Fire and flood management of coastal swamp enabled first rice paddy cultivation in east China

A novel approach for quantitatively distinguishing between anthropogenic and natural effects on paleovegetation

How to distinguish and quantify past human impacts on vegetation is a significant challenge in paleoecology. Here, we propose a novel method, the error inflection point-discriminant technique. It finds out the inflection points (IPs) of the regression errors of pollen-climate transfer functions using modern pollen spectra from vegetation with different values of the Human Influence Index (HII), which represent the HII threshold values of native/secondary and secondary/artificial vegetation systems. Our results show that the HII value at the native/secondary vegetation IPs is approximately 22 and globally uniform, whereas it varies regionally for the secondary/artificial vegetation IPs. In a case study of the Liangzhu archaeological site in the lower Yangtze River, discriminant functions for pollen spectra from three vegetation types and pollen-climate transfer functions of the native vegetation were established to reconstruct paleovegetation and paleoclimate over the past 6,600 years. Our study demonstrates this method's feasibility for quantitatively distinguishing human impacts on paleovegetation and assessing quantitative paleoclimate reconstructions using pollen data.

Genomic variations combined with epigenetic modifications rewire open chromatin in rice

Cis-regulatory elements (CREs) fine-tune gene transcription in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global sequence and structural variations (SVs) are responsible for multilevel changes between indica and japonica rice (Oryza sativa) is still not fully elucidated. To address this, we conducted multiomic studies using MNase hypersensitivity sequencing (MH-seq) in combination with RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and bisulfite sequencing (BS-seq) between the japonica rice variety Nipponbare (NIP) and indica rice variety 93-11. We found that differential MNase hypersensitive sites (MHSs) exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Notably, through MHS-genome-wide association studies (GWAS) integration, we found that key sequence variations may be associated with differences of agronomic traits between NIP and 93-11, which is partly achieved by MHSs harboring CREs. In addition, SV-derived differential MHSs caused by transposable element (TE) insertion, especially by noncommon TEs among rice varieties, were associated with genes with distinct functions, indicating that TE-driven gene neo- or subfunctionalization is mediated by changes of chromatin openness. This study thus provides insights into how sequence and genomic SVs control agronomic traits of NIP and 93-11; it also provides genome-editing targets for molecular breeding aiming at improving favorable agronomic properties.

The firing temperatures of burnt clay from the Chinese neolithic cultural relics and its paleoenvironmental imprints

The impact of human-induced fires on the surrounding environment has been particularly significant during the Anthropocene epoch. Neolithic burnt clay, which is widely distributed in the archaeological relics of ancient civilizations across the Eurasian continent, provides pivotal information about the ancient firing stories. However, understanding of the paleoenvironmental imprints of fire in burnt clay has been largely limited by the lack of sufficient analytical data on comprehensive knowledge of ancient firing conditions. In this study, a detailed magnetic analysis was conducted on burnt clay materials from a Neolithic site in Fujian, southeastern China, which presented a burnt clay-based record of the Neolithic firing temperature in relation to paleoenvironmental conditions. Based on magnetic analysis, the ancient firing temperature was determined to be approximately 620 °C, which is comparable with other records from Eurasian Neolithic sites. Frequency-dependent magnetic susceptibility provides alternative indicative information for ancient firing conditions in addition to conventional magnetic susceptibility. Furthermore, magnetic properties of burnt clay may decode the in-situ source characteristics with respect to geological background. In addition, a potential link between temporal variations in ancient firing temperatures in burnt clay and surrounding paleoenvironmental changes is tentatively interpreted by local environmental feedback of temperature-moisture conditions and anthropogenic activity. This study further confirms the archaeological potential of thermomagnetic properties as useful indicators in paleoenvironmental studies. More work combining paleoenvironmental and archaeological archives is critically essential to understand ancient firing history in the context of environmental conditions.

Single-Cell RNA sequencing of leaf sheath cells reveals the mechanism of rice resistance to brown planthopper (Nilaparvata lugens)

The brown planthopper (BPH) (Nilaparvata lugens) sucks rice sap causing leaves to turn yellow and wither, often leading to reduced or zero yields. Rice co-evolved to resist damage by BPH. However, the molecular mechanisms, including the cells and tissues, involved in the resistance are still rarely reported. Single-cell sequencing technology allows us to analyze different cell types involved in BPH resistance. Here, using single-cell sequencing technology, we compared the response offered by the leaf sheaths of the susceptible (TN1) and resistant (YHY15) rice varieties to BPH (48 hours after infestation). We found that the 14,699 and 16,237 cells (identified via transcriptomics) in TN1 and YHY15 could be annotated using cell-specific marker genes into nine cell-type clusters. The two rice varieties showed significant differences in cell types (such as mestome sheath cells, guard cells, mesophyll cells, xylem cells, bulliform cells, and phloem cells) in the rice resistance mechanism to BPH. Further analysis revealed that although mesophyll, xylem, and phloem cells are involved in the BPH resistance response, the molecular mechanism used by each cell type is different. Mesophyll cell may regulate the expression of genes related to vanillin, capsaicin, and ROS production, phloem cell may regulate the cell wall extension related genes, and xylem cell may be involved in BPH resistance response by controlling the expression of chitin and pectin related genes. Thus, rice resistance to BPH is a complicated process involving multiple insect resistance factors. The results presented here will significantly promote the investigation of the molecular mechanisms underlying the resistance of rice to insects and accelerate the breeding of insect-resistant rice varieties.

Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice

Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.

