated based on the genetic background of cultivated rice, leading to misinterpretation of rice domestication. Here, we review several genetic changes and discuss the importance of evaluating these traits in the wild rice genetic background to understand the process of rice domestication. In this review, we also provide a phenotypic evaluation of domestication-related traits.

Role of dynamic environmental change in sustaining the protracted process of rice domestication in the lower Yangtze River

Recent increases in archaeobotanical and genetic evidence offer insights into agricultural origins and plant domestication, which suggest a protracted process taking thousands of years that began by 10,000 cal a BP or in the late Pleistocene. Compared to the cereal domestication that was accomplished in the early Holocene in Southwest Asia and Mesoamerica, the reasons for the delay in rice domestication in China until the middle Holocene remain unclear. In the present study, the dynamic influence of environmental change on rice domestication was revealed by evidence from sedimentary facies and phytolith analysis of the high-resolution HMD1602 core from the Hemudu site. Rice phytoliths were recovered from beneath the neritic sediment at this site for the first time, which pushes the history of human activities and the process of rice domestication in the Yaojiang Valley back to 8200-7600 cal a BP. The process of rice domestication at the Hemudu site developed discontinuously with an obvious interruption during 7600-7100 cal a BP, which was significantly influenced by marine transgression and palaeo-typhoon events. Furthermore, synthesis of palaeoenvironmental and archaeobotanical records suggests that rice exploitation and domestication was interrupted three times during 13,000-10000, 7900-7400 and 6400-5600 cal a BP, respectively. The first interruption of rice exploitation was induced by the Younger Dryas, which triggered the onset of cultivation at approximately 10,000 cal a BP in Southwest Asia and China, while the second two interruptions of rice domestication were caused by marine transgressions, which postponed the domestication of only rice. Therefore, the delayed accomplishment of rice domestication until the middle Holocene resulted from an unstable climatic environment and sea-level fluctuations, which ultimately led to the discontinuous process of rice domestication.

Bulliform Phytolith Size of Rice and Its Correlation With Hydrothermal Environment: A Preliminary Morphological Study on Species in Southern China.

In the last decade, our understanding of rice domestication has improved by new archaeological findings using advanced analytical techniques such as morphological and morphometric analyses on rice grains, spikelet bases and phytoliths, and ancient DNA analysis on rice remains. Previous studies have considered the size of rice bulliform phytoliths as a proxy for tracking the domestication process. These phytoliths are often abundant and well preserved in sediments, and their shape is under the control of numerous genes, which may shift toward larger sizes by genetic mutation in domestication. Therefore, it has been assumed that the bulliforms of domesticated rice are usually larger than those of wild ones; however, morphometric data supporting this assumption are lacking in the literature, thereby requiring additional evidence to test its veracity. In this study, the vertical and horizonal lengths of bulliform phytoliths were measured in four rice species (domesticated Oryza sativa and wild Oryza rufipogon, Oryza officinalis, and Oryza meyeriana) from different regions of southern China. We found that the bulliform morphometric data of wild and domesticated rice overlapped and that there was no statistically significant difference between them. Therefore, bulliform size could not be used as a diagnostic indicator to distinguish domesticated rice from wild species and is a supporting rather than conclusive proxy for determining the domesticated status of rice in archaeological research. We further found that larger rice bulliform sizes likely occurred at the locations with higher temperature, precipitation, and water levels, indicating hydrothermal environment is an alternative factor influencing the size of rice bulliform phytoliths. For further archaeological use of an increasing size trend of bulliform phytoliths to reveal the process of rice domestication, we present some suggestions for controlling the influence of hydrothermal factors. Even so, the combination of bulliform phytolith size with other established criteria is strongly suggested to provide precise identification of wild and domesticated rice in future research.

Phytoliths reveal the earliest interplay of rice and broomcorn millet at the site of Shuangdun (ca. 7.3–6.8 ka BP) in the middle Huai River valley, China

