Rice origins and cultural history
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ScienceDirect.com - Agricultural Water Management - Genotypic trade-offs between water productivity and weed competition under the System of Rice Intensification in the Sahel

ScienceDirect.com - Agricultural Water Management - Genotypic trade-offs between water productivity and weed competition under the System of Rice Intensification in the Sahel | Rice origins and cultural history | Scoop.it

Yield, water productivity and weed-inflicted Relative Yield Losses (RYL) under Recommended Management Practices (RMP) were compared with the System of Rice Intensification (SRI) under double-cropping for two seasons and at two locations in the Senegal River Valley. Seven genotypes from Oryza sativa and Oryza glaberrima species and their interspecific crosses, were grown under weed-free conditions and in competition with weeds. Weed-free grain yields in SRI were never significantly different than those obtained with RMP. An average of 27% (range 18–46%) less water was applied to SRI than required for continuous flooding in RMP, resulting in consistently higher water productivity with SRI. However, when subjected to weed competition, mean SRI yields were significantly lower than RMP in three of four experimental iterations (an average of 28% less). Across experiments, weed-inflicted RYL was greater in SRI than RMP in 81% of observed cases. Weeds reduced the water productivity enhancing benefits of SRI by an average of 38% compared to weed-free treatments, resulting in significantly lower water productivity with SRI in three of four experiments. Rice genotypes Jaya and Sahel-202 were identified as relatively weed-competitive under each crop management system, however both have intermediate-length cycles and required more irrigation than shorter-duration genotypes. When weeds are carefully controlled, good yields and significant water savings can be achieved with SRI. However, this specific requirement of careful weed control might be difficult to meet by farmers coping with high weed infestations or with limited access to tools, inputs or labor to address them. Weed-competitive genotypes could help reduce weed-inflicted yield losses associated with SRI and other water-saving rice production systems, though future breeding efforts should address the trade-offs between weed competitive traits, water productivity and crop duration to meet the needs of farmers practicing double rice cropping.

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Rice origins and cultural history
Rounding up the archaeology, cultural history and domestication evidence for rice, and perhaps some other comparisons to other crops
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Barnyard grasses were processed with rice around 10000 years ago

Barnyard grasses were processed with rice around 10000 years ago | Rice origins and cultural history | Scoop.it
Rice (Oryza sativa) is regarded as the only grass that was selected for cultivation and eventual domestication in the Yangtze basin of China. Although both macro-fossils and micro-fossils of rice have been recovered from the Early Neolithic site of Shangshan, dating to more than 10,000 years before present (BP), we report evidence of phytolith and starch microfossils taken from stone tools, both for grinding and cutting, and cultural layers, that indicating barnyard grass (Echinochloa spp.) was
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Evidence for wild millet grass gathering and processing alongside rice in the millennia before clear evidence for the domestication process.

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PLOS ONE: A New Chronology for the Bronze Age of Northeastern Thailand and Its Implications for Southeast Asian Prehistory

PLOS ONE: A New Chronology for the Bronze Age of Northeastern Thailand and Its Implications for Southeast Asian Prehistory | Rice origins and cultural history | Scoop.it
There are two models for the origins and timing of the Bronze Age in Southeast Asia. The first centres on the sites of Ban Chiang and Non Nok Tha in Northeast Thailand. It places the first evidence for bronze technology in about 2000 B.C., and identifies the origin by means of direct contact with specialists of the Seima Turbino metallurgical tradition of Central Eurasia. The second is based on the site of Ban Non Wat, 280 km southwest of Ban Chiang, where extensive radiocarbon dating places the transition into the Bronze Age in the 11th century B.C. with likely origins in a southward expansion of technological expertise rooted in the early states of the Yellow and Yangtze valleys, China. We have redated Ban Chiang and Non Nok Tha, as well as the sites of Ban Na Di and Ban Lum Khao, and here present 105 radiocarbon determinations that strongly support the latter model. The statistical analysis of the results using a Bayesian approach allows us to examine the data at a regional level, elucidate the timing of arrival of copper base technology in Southeast Asia and consider its social impact.
Dorian Q Fuller's insight:

The latest Bayesian chronology for the transition from the Neolithic to the Bronze Age in Thailand, based on quite alot of high quality dates. Among other things it highlights the discrepancy between a short chronology based on dates from burials bone and shell and an older long chronology based on dating the organic fraction of ceramics. While it has long been assumed that dating the organics from pottery dates that rice chaff temper, various studies make it apparent that there is old carbon (presumably from organic rich clays potters used) that confounds this. Here the pottery organics dates are around 700 years too old. This problem also affects other regions, like the middle Yangtze where ceramic "temper" dates from Pengtoushan are consistently almost a millennium too old compared to better dated contexts at Bashidang, or Saharan millet tempered ceramics that are around 500 years too old. While pottery impressions may be a useful way to mark the presence of a crop-- direct dates on pottery are not so reliable for fixing this presence in time.

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Antiquity - Phytoliths and rice: from wet to dry and back again in the Neolithic Lower Yangtze - Cambridge Journals Online

Antiquity - Phytoliths and rice: from wet to dry and back again in the Neolithic Lower Yangtze - Cambridge Journals Online | Rice origins and cultural history | Scoop.it
The cultivation of rice has had a major impact on both societies and their environments in Asia, and in China in particular. Phytolith assemblages from three Neolithic sites in the Lower Yangtze valley reveal that in early rice fields the emphasis was on drainage to limit the amount of water and force the rice to produce seed. It was only in the later third millennium BC that the strategy changed and irrigated paddies came into use. The results demonstrate that plant remains, including weed assemblages, can reveal wetter or drier growing conditions, showing changes in rice cultivation from flooded and drained fields to large, intensively irrigated paddies.
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The phytolith wet:dry index applied to the evolution of rice in the Lower Yangtze

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Dorian Q Fuller's curator insight, October 12, 2015 10:05 AM

The evolution of cultivation in the Lower Yangtze, as seen through phytoliths and field systms

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Antiquity - Rainfall and circular moated sites in north-east Thailand - Cambridge Journals Online

Antiquity - Rainfall and circular moated sites in north-east Thailand - Cambridge Journals Online | Rice origins and cultural history | Scoop.it
The existence of moated mounds in the archaeological record of north-east Thailand has long been known, the majority constructed during the earlier first millennium AD. Despite considerable research, the purpose of the substantial and sometimes multiple moats surrounding raised occupation mounds has remained a mystery. Combining locational, hydrological and rainfall data with the archaeological evidence, this study of the moated mounds of the Khorat Plateau seeks to resolve the question through statistical analysis. The results suggest that water storage may have been the primary purpose of the moats, enabling communities to survive dry seasons and droughts.
Dorian Q Fuller's insight:

Water storage that was likely important in irrigating rice and the Iron shift from rainfed to irrigated rice cultivation

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Britons may have imported wheat long before farming it - life - 26 February 2015 - New Scientist

Britons may have imported wheat long before farming it - life - 26 February 2015 - New Scientist | Rice origins and cultural history | Scoop.it
The discovery of DNA in the southern part of the UK from what appears to be ancient wheat flour hints at a trade in what would have been a prestigious food
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This study is not about rice, but its method may have wide reperscussions in the study of other crops like rice.

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The Future of Domestication Studies

The Future of Domestication Studies | Rice origins and cultural history | Scoop.it
Research by Dorian Fuller, UCL colleagues and collaborative partners is being featured in a special issue of the Proceedings of the National Academy of Sciences of the United States of America (PNAS). The papers are part of a collection entitled: "The Modern View of Domestication", edited by Greger Larson and Dolores R. Piperno, Special Feature of The Proceedings of the National Academy of Sciences, USA (29 April 2014). Early Edition online content is available now via the links below
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Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation - Springer

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation - Springer | Rice origins and cultural history | Scoop.it

Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

Dorian Q Fuller's insight:

Taking a crop to it climatic limits has always proved a challenge, as much a challenge for breeders in the last century (explored in this article) as for those farming expanders of prehistory (e.g.http://archaeobotanist.blogspot.co.uk/2012/02/taking-agriculture-to-edge-arctic.html)

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East Africa and Madagascar in the Indian Ocean world - Online First - Springer

East Africa and Madagascar in the Indian Ocean world - Online First - Springer | Rice origins and cultural history | Scoop.it

The Indian Ocean has long been a forum for contact, trade and the transfer of goods, technologies and ideas between geographically distant groups of people. Another, less studied, outcome of expanding maritime connectivity in the region is the translocation of a range of species of plants and animals, both domestic and wild. A significant number of these translocations can now be seen to involve Africa, either providing or receiving species, suggesting that Africa’s role in the emergence of an increasingly connected Indian Ocean world deserves more systematic consideration. While the earliest international contacts with the East African coast remain poorly understood, in part due to a paucity of archaeobotanical and zooarchaeological studies, some evidence for early African coastal activity is provided by the discovery of early hunter-gatherer sites on offshore islands, and, possibly, by the translocation of wild animals among these islands, and between them and the mainland. From the seventh century, however, clear evidence for participation in the Indian Ocean world emerges, in the form of a range of introduced species, including commensal and domestic animals, and agricultural crops. New genetic studies demonstrate that the flow of species to the coast is complex, with more than one source frequently indicated. The East African coast and Madagascar appear to have been significant centres of genetic admixture, drawing upon Southeast Asian, South Asian and Middle Eastern genetic varieties, and sometimes yielding unique hybrid species. The biological patterns reflect a deeply networked trade and contact situation, and support East Africa’s key role in the events and transformations of the early Indian Ocean world.

 

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Includes an updated review of the evidence for the arrival of Asian rice in Africa

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Dorian Q Fuller's curator insight, November 28, 2013 12:04 PM

The latest output of the SEALINKs project, a regional review of the SE East African coast and Madgascar, with an emphasis on the archaeobotanical and archaeozoological evidence, and reviews of key crops, livestock (like chickens) and commensals (from rates to geckos).

Dorian Q Fuller's curator insight, November 29, 2013 5:51 AM

This article includes a section reviewing the evidence for the arrival of farming in coastal East Africa and its offshore islands, all quite recents <2000 years, based on current archaeobotanical data.

Eve Emshwiller's curator insight, December 14, 2013 8:32 PM

Looks good to use for the topic on "Global Movement of People and Plants."

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The Archaeobotanist: Origins of Rice Podcasts

The Archaeobotanist: Origins of Rice Podcasts | Rice origins and cultural history | Scoop.it
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Dorian Q Fuller's curator insight, November 14, 2013 2:51 AM

Link to recent IRRI radio (Rice Today) interview on the archaeobotany of rice origins (with yours trully)

Eve Emshwiller's curator insight, December 14, 2013 9:12 PM

Nice podcasts about domestication of rice, featuring both Dorian Fuller (archaeological studies) and Susan McCouch (molecular studies).  

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High-quality reference genes for quantifying the transcriptional responses of Oryza sativa L. (ssp. indica and japonica) to abiotic stress conditions - Springer

High-quality reference genes for quantifying the transcriptional responses of Oryza sativa L. (ssp. indica and japonica) to abiotic stress conditions - Springer | Rice origins and cultural history | Scoop.it

Rice (Oryza sativa L.) is important to food security and is also an excellent model plant for numerous cereal crops. A functional genomics study in rice includes characterization of the expression dynamics of genes by quantitative real-time PCR (qPCR) analysis; this is a significant key for developing rice varieties that perform well in the face of adverse climate change. The qPCR analysis requires the use of appropriate reference genes in order to make any quantitative interpretations meaningful. Here, the new potential reference genes were selected from a huge public database of rice microarray experiments. The expression stability of 14 candidates and 4 conventional reference genes was validated by geNormPLUS and NormFinder software. Seven candidates are superior to the conventionally used reference genes in qPCR and three genes can be used reliably for quantitating the expression of genes involved in abiotic stress responses. These high-quality references EP (LOC_Os05g08980), HNR (LOC_Os01g71770), and TBC(LOC_Os09g34040) worked very well in three indica genotypes and one japonica genotype. One ofindica genotypes including the Jasmine rice, KDML105 developed in Thailand for which no reference genes have been reported until now.