New evidence for rice harvesting in the early Neolithic Lower Yangtze River, China

The Lower Yangtze River of China has been identified as an independent center of rice domestication, but tracing the earliest evidence for rice cultivation practices has been challenging. Here we report the first evidence for rice harvesting, based on use-wear and phytolith residue analyses of 52 flaked stone tools (10000-7000 BP) from the Shangshan and Hehuashan sites. The tools reflect two harvesting methods: reaping the panicles at the top and cutting the stalk near the base. Thus, our research provides a new method for investigating prehistoric cereal cultivation, and the data lend support to the evidence of rice domestication in the early Holocene. The results also show the complexity of rice harvesting strategies several millennia before the emergence of full-fledged agriculture in the Lower Yangtze.

Changes of Neolithic subsistence in south Hangzhou Bay coast, eastern China: An adaptive strategy to landscape processes

The transition from hunting and gathering to agricultural subsistence is a striking feature of the Neolithic revolution worldwide. Known as the cradle of a series of representative Neolithic cultures, south Hangzhou Bay (SHB) witnessed substantial changes in both landscape and human subsistence during the Holocene, yet the relationship between them was not well established. Here, we combined archaeobotanical results from sediment cores with archaeological findings to illustrate the subsistence changes during the Neolithic regime in the context of the landscape process in SHB. Our result showed that SHB was inundated by marine transgression 8,200 years ago without significant human imprints. At 8,200-7,600 cal yr. BP, the initial coastal wetland formation at locations with the semi-enclosed landscape would have facilitated the activities of hunting-gathering, incipient rice cultivation, and collecting seafood if accessible. Pollen and phytoliths evidence from multiple sediment cores in the Yaojiang Valley (YJV) suggested a desalinization process of wetland in the following hundreds of years. This amelioration of the environment had favored the intermittent rice cultivation at various locations in the YJV, where archaeological evidence was absent. Since 7,000-6,600 cal yr. BP, as freshwater wetland expanded with coastal progradation, a wide variety of food resources became available. Meanwhile, rice domestication began to serve as a crucial food supplement as evidenced by both microfossil results and archaeological findings. With the expansion of the coastal plain after 5,500 cal yr. BP, rice farming became widespread and rice consumption was increasingly important in the diet, as supported by discoveries of upgraded farming tools, abundant rice remains, and ancient rice paddies. Above all, the change of subsistence from hunting-gathering to rice farming exhibited an adaptive strategy in response to landscape evolution from an initial marine-influenced setting to a later coastal plain.

Subsistence, Environment, and Society in the Taihu Lake Area during the Neolithic Era from a Dietary Perspective

The Taihu Lake region is an important area where China’s rice agriculture originated and where early Chinese civilisation formed. Knowing how this ecologically sensitive area’s Neolithic residents adapted to environmental changes and utilised natural resources is key to understanding the origins of their agricultural practices and civilisation. Focusing on food resources, we systematically organised data from archaeobotanical and zooarchaeological research, human bone stable isotopic analyses, and fatty acid and proteome residue analyses on the Taihu Lake area’s Neolithic findings to explore the interrelationships between subsistence, the environment, and society through qualitative and quantitative analysis supported by paleoenvironmental and archaeological evidence. The results showed that during the Neolithic era (7.0–4.3 ka BP), under a suitable climate with stable freshwater wetland environments, 38 varieties of edible animals and plants were available to humans in the Taihu Lake area. Despite agriculture being an important food source, rice cultivation and husbandry developed at different paces. Paddy rice cultivation began in wetlands and had always dominated the subsistence economy, as although gathering was universal and diverse, it produced a relatively low volume of food. In contrast, husbandry did not provide sufficient meat throughout the 2000 years of the Majiabang and Songze Cultures. Thus, fishing for freshwater organisms and hunting for wild mammals were the main meat sources before the domestication of pigs became the primary source of meat during the Liangzhu Cultural period. With the available wetland ecological resources and paddy rice farming (the sole crop), the Taihu Lake area transformed into an agricultural society in which rice cultivation dominated the Songze Culture’s subsistence economy, which was also the first to exhibit social complexity. Then, finally, early civilisation developed in the Liangzhu Cultural period. This study contributes to understanding the unique evolutionary path of early Chinese civilisation and has important implications on sustainable resource utilisation for constructing ecological civilisations in present-day societies.

Human activities have reduced plant diversity in eastern China over the last two millennia

Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south-north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period.

Traditional agricultural management of Kam Sweet Rice (Oryza sativa L.) in southeast Guizhou Province, China

BACKGROUND

The Dong people mainly live in Hunan, Guangxi and Guizhou provinces, China, with a long history of glutinous rice cultivation, among which Kam Sweet Rice (KSR) is a group of rice landraces that has been domesticated for thousands of years by the Dong people. The core distribution area of KSR is Liping, Congjiang and Rongjiang County of southeast, Guizhou Province. Paddy fields, forests, livestock and cottages have formed a special artificial wetland ecosystem in local area, and the Dong people have also formed a set of traditional farming systems of KSR for variety breeding, field management, and soil and water conservation. However, this traditional agricultural management has not been reported at multiple levels based on landraces, species and ecosystems.

METHODS

Fieldwork was conducted in ten villages in southeast Guizhou from 2019 to 2021. A total of 229 informants were interviewed from the villages. Semi-structured and key informant interviews were administered to collect ethnoecological data on the characteristics and traditional utilization of KSR, traditional farming systems and agricultural management of the Dong people.