The middle Huai River valley, located in the climatic, cultural and agricultural transitional zone in the central-eastern China during the Neolithic, occupies an important position in the study of the origins, development and spread of rice and millet farming in China. Previous studies indicate that rice agriculture has extended to the middle Huai River valley since 8.5 ka BP, and rice domestication was in the early stage between 8.5 and 7.5 ka BP, while the earliest evidence of millet remains discovered in this region was as late as ca. 5.0 ka BP. However, the process of rice domestication after 7.5 ka BP in this region, and when and where foxtail millet and broomcorn millet first extended respectively into this valley and interplayed with rice during the Neolithic period are still unknown. In this study, phytolith analysis of the soil samples from the Shuangdun site during the archaeological excavation, which is a representative site of the Shuangdun Culture in the middle Huai River valley dating back to 7.3–6.8 ka BP, reveals evidence of crops in the middle Huai River valley, China. Our results show that rice with japonica characteristics was the dominant crop at the Shuangdun site, which had a higher domestication rate than that at the Shunshanji site during 8.5–7.5 ka BP in terms of the morphological and morphometric analyses of rice bulliform and double-peaked glume cells, while broomcorn millet only occupied a small proportion of the total amount based on analysis of the quantity and ubiquity of phytoliths. Our data extend the record of broomcorn millet use in the middle Huai River valley by nearly 2000 years. The analysis in this paper not only provides significant evidence for illustrating the transformation of crop structure and the domestication process of rice in the middle Huai River valley, but also brings some clues for mapping the spatiotemporal route for the spread of rice and millets in central-eastern China during the Neolithic.

Multiple indicators of rice remains and the process of rice domestication: A case study in the lower Yangtze River region, China

The process of rice domestication has been studied for decades based on changing morphological characteristics in assemblages of both macroremains, such as charred seeds and spikelet bases, and microremains, such as phytoliths, esp. bulliform and double-peaked phytoliths. The applicability of these indicators in determining if a specific assemblage is wild or domesticated, however, is rarely discussed. To understand the significance of these indicators in the determination of domestication, we collected 38 archaeological samples from eight Neolithic sites, dating from 10-2ka BP, in the lower Yangtze River region to analyze and compare the changes of these different indicators over eight thousand years. The data demonstrate that the comprehensive analysis of multiple indicators may be the best method to study the process of rice domestication developed thus far. An assemblage of rice remains can be identified as domesticated forms if they meet the following criteria simultaneously: 1) the proportion of domesticated-type bulliform phytoliths is more than 73%; and 2) the proportion of domesticated-type rice spikelet bases is higher than 75%. Furthermore, we found that each indicator tends to change steadily and gradually over time, and each stabilized at a different time, suggesting that the characteristics of domesticated rice developed slowly and successively. Changes of multiple indicators during the period between 10,000–2,000 yr BP indicate that the process of rice domestication in the lower Yangtze River region lasted as long as ca. 6,000 years during the Neolithic, and can be divided into three stages with the turning points in the middle Hemudu-late Majiabang culture (6,500–5,800yr BP) and the late Liangzhu culture (4,600–4,300yr BP).

Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits.

Cultivated rice (Oryza sativa) originated from common wild rice (Oryza rufipogon) and inherited its advantages. However, during the rice domestication process, some valuable features of wild rice, such as tolerance to biotic and abiotic stress, were lost. To fully utilize wild rice germplasm resources, we constructed a set of introgression lines (ILs) using a common wild rice material from Lingshui, China. A set of high-resolution InDel molecular markers with an average interval of 2.39Mb were designed to carry out marker-assisted selection and identification of segment characteristics. The ILs contained 77 lines including 1.286 introgressed fragments with an average length of 6.511Mb, covering 93.59% of the donor parent's chromosomes. The agricultural traits of 77 lines were investigated. Many old quantitative trait loci (QTLs) involved in plant height, awn length, seed traits and other characteristics reappeared in our ILs, proving that our system was reliable. Further, many new QTLs were identified. A QTL related to drought tolerance located on chromosome 4 was thoroughly elaborated. This set of ILs provides a new resource for utilizing the excellent features of wild rice.

Understanding of Rice Domestication Process based on DNA Changes in Domestication-trait Genes.

Understanding of Rice Domestication Process based on DNA Changes in Domestication-trait Genes.

Rice bulliform phytoliths reveal the process of rice domestication in the Neolithic Lower Yangtze River region

Abstract Recent studies have shown that the proportion of rice bulliform phytoliths with ≥9 fish-scale decorations can be used as a criterion to differentiate wild rice from its domesticated counterpart. The analysis of rice bulliform phytoliths recovered from 38 samples collected from eight archaeological sites dated to around 10,000–2200 BP suggests that the process of rice domestication in the Lower Yangtze River region lasted for around 6000 years and can be divided into three stages. Stage I was from around 10,000 to 6500 BP. The process of domestication was very slow, and even went backwards. Stage II was between 6500 and 5600 BP, when the process was accelerated. During stage III, from 4500 to 2200 BP, the domestication process eventually resulted in the breed of the modern rice.

Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China.

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.