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Trends in Genetics - Resequencing rice genomes: an emerging new era of rice genomics

Trends in Genetics - Resequencing rice genomes: an emerging new era of rice genomics | Rice origins and cultural history | Scoop.it

Rice is a model system for crop genomics studies. Much of the early work on rice genomics focused on analyzing genome-wide genetic variation to further understand rice gene functions in agronomic traits and to generate data and resources for rice research. The advent of next-generation high-throughput DNA sequencing technologies and the completion of high-quality reference genome sequences have enabled the development of sequencing-based genotyping and genome-wide association studies (GWAS) that have significantly advanced rice genetics research. This has led to the emergence of a new era of rice genomics aimed at bridging the knowledge gap between genotype and phenotype in rice. These technologies have also led to pyramid breeding through genomics-assisted selection, which will be useful in breeding elite varieties suitable for sustainable agriculture. Here, we review the recent advances in rice genomics and discuss the future of this line of research.


Via Jennifer Mach, Ricardo Oliva
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Archaeobotanical implications of phytolith assemblages from cultivated rice systems, wild rice stands and macro-regional patterns

Archaeobotanical implications of phytolith assemblages from cultivated rice systems, wild rice stands and macro-regional patterns | Rice origins and cultural history | Scoop.it

Rice can be cultivated in a range of arable systems, including upland rainfed, lowland rainfed or irrigated, flooded or décrue, and deep water cultivation. These agricultural regimes represent ecosystems controlled to large degree by agricultural practices, and can be shown to produce different weed flora assemblages. In order to reconstruct early rice cultivation systems it is necessary to better establish how ancient rice farming practices may be seen using archaeobotanical data. This paper focuses on using modern analogue phytolith assemblages of associated crop weeds found within cultivation regimes, as well as in wild rice stands (unplanted stands of Oryza nivara or O. rufipogon), as a means of interpreting archaeobotanical assemblages. Rice weeds and sediment samples have been recorded and collected from a range of arable systems and wild stands in India. The husks, leaves and culms of associated weeds were processed for phytolith reference samples, and sediment samples were processed for phytoliths in order to establish patterns identifiable to specific systems. The preliminary results of the phytolith analysis of samples from these modern fields demonstrate that phytolith assemblage statistics show correlation with variation in rice cultivation systems on the basis of differences in environmental conditions and regimes, with wetness being one major factor. Analysis of phytoliths from archaeological samples from contrasting systems in Neolithic China and India demonstrate how this method can be applied to separate archaeological regions and periods based on inferred differences in past agricultural practices, identifying wet cultivation systems in China, dry millet-dominated agriculture of north China and rainfed/dry rice in Neolithic India.

Dorian Q Fuller's insight:

We present a new methodology for identifying ancient rice arable systems.

We create modern analogues of phytolith assemblages of rice weeds from modern fields.

These analogues are used as models to understand archaeobotanical samples.

We present an analysis of different systems from Neolithic India and China.

More studiies applying and improving on this study are underway now as part of the rice project, which recieved further NERC support: http://www.ucl.ac.uk/archaeology/calendar/articles/20130509b

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Dorian Q Fuller's curator insight, May 17, 2013 4:15 AM

next we will be expanding on this sort of analysis in the Lower Yangtze...watch this space.