RESULTS

(1): A total of 57 KSR landraces were recorded as used by the Dong people in southeast Guizhou. We analyzed the cultural importance index (CII) of all KSRs. KSR with high CII often has a pleasant taste, special biological characteristics of cold resistance, disease and insect resistance and high utilization in the traditional culture of Dong people. (2) There is a clear division of labor between men and women in the breeding, seed retention, field management and grain storage management of different landraces of KSR in Dong communities. In order to resist natural disasters and insect pests, the cultivation of KSR is usually managed by multi-variety mixed planting. These agricultural management modes are the result of Dong people's understanding and adaptation to the local natural geographical environment, as well as the experience and wisdom crystallization of Dong people's long-term practice. (3) The traditional farmland of Dong People is a typical artificial wetland ecosystem that is planted with mixed KSR landraces with rich traditional wisdom. In addition, the economic benefit of the rice-fish-duck symbiotic system was 3.07 times that of hybrid rice alone; therefore, the rice-fish-duck system not only has the function of maintaining soil, water and ecological balance but also improves the income of Dong people.

CONCLUSION

KSR is a special kind of rice that has been domesticated and cultivated by Dong people for thousands of years. Dong people have also formed traditional agriculture dominated by KSR cultivation. The traditional agricultural management of Dong people provides suitable habitats for flora and fauna with biodiversity protection, and convenient conditions for rational utilization and distribution of water resources were also provided. This traditional management mode is of great significance for environmental protection, climate change response, community resource management, sustainable utilization and agricultural transformation in modern society. Therefore, we call for interdisciplinary research in natural and social sciences, in-depth study of the ecological culture of ethnic areas, and sort out treasures conducive to the development of all mankind.

Proto Kranz-like leaf traits and cellular ionic regulation are associated with salinity tolerance in a halophytic wild rice

Species of wild rice (Oryza spp.) possess a wide range of stress tolerance traits that can be potentially utilized in breeding climate-resilient cultivated rice cultivars (Oryza sativa) thereby aiding global food security. In this study, we conducted a greenhouse trial to evaluate the salinity tolerance of six wild rice species, one cultivated rice cultivar (IR64) and one landrace (Pokkali) using a range of electrophysiological, imaging, and whole-plant physiological techniques. Three wild species (O. latifolia, O. officinalis and O. coarctata) were found to possess superior salinity stress tolerance. The underlying mechanisms, however, were strikingly different. Na+ accumulation in leaves of O. latifolia, O. officinalis and O. coarctata were significantly higher than the tolerant landrace, Pokkali. Na+ accumulation in mesophyll cells was only observed in O. coarctata, suggesting that O. officinalis and O. latifolia avoid Na+ accumulation in mesophyll by allocating Na+ to other parts of the leaf. The finding also suggests that O. coarctata might be able to employ Na+ as osmolyte without affecting its growth. Further study of Na+ allocation in leaves will be helpful to understand the mechanisms of Na+ accumulation in these species. In addition, O. coarctata showed Proto Kranz-like leaf anatomy (enlarged bundle sheath cells and lower numbers of mesophyll cells), and higher expression of C4-related genes (e.g., NADPME, PPDK) and was a clear outlier with respect to salinity tolerance among the studied wild and cultivated Oryza species. The unique phylogenetic relationship of O. coarctata with C4 grasses suggests the potential of this species for breeding rice with high photosynthetic rate under salinity stress in the future.

Remarkable signals of the ancient Chinese civilization since the Early Bronze Age in the marine environment

The signals of fire activity induced from climate and ancient human activities could be recorded in sedimentary strata. We examined a 6000-year black‑carbon (BC) record-including char and soot-of a sediment core from the South Yellow Sea. The climate change had a threshold effect on the fire regime, and dominated the char emissions. The soot/BC signals depicted that the anthropogenic emissions related to the evolution of the Chinese civilization since the Early Bronze Age (~4 ka) have overwhelmed natural soot emissions. The soot variation in the record closely matched periods when there was large-scale use of coal or charcoal after the Han Dynasty and when indigenous coking technology was promoted after the Tang Dynasty; low soot-abundance in the record coincided with periods of social unrest. This work illustrates how soot signals can be a robust tracer of civilization evolution.

Analysis of the Structure and Ecological Function of an Extreme Landscape in a Tropical Region of West Java, Indonesia

An extreme landscape is a spatially heterogeneous area with unusual topography that is prone to natural disasters but still exhibits interrelated structures and functions. One of the important functions of an extreme landscape is its ecological function. This study aimed to determine the structure and reveal the ecological functions of an extreme landscape in a tropical region of West Java, with special reference to Rongga Sub-district. The method used was a combination of remote sensing techniques and geographic information systems, which were required to process, analyze, and interpret Landsat 8 OLI/TIRS data. The landscape structure was quantified by landscape metrics, after which an analysis of ecological functions was carried out based on the constituent elements of the landscape. The results showed that the landscape structure of Rongga Sub-district consists of various elements of agroforestry land, open fields, settlements, shrubs, plantations, and rainfed and irrigated rice fields. Additionally, secondary forest land acted as a landscape matrix where rivers crossed as natural corridors. The amount of each element varied; agroforestry land had the highest value, indicating that this element showed a high degree of human intervention. Each patch was adjacent to other patch types, and the landscape diversity was quite high. The extreme topography of Rongga Sub-district supports the landscape connectivity and consequently the presence of wild animals in this area. Therefore, Rongga Sub-district has an essential ecological function as a refuge for protected animals living in non-conservation areas.