Morphological trend analysis of rice phytolith during the early Neolithic in the Lower Yangtze

The investigation of rice domestication process is important for understanding how agriculture evolved in China. In this paper, we studied samples of rice phytoliths from the Shangshan (around c. 11,000–9000 cal. BP), Kuahuqiao (around c. 8200–7200 cal. BP) and Hemudu (around c. 7000–6500 cal. BP) periods in the lower valley of Yangtze River. Using two different techniques it was demonstrated that rice phytoliths could be separated into wild rice and domesticated varieties. Through time the percentage of wild rice phytoliths decreases while the percentage of domesticated rice phytoliths increases. The changes in morphological characteristics of double-peaked glume cells and scale-like decorations numbers of cuneiform bulliform cells indicates that human intervention likely impacted rice during the Shangshan, Kuahuqiao and Hemudu Periods. Based on morphological characteristics when classifying the rice phytoliths into wild rice and domesticated rice varieties of double-peaked glume cells, a large percentage of phytoliths could not be assigned to either a wild or domesticated variety. The large percentage of the uncertain type indicates that early domesticated rice phytolith may be neither completely wild nor fully domesticated in morphology. The result of this study indicates the evolution from wild rice to domestic rice occur between 12,000 and 7000 cal. BP.

Archaeological and genetic insights into the origins of domesticated rice.

Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world's population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.

Haplotype variation at Badh2, the gene determining fragrance in rice

Fragrance is an important component of end-use quality in rice. A set of 516 fragrant rice accessions were genotyped and over 80% of them carried the badh2.7 allele. A subset of 144 mostly fragrant accessions, including nine of Oryza rufipogon, was then subjected to a detailed diversity and haplotype analysis. The level of linkage disequilibrium in the Badh2 region was higher among the fragrant accessions. Re-sequencing in the Badh2 region showed that badh2.7, badh2.2 and badh2.4–5 all arose in the japonica genepool, and spread later into the indica genepool as a result of deliberate crossing. However, loss-of-function alleles of Badh2 are also found in the indica genepools, and then transferred into japonica. Evidence for three new possible FNPs was obtained from the Badh2 sequence of 62 fragrant accessions. Based on these data, we have elaborated a model for the evolution of Badh2 and its participation in the rice domestication process.

Major domestication traits in Asian rice

Rice (Oryza sativa L.) is an excellent model plant in elucidation of cereal domestication. Loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. Loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. Two major shattering QTLs, Sh4 and qSH1, have displayed different domestication histories. Weakened seed dormancy is essential for synchronous germination in agricultural production. Genes Sdr4, qSD7-1, and qSD12 impose a global and complementary adaptation strategies in controlling seed dormancy. The prostate growth habit of wild rice is an adaptation to disturbed habitats, while the erect growth habit of rice cultivars meet the needs of compact planting, and such a plant architecture is mainly controlled by PROG1. The outcrossing habit of wild rice promotes propagation of domestication genes among different populations, while the self-pollinating habit of cultivated rice facilitates fixation of domestication genes. Currently, the researches on rice domestication mainly focus on individual genes or multiple neutral markers, and much less attention has been paid to the evolution of network controlling domestication traits. With the progress in functional genomics research, the molecular mechanism of domestication traits is emerging. Rice domestication researches based on network will be more comprehensive and better reflect rice domestica-tion process. Here, we reviewed most progresses in molecular mechanisms of rice domestication traits, in order to provide the new insights for rice domestication and molecular breeding.

The Domestication Process and Domestication Rate in Rice: Spikelet Bases from the Lower Yangtze

The process of rice domestication occurred in the Lower Yangtze region of Zhejiang, China, between 6900 and 6600 years ago. Archaeobotanical evidence from the site of Tianluoshan shows that the proportion of nonshattering domesticated rice (Oryza sativa) spikelet bases increased over this period from 27% to 39%. Over the same period, rice remains increased from 8% to 24% of all plant remains, which suggests an increased consumption relative to wild gathered foods. In addition, an assemblage of annual grasses, sedges, and other herbaceous plants indicates the presence of arable weeds, typical of cultivated rice, that also increased over this period.

The Process of Rice Domestication: A New Model Based on Recent Data

Abstract Rice domestication involved a complex process of selection by ancient humans, leading to the development of a new species, Oryza sativa, during the last 10,000 years. Recent rice genome research and the cloning of domestication-related genes have provided novel knowledge about the domestication process, although recent reviews have revealed more complexity than previously suspected. Some of this additional complexity may arise from a poor fit between the new data and previous models. DNA divergence observed in existing landraces, cultivars, and wild relatives can now be determined accurately, so the order of major DNA changes such as single nucleotide polymorphisms during the domestication process can be abducted owing to relatively low mutation rates. Therefore, a new model to explain the selection process during rice domestication, such as the one proposed for further discussion in this paper, is needed to accommodate the new DNA evidence.