Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (~2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.     

Characteristics of the short rachillae of rice from archaeological sites dating to 7000 years ago

The abscission layer formed on a pedicel situated at the basal part of a short rachilla is an important characteristic for discriminating between wild, japonica, and indica rice. The short rachillae of paddy rice grains excavated from the Kuahuqiao, Luojiajiao, and Tianluoshan sites, located in the lower reaches of the Yangtze River and dating to 7000 years old, were observed. The results showed that the short rachillae could be divided into two types: a wild type and japonica type. These results indicated that the rice had been domesticated, but was a primitive cultivated rice that retained some of the characteristics of wild rice. The results also suggested that the rice was changing to resemble japonica type rice. Based on the ratios of wild and japonica types, it was inferred that rice domestication began 10000 years ago.     

水稻的起源与驯化——来自基因组学的证据

 水稻是世界上最重要的粮食作物, 约1 万年前开始被驯化。由于水稻与其祖先野生种存在一定的遗传分化, 水稻的起源和驯化问题长期存在争议。本文综述了水稻起源和驯化方面的研究成果, 特别是近年来基因组学方面的证据, 认为水稻2 个亚种独立起源于野生祖先种内很早就分化的不同类群, 但一些驯化基因--控制重要农艺性状的基因, 可能首先在一个亚种中被驯化, 然后通过基因渐渗, 扩散到另一个亚种中。因此, 水稻驯化的关键是研究驯化基因的起源和扩散方式。随着大规模基因组测序技术的发展和相应数据分析方法的建立, 在全基因组水平对水稻及其祖先进行大规模分析, 已成为揭示水稻起源与驯化之谜的必由之路。     

Diets, eco-environments and seasonal variations recorded in the oxygen and carbon isotopic compositions of mammal tooth enamel from the Shunshanji site, Sihong County, Jiangsu Province, China

The carbon and oxygen isotopic compositions of the tooth enamel of mammals, including deer, wild pigs, buffaloes and domesticated pigs from the Shunshanji site, Sihong County, Jiangsu Province, China, were analyzed to reconstruct the mammals’ ecoenvironments and diets, and to evaluate seasonal variations in the study area. Carbon isotopic compositions of buck samples revealed that the deer ate completely C₃ plants and the environments they inhabited were relatively open and that wild pigs ate primarily C₃ plants. Oxygen isotopic compositions indicated that the body sources of these two mammals were different, i.e. the deer and pigs lived in different niches within a relatively similar ecosystem. Modern domesticated pigs were isotopically more positive than the ancient wild pigs in carbon δ ¹³C values, suggesting the former ingested more C₃ plants relative to the latter. Although the δ ¹⁸O data showed modern domesticated and ancient pigs had similar oxygen isotope compositions, their water sources were different. The carbon and oxygen isotopic patterns of premolar microsamples of ancient and modern buffaloes indicated that the plants ingested by the ancient buffalo varied with seasonal shifts, but plants ingested by the modern buffalo were relatively constant. The eco-environment of the modern buffalo was more open, warmer and drier than eco-environment of the ancient buffalo, which may be the result of the deforestation and other human activities. Ancient and modern seasonal changes were clearly recorded in the isotopic patterns and the seasonal variation amplitudes of the ancient and modern eco-environments were similar.     

Archaeological discovery and research on the remains of the paleoflood of the Yuxi site

The research of the paleoflood remains from archaeological sites is one of the most important jobs in the environmental archaeology.Based on the traditional archaeological methods and the archaeological finds from the Yuxi site,Fengdu County of Chongqing,the paper analyzes the difference between the cultural layers and the possible paleoflood layers from various angles,such as contents,shapes of gravels,pottery,etc.,identifies the possible paleoflood deposit layers,i.e.the paleoflood remains of the Yangtze River,and discusses the periodicity of the floods.     

Molecular evolution of rice S 5 n and functional comparison among different sequences

The wide compatibility gene, S ₅ ⁿ , can overcome embryo sac sterility between indica and japonica subspecies of rice. Therefore, it is very important to characterize the features of the S ₅ ⁿ sequence to reveal the origin and evolution of S ₅ ⁿ . In this paper, 26 cultivated rice haplotypes and 22 wild rice accessions harboring S ₅ ⁿ were used to sequence S ₅ ⁿ . The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S ₅ ⁿ sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710?C1719 bp, including wild (O. nivara) and cultivated rice, such as IRW501 and Yuetai B. S ₅ ⁿ sequences were not biased and evolved neutrally. The 48 materials could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice clustered into another group. Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found to lack 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S ₅ ⁿ coding regions were crossed with testers (typically indica and japonica) to produced test cross F₁ populations. The F₁s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S ₅ ⁿ -containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, indirectly proving that S ₅ ⁿ is a non-functional gene.     