Rice aquaporin OsPIP2;2 is a water-transporting facilitator in relevance to drought-tolerant responses

In rice (Oryza sativa), the PLASMA MEMBRANE INTRINSIC PROTEIN (PIP) family of aquaporin has 11 members, OsPIP1;1 to OsPIP1;3, and OsPIP2;1 to OsPIP2;8, which are hypothesized to facilitate the transport of H2O and other small compounds across cell membranes. To date, however, only OsPIP1;2, OsPIP2;1, and OsPIP2;4 have been demonstrated for substrate selectivity in their source plant (rice). In this study, OsPIP2;2 was characterized as the most efficient facilitator of H2O transport across cell membranes in comparison with the other 10 OsPIPs. In concomitant tests of all OsPIPs, four genes (OsPIP1;3, OsPIP2;1, OsPIP2;2, and OsPIP2;4) were induced to express in leaves of rice plants following a physiological drought stress, while OsPIP2;2 was expressed to the highest level. After de novo expression in frog oocytes and yeast cells, the four OsPIP proteins were localized to the plasma membranes in trimer and tetramer and displayed the activity to increase the membrane permeability to H2O. In comparison, OsPIP2;2 was most supportive to H2O import to oocytes and yeast cells. After de novo expression in tobacco protoplasts, OsPIP2;2 exceeded OsPIP1;3, OsPIP2;1, and OsPIP2;4 to support H2O transport across the plasma membranes. OsPIP2;2-mediated H2O transport was accompanied by drought-tolerant responses, including increases in concentrations of proline and polyamines, both of which are physiological markers of drought tolerance. In rice protoplasts, H2O transport and drought-tolerant responses, which included expression of marker genes of drought tolerance pathway, were considerably enhanced by OsPIP2;2 overexpression but strongly inhibited by the gene silencing. Furthermore, OsPIP2;2 played a role in maintenance of the cell membrane integrity and effectively protected rice cells from electrolyte leakage caused by the physiological drought stress. These results suggest that OsPIP2;2 is a predominant facilitator of H2O transport in relevance to drought tolerance in the plant.

History of Mid- and Late Holocene Palaeofloods in the Yangtze Coastal Lowlands, East China: Evaluation of Non-Pollen Palynomorph Evidence, Review and Synthesis

The surface of the lowland deltaic plain around Taihu (Lake Tai), south of the Yangtze river mouth in eastern China, lies near sea level and until recent drainage and development by human societies was mostly covered by wetlands of various types. It was created by regular overbank flooding, mainly from the Yangtze, and the deposition of mostly mineral sediments over the several millennia since sea level regained its current altitude in the early mid-Holocene and progradation of the Yangtze delta began. Fluvial activity has therefore been the dominant influence on sedimentation in the Taihu lowlands, and in the lower Yangtze valley generally, and has determined the character of the mainly inorganic sediment sequences that have accumulated there, with autochthonous deposition of organic sediments within the local wetland plant communities playing a minor role. The presence of both clastic flood horizons and peat layers within the deposits of the Taihu plain attests to great variability in the magnitude of fluvial input from the Yangtze, with repeated extreme floods occurring at some periods, but with periods when the growth of peat layers shows low water tables, little exogenic sediment input and so little fluvial influence. We have examined the published evidence for these different depositional environments in the lower Yangtze and the Taihu plain during the Holocene, comparing the flood history with the middle and upper reaches of the Yangtze catchment. Discrete phases of high or low flooding influence are recognised, and these correspond with large-scale Holocene climate history. Intensified human land use in recent millennia has complicated this relationship, amplifying the flooding signal. Our palynological research shows that algal microfossil type and abundance is a useful proxy for changing water depth and quality in the aquatic environments of the Holocene Taihu wetlands, and can recognise flooding events that are not registered in the floodplain lithological sequences.

The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.

Identification and characterization of An-4, a potential quantitative trait locus for awn development in rice

BACKGROUND

Awn of rice is an important domestication trait closely associated with yield traits. Therefore, the identification of genes for awn development is of great significance for the elucidation of molecular mechanism of awn development and the genetic improvement of yield traits in rice.

RESULTS

In this study, using chromosome segment substitution lines (CSSLs) derived from a long-awned Guangxi common wild rice (GXCWR, Oryza rufipogon Griff.) and a short-awned indica cultivar 9311, we identified An-4, a potential quantitative trait locus (QTL) for awn development. Then, An-4 was fine mapped into a 56-kb region of chromosome 2, which contained four annotated genes. Among these four annotated genes, Os02g0594800 was concluded to be the potential candidate gene for An-4. An-4 exhibited pleiotropic effects on awn development and several yield traits. Scanning electron microscopy (SEM) analysis showed that An-4 significantly promoted awn development at Sp7 and Sp8 stage of spikelet development. Transcriptome analysis suggested that An-4 might influence the development of awn by regulating the expression of genes related to growth, developmental process, channel regulation and extracellular region. By contrast to those of 9311, the expression level of OsRR5 in CSSL128 was significantly down-regulated, whereas the expression levels of OsCKX2 and OsGA2ox5 in CSSL128 were significantly up-regulated. In addition, our study showed that An-4 had additive effects with other genes for awn development, such as An-1, An-2/LABA1 and An-3/GAD1/RAE2.

CONCLUSIONS

The identification of An-4 lays a foundation for cloning of An-4 and further elucidation of the molecular mechanism of awn development. Moreover, the identification of favorable allelic variation of An-4 from 9311 will be useful to improve rice yield traits.

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.

Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.

Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.

Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.

Using a process-based model to understand dynamics of Chinese agricultural and water technology development from 8000 BC to 1911 AD

Advancements in technology are inextricably bound to our society and the natural environment. However, how the development process of a technology system interacts with both remains unclear. We propose a process model to understand the complex dynamics among technology, society, and the environment via seven interactive elements: technologies, actors, receiving bodies, natural contexts, social contexts, temporal-spatial contexts, and outcomes. The model was applied to agricultural and water technology development in China from 8000 BC to 1911 AD. Our findings show that these elements did not play equally important roles in different periods of the development in ancient China, with social contexts most dominating during the earlier periods and both social and environmental concerns arising towards the later periods. The proposed model, by identifying the elements in the technology development that should be strengthened, can act as an analysis device to assist in reconfiguring a more sustainable socio-technological system.

Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides

Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.

Holocene coastal evolution preceded the expansion of paddy field rice farming

Rice agriculture is the foundation of Asian civilizations south of the Yangtze River. Although rice history is well documented for its lower Yangtze homeland area, the early southward expansion of paddy rice farming is poorly known. Our study investigates this process using a compilation of paleoenvironmental proxies from coastal sediment cores from southeast China to Thailand and Island Southeast Asia. We propose that a shortage of land suitable for paddy fields, caused by marine transgression, constrained rice agriculture during the mid-Holocene. Rapid expansion of coastal plains, particularly in deltaic basins, over the past three millennia has coincided with increases in land suitable for rice cultivation. Our study also helps explain the past population movements of rice farmers.

Early to Mid-Holocene Palaeoenvironment Change and Sedimentary Evolution in the Xianghu Area, Zhejiang

A 2.5 m long sediment core (XH-2) obtained from Xianghu area, near the Kuahuqiao site, were analyzed for grain size, diatom index, and geochemistry of organic carbon. The results of the total organic carbon (TOC) and stable organic carbon isotope (δ¹³C) in sediment samples from core XH-2 in the Xianghu area in Zhejiang Province have revealed the evolution history of sedimentary environmental and climatic changes during the breeding–prosperity–decline period of the Kuahuqiao culture. During 9300–8200 cal a BP, TOC contents were relatively high and stable, whereas δ¹³C values tended to be negative. This condition indicated that the climate was humid, and the sedimentary environment in the Xianghu area was stable. During 8200–7500 cal a BP, TOC contents presented a fluctuating declining trend, and δ¹³C values were significantly high, implying that the climate was arid, and the Xianghu area was gradually reduced to land. Thus, conducive conditions were provided for the development of the Kuohuqiao culture (7700–7400 cal a BP). From 7500 cal a BP, TOC contents obviously declined, and δ¹³C values were partially low, suggesting strengthened hydrodynamic force and wet conditions in the Xianghu area. This condition was related to the rise in sea level at approximately 7400 cal a BP, and the Kuahuqiao site became obsolete due to the transgression event. The TOC contents in core XH-2 were remarkably influenced by grain size, whereas no significant correlation existed between the δ¹³C variability and grain size. Sedimentary environment changes in the Xianghu area from 9300 to 6600 cal a BP, which was reflected by the TOC and δ¹³C records in core XH-2, accorded with the diatom results in this core and those in the Baima Lake area.

Abundance and morphology of charcoal in sediments provide no evidence of massive slash-and-burn agriculture during the Neolithic Kuahuqiao culture, China

It remains debatable whether slash-and-burn practices were adopted in rice cultivation by the Neolithic Kuahuqiao culture in the Ningshao Plain, one of the birthplaces of rice farming. Here, we established charcoal-based indices to reconstruct the history of fire and vegetation in the Ningshao Plain since the last glacial period. We collected representative modern vegetation and conducted combustion and fragmentation experiments to simulate fire and depositional processes, respectively. Charcoals from modern vegetation show clear morphological differences between herbaceous and woody plants. In particular, the length to width ratios (L/W) of herbaceous charcoals were systematically higher than those of woody charcoals, and the associated end-member values were 4.50 and 1.94, respectively. These values were then applied to sediment cores (KHQ-14/15) collected in proximity to the Kuahuqiao archaeological site. Results show that the amount of combusted herbaceous plants increased sharply after the Holocene, and the most remarkable rise occurred around 8550 yr B.P. This observation may reflect local environment (sedimentary and/or climatic) changes or small-scale early human activities. During the Kuahuqiao cultural period (8250−7450 yr B.P.), the relative abundance of woody charcoals increased, but the overall fire intensity decreased. This finding suggests that the Kuahuqiao farming was restricted to a small geographic area and large-scale slash-and-burn farming activities were not adopted.

Late Pleistocene-Holocene vegetation history and anthropogenic activities deduced from pollen spectra and archaeological data at Guxu Lake, eastern China

This study presents high-resolution pollen and charcoal records from Guxu Lake in the Taihu Lake Basin, eastern China, spanning the last 23,000 years. The sedimentary sequences revealed dynamic terrestrial and lacustrine environments during 23.0-11.7 cal ka BP, the climate was relatively cold and dry, and the vegetation was dominated by evergreen-deciduous broadleaf and coniferous mixed forest. During 11.7-4.4 cal ka BP, the Quercus- and Castanopsis-dominated evergreen-deciduous broadleaf mixed forest expanded, while the Poaceae and Artemisia were still the major terrestrial herbs under warmer and more humid conditions. After this period, the climate became relatively cool and dry again, and the vegetation landscape was comparatively stable, as it remains today. Wild rice likely grew before Neolithic humans occupied this area. The variations in Oryza-type Poaceae pollen spectra and distributions of Neolithic archaeological sites indicate rice agriculture may have first appeared and developed with human occupation in ca. 7.0-4.4 ka BP. During the historical period, beginning approximately 4 ka BP, a clear signal of intensified anthropogenic disturbance is evident from the clearing of forests, high charcoal concentrations and the presence of rice pollen in large quantities. These results suggest more intensified rice farming was widespread, with increasing human impact on the environment.