Starch grains reveal early root crop horticulture in the Panamanian tropical forest

Native American populations are known to have cultivated a large number of plants and domesticated them for their starch-rich underground organs. Suggestions that the likely source of many of these crops, the tropical forest, was an early and influential centre of plant husbandry have long been controversial because the organic remains of roots and tubers are poorly preserved in archaeological sediments from the humid tropics. Here we report the occurrence of starch grains identifiable as manioc (Manihot esculenta Crantz), yams (Dioscorea sp.) and arrowroot (Maranta arundinacea L.) on assemblages of plant milling stones from preceramic horizons at the Aguadulce Shelter, Panama, dated between 7,000 and 5,000 years before present (BP). The artefacts also contain maize starch (Zea mays L.), indicating that early horticultural systems in this region were mixtures of root and seed crops. The data provide the earliest direct evidence for root crop cultivation in the Americas, and support an ancient and independent emergence of plant domestication in the lowland Neotropical forest.     

Early maize agriculture and interzonal interaction in southern Peru

Over the past decade, increasing attention to the recovery and identification of plant microfossil remains from archaeological sites located in lowland South America has significantly increased knowledge of pre-Columbian plant domestication and crop plant dispersals in tropical forests and other regions. Along the Andean mountain chain, however, the chronology and trajectory of plant domestication are still poorly understood for both important indigenous staple crops such as the potato (Solanum sp.) and others exogenous to the region, for example, maize (Zea mays). Here we report the analyses of plant microremains from a late preceramic house (3,431 +/- 45 to 3,745 +/- 65 14C bp or approximately 3,600 to 4,000 calibrated years bp) in the highland southern Peruvian site of Waynuna. Our results extend the record of maize by at least a millennium in the southern Andes, show on-site processing of maize into flour, provide direct evidence for the deliberate movement of plant foods by humans from the tropical forest to the highlands, and confirm the potential of plant microfossil analysis in understanding ancient plant use and migration in this region.     

Component and simulation of the 4,000-year-old noodles excavated from the archaeological site of Lajia in Qinghai,China

Noodles are a global food, but the periods when and places where they were made and originated, as well as their ingredients and the cooking methods used to manu- facture them, have remained contentious. In the 2005 edi- tion of the journal Nature, we wrote a summary of the millet noodle specimens found in the Late Neolithic Qijia cultural stratum of the Lajia archaeological site in Qinghai Province, China. However, how the ancient people made millet noodles remains controversial. This paper provides a systematic analysis of the remains of noodles found within an earthenware bowl at the Lajia ＂noodle house＂ in terms of their plant composition including phytoliths, starch and biomarkers. It provides evidence of how people used millet 4,000 years ago and, most specifically, of the principal methods used for producing millet-based noodles. Further, we show how we used traditional hele tools to make hele millet noodles, with especial reference to the gelatinized hydrogel-forming method, to simulate morphology con- sistent with the composition and form of the unearthed millet noodles. The results of this study provide new evi- dence and new insights into the cultural characteristics of the prehistoric human diet.     

Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the polymorphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the “InDel molecular index” that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.     

Environmental archaeology of the Dachang region in the Daning Valley,the Three Gorges reservoir region of the Yangtze River,China

Environmental archaeology of archaeological sites on both sides of the Dachang section in the Daning River,the Three Gorges of the Yangtze River,shows that riverbed evolution has a great influence on the distribution of archaeological sites during the prehistorical and historical period,and it restricts human activity and the development of ancient culture.Field investigation,dating data,paleocurrent analysis of 100 gravels on the riverbed and archaeological excavation reveal that the riverbed of the Dachang section developed in the Shuangyantang region during the early stage,after about 30 kaBP it shifted westward gradually and reached the present place.Along with the westward shift,the focus of ancient culture changed for several times.In the Western Zhou Dynasty’s period,the east riverbank of the Daning River was the main residential area.During the Han Dynasty,along with the westward shift,the living space of ancient people was no longer confined to the east riverbank and the focus of culture moved westward.Then the Zhangjiawan site became the main dwelling district.In the late Han Dynasty, the villages were flooded and the ancients had to immigrate to a high place.Tombs of the Han and the Jin Dynasties outcropped on the flood plain of the east bank because their surface sediments were eroded by several flood events and the westward shift of the riverbed.     