Gene flow across host-associated populations of the rice stem borer Chilo suppressalis Walker (Lepidoptera: Crambidae): implications for Bt resistance management in rice

BACKGROUND

The rice stem borer, Chilo suppressalis, is a serious pest of rice, but also damages an aquatic vegetable, water oats (Zizania latifolia Turcz.). The time at which mating occurs is different between populations of rice stem borer associated with rice and those associated with water-oats, which suggests that undetected cryptic species may be associated with these plant hosts. If true, this would have significant management implications. This study is the first empirical test of this idea, using population genetic tools from two sampling cohorts. We genotyped 320 rice stem borer individuals from 2014, collected from rice and water-oats across five locations (where they exist in sympatry), using seven microsatellite loci.

RESULTS

We found no genetic structuring associated with host plant species. On water oats, some rice stem borers were found that had a similar mating time to the rice population, so in 2016, a second cohort of samples was screened by their timing of mating to get 'pure rice feeders' and 'pure water oats feeders'. These samples were genotyped with microsatellites, mitochondrial DNA (mtDNA) (COI and COII), and a nuclear gene (EF1-α). Our mtDNA data suggest a relatively low amount of population subdivision associated with plant host, but the microsatellite data revealed no such genetic structure, and we were only able to identify one haplotype of EF1-α.

CONCLUSIONS

Our results indicate gene flow between rice and water oats populations of rice stem borer, indicating that water oats will likely provide a refuge for resistance management of Bt rice. © 2019 Society of Chemical Industry.

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Rice (Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice (O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near-isogenic NIL-GLA are separately controlled by variations within the GLA (Grain Length and Awn Development) gene, a new allele of GAD1/RAE2, which encodes one member of the EFPL (epidermal patterning factor-like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL) in the promoter region of GLA (GLA^VGL ) increases grain length by promoting transcription of GLA. Absence of InDel3 (variation for awn formation, VA) in the coding region (CDS) of GLA (GLA^va ) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An-1, an important gene for awn formation, was preferentially domesticated and its mutation to an-1 was followed by GLA and An-2. Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica, whereas short-grained and awnless phenotypes with good quality were selected in japonica. Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.

Effects of Winter Cover Crops on Rice Pests, Natural Enemies, and Grain Yield in a Rice Rotation System

Rotations that include winter cover crops are widely used in agricultural systems and can provide numerous agroecological and economic benefits. However, the effects of winter cover crops on arthropod diversity, specifically rice pests and related natural enemies in rice rotation systems, are still largely unknown. We compared the effects of three winter cover crops, rapeseed, Brassica napus L. (Brassicales: Brassicaceae), Chinese milkvetch, Astragalus sinicus L. (Fabales: Fabaceae), and garlic, Allium sativum L. (Asparagales: Amaryllidaceae), on arthropods species diversity and evenness, densities of populations of major rice pests and major natural enemies, and grain yield in an experimental double cropping rotational rice field in Jiangxi Province, China. We did not observe any effects of cover crops on arthropod species diversity and evenness. The presence of prior cover crops also had no effect on the number of plants infested by the two major rice pests, Chilo suppressalis Walker (Lepidoptera: Pyralidae) and Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae). Our study did not show any effects of rapeseed and Chinese milkvetch on grain yield. However, grain yield was increased in the garlic treatment. Our results suggest that although the winter cover crops we tested in our study do not affect the number of rice plants infected by major rice pests, they do not negatively affect the arthropod community and grain yields in rice rotation systems. Therefore, planting of winter cover crops may increase agricultural land utilization and have an overall economic benefit in rice rotational systems.

A paleopathological approach to early human adaptation for wet-rice agriculture: The first case of Neolithic spinal tuberculosis at the Yangtze River Delta of China

The earliest evidence of human tuberculosis can be traced to at least the early dynastic periods, when full-scaled wet-rice agriculture began or entered its early developmental stages, in circum-China countries (Japan, Korea, and Thailand). Early studies indicated that the initial spread of tuberculosis coincided with the development of wet-rice agriculture. It has been proposed that the adaptation to agriculture changed human social/living environments, coincidentally favoring survival and spread of pathogenic Mycobacterial strains that cause tuberculosis. Here we present a possible case of spinal tuberculosis evident in the remains of a young female (M191) found among 184 skeletal individuals who were Neolithic wet-rice agriculturalists from the Yangtze River Delta of China, associated with Songze culture (3900-3200 B.C.). This early evidence of tuberculosis in East Asia serves as an example of early human morbidity following the adoption of the wet-rice agriculture.

A 110-year pollen record of land use and land cover changes in an anthropogenic watershed landscape, eastern China: Understanding past human-environment interactions

Land use and land cover changes (LUCCs) have largely altered terrestrial ecosystems and landscapes during the Anthropocene. Reconstructing past LUCCs is necessary to better understand terrestrial ecosystem succession and human-environment interactions so that ecosystem services can be used conservatively and developed sustainably. In this paper, we reconstructed the LUCCs over the past century in a typical anthropogenic watershed based on a high-resolution pollen record from Changdang Lake, eastern China. The sediment core was ²¹⁰Pb dated and constrained cluster analysis identified different periods of LUCCs associated with the 110-year pollen record. Multi-sedimentary proxies, historical records, and remote sensing LUCC maps were analyzed to complement the palynological results. Our results demonstrate that pollen records can accurately capture LUCCs during different historical periods. Extra-regional arboreal pollen, fern spores, and pollen concentration can record the hydrological variations of waterbodies under both climatic and anthropogenic impacts. Multiple agriculture-related pollen indicators, such as cereal, Cruciferae, and wetland taxa are significantly related to the corresponding vegetation cover and landscape variations. Specifically, the anthropochore taxa to wetland taxa ratio is a good indicator of agricultural intensity. Dominant arboreal pollen (Pinus and Quercus) and the arboreal taxa to non-arboreal taxa ratio reflects the forestry landscape changes. Urban greening arboreal pollen (including Platanus, Salix, and Ulmus) is found to be an indirect indicator of urbanization. In addition, agriculture and urbanization in the region are causing the pollen diversity to increase in lake sediments. This study from a shallow lake in eastern China contributes to our understanding of pollen-based LUCC studies in similar climatic and anthropogenic regions around the world.

Phytolith assemblage analysis for the identification of rice paddy

The rice arable system is of importance to both society and the environment. The emergence of rice paddies was a crucial step in the transition from pre-domestic cultivation to systematic land use and management. However, many aspects of the formation of rice farming systems remain unclear. An important reason is the lack of reliable methods for identifying early rice paddies. One possible means of remedying this knowledge deficit is through analysis of phytolith assemblages, which are closely related to their parent plant communities. In this study, phytolith assemblages from 27 surface soil samples from wild rice fields, 91 surface soil samples from modern rice paddies, and 50 soil samples from non-rice fields were analysed to establish a discriminant function. This discriminant function enabled classification of 89.3% of the samples into appropriate groups. Further, the results suggested that phytolith assemblages can be used to identify rice fields and differentiate between wild rice fields and domesticated rice fields. The method was demonstrated to be an effective way of utilising the large amounts of unidentifiable phytoliths discovered at archaeological sites to provide a modern analogue that may be a valuable key to unlocking the past.

Comparative transcriptome analysis reveals host-associated differentiation in Chilo suppressalis (Lepidoptera: Crambidae)

The striped stem borer, Chilo suppressalis Walker (Lepidoptera: Crambidae), is one of the most serious rice pests. Besides attacking rice, it also feeds on an economically important vegetable crop, water-oat Zizania latifolia. The species feeding on water-oat has higher growth and survival rate than those on rice, suggesting their success in adaptation to the new host plant. However, little is known about the molecular mechanisms of host plant adaptation. Here we investigated the midgut transcriptome responses of C. suppressalis larvae reared on rice and water-oat. A total of 1,633 differentially expressed genes were identified, with a greater number up-regulated on the more delicious new host. The up-regulation of most digestive and detoxification-related genes may be the result of adaptation to the changes in nutritional requirements and toxic chemicals during host shift. In contrast, down-regulation of ribosomal genes may be related to their better development performance when feeding on the new host. In conclusion, our results suggest that transcriptional regulation of genes related to digestion, detoxification and ribosome may play an important role in adaptation of C. suppressalis to a new host plant.

Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia

Austronesian diffusion is considered one of the greatest dispersals in human history; it led to the peopling of an extremely vast region, ranging from Madagascar in the Indian Ocean to Easter Island in Remote Oceania. The Y-chromosome haplogroup O3a2b*-P164(xM134), a predominant paternal lineage of Austronesian populations, is found at high frequencies in Polynesian populations. However, the internal phylogeny of this haplogroup remains poorly investigated. In this study, we analyzed -seventeen Y-chromosome sequences of haplogroup O3a2b*-P164(xM134) and generated a revised phylogenetic tree of this lineage based on 310 non-private Y-chromosome polymorphisms. We discovered that all available O3a2b*-P164(xM134) samples belong to the newly defined haplogroup O3a2b2-N6 and samples from Austronesian populations belong to the sublineage O3a2b2a2-F706. Additionally, we genotyped a series of Y-chromosome polymorphisms in a large collection of samples from China. We confirmed that the sublineage O3a2b2a2b-B451 is unique to Austronesian populations. We found that O3a2b2-N6 samples are widely distributed on the eastern coastal regions of Asia, from Korea to Vietnam. Furthermore, we propose- that the O3a2b2a2b-B451 lineage represents a genetic connection between ancestors of Austronesian populations and ancient populations in North China, where foxtail millet was domesticated about 11,000 years ago. The large number of newly defined Y-chromosome polymorphisms and the revised phylogenetic tree of O3a2b2-N6 will be helpful to explore the origin of proto-Austronesians and the early diffusion process of Austronesian populations.

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.

Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice

Awn is one of the most important domesticated traits in rice (Oryza sativa). Understanding the genetic basis of awn length is important for grain harvest and production, because long awn length is disadvantageous for both grain harvest and milling. We investigated the awn length of 529 rice cultivars and performed a Genomewide association studies (GWAS) in the indica and japonica subpopulations, and the whole population. In total, we found 17 loci associated with awn length. Of these loci, seven were linked to previously reported quantitative trait loci, and one was linked to the awn gene An-1. Nine novel loci were repeatedly identified in different environments. One of the nine associations was identified in both the whole and japonica populations. Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1. These results may provide potentially favourable haplotypes for molecular breeding in rice.

Fine Mapping of Two Additive Effect Genes for Awn Development in Rice (Oryza sativa L.)