Response of rice cultivation to fluctuating sea level during the Mid-Holocene

Archaeological analysis of a section of ancient rice fields at Tianluoshan for diatoms, seeds and phytoliths has shown that the highest local sea level in eastern China during the Holocene appeared before 7.0 ka BP. Entering the Mid-Holocene, as seawater regressed, a vast wetland plain appeared in the coastal area, where farmers of the Neolithic Hemudu culture cultivated rice. However, there were still several sea-level fluctuations in the Mid-Holocene, of which the biggest were from 6.4 to 6.3 ka BP and from 4.6 to 2.1 ka BP. In addition, in the period dominated by wetland grass vegetation, 6.3 to 4.6 ka BP, smaller fluctuations appar- ently pushed the coastline back on to the land. Even though the sea-level rises associated with these shoreline transgressions did not have the intensity of the highest sea level period, there still would have been profound impacts on the lives and production activities of people living in the region. Archaeological evidence from ancient rice fields at Tianluoshan shows that larger sea-level rise events pushed seawater onto the land and inundated large areas of rice fields, whereas weaker sea-level rise events resulted in the intrusion of seawater along rivers, causing an increase in soil salinity and a decrease in rice yields. The impact of sea-level rise on rice cultivation caused changes in local diet. In regions where rice production fell, the prevalence of gathering and hunting rose. High sea levels in the early Holocene imply that the origin of rice cultivation in the eastern coastal plain is likely to have been in small nearby mountain basins.     

Origin of the Chinese cultivated rice (Oryza sativa L.)

The following new research progresses are summarized and discussed, which are related to 3 main problems in origin of rice cultivation in China: 1. new hypothesis of rice cultivation in China— middle Yangtze River and upper Huai River regions; 2. primitive cultivated rice and the strengthen period of domestication; 3. genetic diversity centers of cultivated rice in China; 4. China and South Asia might be two independent systems of origin and differentiation of Asian cultivated rice; 5. morphological classification of common wild rice of China; 6. primitive progenitor of common wild rice; 7. direct progenitor of cultivated rice; 8. present or not the annual wild rice in China; 9. differentiation or not the common wild rice into Indica and Japonica; 10. origin and differentiation of Indica and Japonica.     

Genetic analysis and fine mapping of the pubescence gene GL6 in rice (Oryza sativa L.)

The pubescence of the leaf blade surface is an important agronomic characteristic for rice morphology and significantly influences rice growth as well as physiological characteristics. This characteristic was analyzed in F1 and F2 plants derived by crossing cultivar 75-1-127 with the indica cultivar Minghui 63, as well as the glabrous cultivar Lemont and indica cultivar 9311. Results indicated that the pubescence of the leaf blade surface was a dominant trait and controlled by a single gene. The GL6 gene was primarily mapped on rice chromosome 6 with recessive F2 population derived from 75-1-127/Minghui 63 by combining bulked segregation analysis and recessive class analysis using the Mapmaker3.0/MapDraw software. The genetic distances between the simple sequence repeat markers RM20491 and RM20547 were 7.2 and 2.2 cM, respectively. The GL6 gene was fine mapped in the interval between InDel-106 and InDel-115 at genetic distances of 0.3 and 0.1 cM, respectively. The large, recessive F2 population was derived from 75-1-127/Minghui 63. A high-resolution genetic and physical map of GL6 was constructed. Derived from the map-based sequences published by the International Rice Genome Sequencing Project, the GL6 gene was localized at an interval of 79 (japonica) and 116.82 kb (9311) bracketed by InDel-106 and InDel-115 within the BAC accession numbers AP008403 and AP005760. Seven annotated genes (japonica) and eight annotated genes (9311) were present. The basis was further set for GL6 cloning and function analysis.     