Awns, important domestication and agronomic traits in rice (Oryza sativa L.), are conferred by polygenes and the environment. Near isogenic line (NIL) pairs BM33 and BM38 were constructed from crosses between awnless japonica cv Nipponbare as recurrent parent, and lines SLG or Funingxiaohongmang (awned japonica accessions), respectively, as donors. In order to study the genetic and molecular mechanism of awning, two unknown, independent genes with additive effects were identified in a cross between the NILs. To map and clone the two genes, a BC4F4 population of 8,103 individuals and a BC4F6 population of 11,206 individuals were constructed. Awn3-1 was fine mapped to a 101.13 kb genomic region between Indel marker In316 and SNP marker S9-1 on chromosome 3. Nine predicted genes in the interval were annotated in the Rice Annotation Project Database (RAP-DB), and Os03g0418600 was identified as the most likely candidate for Awn3-1 through sequence comparisons and RT-PCR assays. Awn4-2 was fine mapped to a 62.4 kb genomic region flanked by simple sequence repeat (SSR) marker M1126 and Indel maker In73 on chromosome 4L. This region contained the previously reported gene An-1 that regulates awn development. Thus, An-1 may be the candidate gene of Awn4-2. These results will facilitate cloning of the awn genes and thereby provide an understanding of the molecular basis of awn development.

Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice.

Crop epigenetics and the molecular hardware of genotype × environment interactions

Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates.

An-2 Encodes a Cytokinin Synthesis Enzyme that Regulates Awn Length and Grain Production in Rice

A wide range of morphological and physiological traits have changed between cultivated rice Oryza sativa and wild rice Oryza rufipogon under domestication. Here, we report cloning of the An-2 gene, encoding the Lonely Guy Like protein 6 (OsLOGL6), which catalyzes the final step of cytokinin synthesis in O. rufipogon. The near-isogenic line harboring a wild allele of An-2 in the genetic background of the awnless indica Guangluai 4 shows that An-2 promotes awn elongation by enhancing cell division, but decreases grain production by reducing grains per panicle and tillers per plant. We reveal that a genetic variation in the An-2 locus has a large impact on reducing awn length and increasing tiller and grain numbers in domesticated rice. Analysis of gene expression patterns suggests that An-1 regulates the formation of awn primordial, and An-2 promotes awn elongation. Nucleotide diversity of the An-2 locus in cultivated rice was found to be significantly reduced compared with that of wild rice, suggesting that the An-2 locus was subjected to artificial selection. We therefore propose that the selection of genetic variation in An-2 was due to reduced awn length and increased grain yield in cultivated rice.

Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat

Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation

Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.

The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Influence of increasing combustion temperature on the AMS 14C dating of modern crop phytoliths

Several attempts have been made to directly date phytoliths, but most (14)C results are not consistent with other independent chronologies. Due to the limited dataset, there is not a clear explanation for these discrepancies. Herein, we report the (14)C ages of phytolith-occluded carbon (PhytOC) from contemporary rice and millet crops that were combusted at different temperatures to investigate the relationship between the combustion temperature and resulting (14)C age. Our results show that the (14)C age of PhytOC increases directly with combustion temperature (up to 1100°C) and results in age overestimations of hundreds of years. Considerably older ages are observed at higher temperatures, suggesting that it may be possible to distinguish between two fractions of organic carbon in phytoliths: labile and recalcitrant carbon. These findings challenge the assumption that PhytOC is homogeneous, an assumption made by those who have previously attempted to directly date phytoliths using (14)C.

Archaeological evidence for peach (Prunus persica) cultivation and domestication in China

The cultivated/domesticated peach (Prunus persica var. persica; Rosaceae, subgenus Amygdalus; synonym: Amygdalus persica) originated in China, but its wild ancestor, as well as where, when, and under what circumstances the peach was domesticated, is poorly known. Five populations of archaeological peach stones recovered from Zhejiang Province, China, document peach use and evolution beginning ca. 8000 BP. The majority of the archaeological sites from which the earliest peach stones have been recovered are from the Yangzi River valley, indicating that this is where early selection for favorable peach varieties likely took place. Furthermore, peach stone morphology through time is consistent with the hypothesis that an unknown wild P. persica was the ancestor of the cultivated peach. The oldest archaeological peach stones are from the Kuahuqiao (8000–7000 BP) and Tianluoshan (7000–6500 BP) sites and both stone samples segregate into two size groups, suggesting early selection of preferred types. The first peach stones in China most similar to modern cultivated forms are from the Liangzhu culture (ca. 5300 to 4300 BP), where the peach stones are significantly larger and more compressed than earlier stones. Similar peach stones are reported from Japan much earlier (6700–6400 BP). This large, compressed-stone peach was introduced to Japan and indicates a yet unidentified source population in China that was similar to the Liangzhu culture peach. This study proposes that the lower Yangzi River valley is a region, if not the region, of early peach selection and domestication and that the process began at least 7500 years ago.

Pollen and phytolith evidence for rice cultivation and vegetation change during the mid-late holocene at the Jiangli site, Suzhou, East China

Pollen and phytolith analyses were undertaken at the Jiangli site in Suzhou, Jiangsu Province, combined with studies on macrofossils by flotation. The concentration of pollen decreased while the percentage of Poaceae pollen in the profile increased from the late phase of the Majiabang Culture to the Songze Culture suggesting that human impact on the local environment intensified gradually. The discovery of rice paddy implies a relatively advanced rice cultivation in this area during the middle-late Holocene. Other than phytoliths, the high percentage of Oryza-type Poaceae pollen (larger than 40 µm) supplied robust evidence for the existence of rice paddy. Moreover, the fact that the farther from the rice paddy, the lower the concentration and percentage of Poaceae pollen also proves that the dispersal and deposition of pollen is inversely proportional to the distance.