Development of ancestors‘ cultivation revealed in phytolith assembalages from Guangfulin relics

Shanghai Museum has got great achievements in re-excavating Guangfulin relics.It is the first time that the cultural remains of Wangyoufang type is found above the Liangzhu cultural remains which comes from East Henan Province,providing previous materials for researching culture evolution around Taihu Lake.Samples were taken from the immature soil layer and cultural layers of Guangfulin relics for phytolith analysis.According to the systemic research for the archaeological remains and phytolith fossil,the phytoliths in Guangfulin relics can be divided into four xones.The development of rice agriculture and living condition of Guangfulin ancestors was discussed based on the existing rice fan-shaped phytolith,rice shell phytolith.diatom fossil and archaeology,evidence in the same layer.The Guangfulin relics has gradually developed since a high sea level 5000 years ago,and the broad rice agriculture has simultaneously developed.The newly re-excavated relics provides valuable materials for the research of ancestors and ancient culture in Shanghai.     

Development of ancestors'''' cultivation revealed in phytolith assemblages from Guangfulin relics

1 Survey The Changjiang Delta Region is one of the cradles of the national culture. 300 cultural sites of Neolithic, which separately belong to 4 archaeology cultural styles, includ-ing Majiabang culture (7—6 kaBP), Songze culture (6—5 kaBP), Liangzhu culture (5—4 kaBP) and Maqiao culture (4—3 kaBP), were excavated and represent the develop-ing steps of continuous ancient culture[1]. After 1949 the archaeologists in Shanghai have been doing a great deal of excavation to ancient rel…     

Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. ¹⁴C analysis showed that this cemetery was used from 217 B.C. to 283 A.D. Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region I (mtDNA HVR-I), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.     

Plant crop remains from the outer burial pit of the Han Yangling Mausoleum and their significance to Early Western Han agriculture

A large amount of carbonized plant remains were discovered in one of the outer burial pits of the Han Yangling Mausoleum, which was built more than 2000 years ago for the Jing Emperor, Liu, Qi (188―141 cal a BC), the fourth emperor of the Western Han Dynasty. The remains are identified by phytolith analysis and macrofossil morphological features. Seeds from foxtail millet (Setaria italica), broomcorn millet (Panicum miliaceum), rice (Oryza sativa) and chenopod (possible Chenopodium giganteum) are identified...     

Biochemical evidence of cannibalism at a prehistoric Puebloan site in southwestern Colorado

The existence of cannibalism is one of the most controversial issues in the archaeology of the American Southwest. Disarticulated, cut-marked and heat-altered human remains from non-burial contexts at prehistoric Puebloan (Anasazi) archaeological sites in the Four Corners region of the American Southwest have been interpreted by some scholars as evidence of cannibalism. Osteological studies indicate that many of the disarticulated bodies found at these sites were processed in a manner consistent with food preparation. Opponents of this interpretation point out that non-cannibalistic practices such as secondary interment, corpse mutilation and ritualized witch executions might account for the assemblages. Osteological evidence alone does not document the actual ingestion of human flesh. Here we show consumption of human flesh did occur as demonstrated in preserved human waste containing identifiable human tissue remains from a site with osteological evidence of cannibalism.     

Generation of selectable marker-free transgenic rice resistant to chewing insects using two co-transformation systems

To produce selectable marker-free (SMF) transgenic rice resistant to chewing insects, the Bacillus thuringiensis cryIA(c) gene (Bt) was introduced into two elite japonica rice varieties by using two Agrobacterium-mediated co-transformation systems. One system is with a single mini-twin T-DNA binary vector in one Agrobacterium strain, which consists of two separate T-DNA regions, one carrying the Bt while the other contains the selectable marker gene, hygromycin resistant gene (HPT). The other system uses two separate binary vectors in two separate Agrobacterium cultures, containing the Bt or HPT gene on individual plasmids. A lot of independent transgenic rice lines harboring both Bt and selectable marker genes were obtained. The results showed that the co-transformation frequency of the Bt gene and HPT gene was much higher by using the mini-twin T-DNA vector system (29.87%) than that by the two separate binary vector systems (4.52%). However, the frequency of the SMF transgenic rice plants obtained from the offspring of co-transgenic plants (21.74%) was lower for the mini-twin T-DNA vector system than that for the latter (50-60%). The data of ELISA implied that the expressed Bt proteins were quantitated as 0.025-0.103% of total leaf soluble proteins in the transgenic plant. Therefore, several elite transgenic rice lines, free of the selectable marker gene, were chosen. The results from both in vitro and in vivo insect bioassays indicated that the SMF transgenic rice was shown to be highly resistant to the striped stem borer and rice leaf folder. Moreover, in a natural field condition without any insecticide applied, all the transgenic rice plants were found to be not injured by the rice leaf folder, whereas the wild types were impaired seriously.