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Phytoliths as a tool for investigations of agricultural origins and dispersals around the world

Phytoliths as a tool for investigations of agricultural origins and dispersals around the world | Rice origins and cultural history | Scoop.it

Agricultural origins and dispersals are subjects of fundamental importance to archaeology as well as many other scholarly disciplines. These investigations are world-wide in scope and require significant amounts of paleobotanical data attesting to the exploitation of wild progenitors of crop plants and subsequent domestication and spread. Accordingly, for the past few decades the development of methods for identifying the remains of wild and domesticated plant species has been a focus of paleo-ethnobotany. Phytolith analysis has increasingly taken its place as an important independent contributor of data in all areas of the globe, and the volume of literature on the subject is now both very substantial and disseminated in a range of international journals. In this paper, experts who have carried out the hands-on work review the utility and importance of phytolith analysis in documenting the domestication and dispersals of crop plants around the world. It will serve as an important resource both to paleo-ethnobotanists and other scholars interested in the development and spread of agriculture.

Dorian Q Fuller's insight:

Includes a summary of approaches to tracking rice in the archaeological phytolith record, including work from the UCL lab on rice cultivation ecology...

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Dorian Q Fuller's curator insight, October 20, 2015 2:22 PM

an updated review of phytolith approaches to tracing early crops, crop varieties and domestications.

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PLOS ONE: From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700–500 BC)

PLOS ONE: From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700–500 BC) | Rice origins and cultural history | Scoop.it
Baligang is a Neolithic site on a northern tributary of the middle Yangtze and provides a long archaeobotanical sequence from the Seventh Millennium BC upto the First Millennium BC. It provides evidence for developments in rice and millet agriculture influenced by shifting cultural affiliation with the north (Yangshao and Longshan) and south (Qujialing and Shijiahe) between 4300 and 1800 BC. This paper reports on plant macro-remains (seeds), from systematic flotation of 123 samples (1700 litres), producing more than 10,000 identifiable remains. The earliest Pre-Yangshao occupation of the sites provide evidence for cultivation of rice ( Oryza sativa ) between 6300–6700 BC. This rice appears already domesticated in on the basis of a dominance of non-shattering spikelet bases. However, in terms of grain size changes has not yet finished, as grains are still thinner than more recent domesaticated rice and are closer in grain shape to wild rices. This early rice was cultivated alongside collection of wild staple foods, especially acorns ( Quercus/Lithicarpus sensu lato). In later periods the sites has evidence for mixed farming of both rice and millets ( Setaria italica and Panicum miliaceum ). Soybean appears on the site in the Shijiahe period (ca.2500 BC) and wheat ( Triticum cf. aestivum ) in the Late Longshan levels (2200–1800 BC). Weed flora suggests an intensification of rice agriculture over time with increasing evidence of wetland weeds. We interpret these data as indicating early opportunistic cultivation of alluvial floodplains and some rainfed rice, developing into more systematic and probably irrigated cultivation starting in the Yangshao period, which intensified in the Qujialing and Shijiahe period, before a shift back to an emphasis on millets with the Late Longshan cultural influence from the north.
Dorian Q Fuller's insight:

An important archaeobotanical sequence from central China, which charts the rise and fall of millets versus rice in this regions between the Yangshao and the Shijiahe period. It also has a much earlier occupation (6300 BC) with non-shattering (domesticated) rice, which makes this earlier than evidence in the Lower Yangtze (or anywhere else at present), but presumably a separate domestication episode...

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Dorian Q Fuller's curator insight, October 15, 2015 7:33 AM

Important evidence for early domestication rice, which is highly non-shattering but still small-grained. This suggests these two trait may be evolving differentially in this region in contrast to the Lower Yangtze, but unfortunately we have no immediately earlier or later assemblages from the region to compare it with, so the extent to which this is a "dead end" or how it fits into a domestication trajectory remains to be determined.

Dorian Q Fuller's curator insight, October 15, 2015 8:53 AM

Important evidence for early domestication rice, which is highly non-shattering but still small-grained. This suggests these two trait may be evolving differentially in this region in contrast to the Lower Yangtze, but unfortunately we have no immediately earlier or later assemblages from the region to compare it with, so the extent to which this is a "dead end" or how it fits into a domestication trajectory remains to be determined.

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How 'Forbidden' Black Rice Flourished For Millennia - NPR

How 'Forbidden' Black Rice Flourished For Millennia - NPR | Rice origins and cultural history | Scoop.it
Once reserved for the exclusive use of Chinese royalty, black rice these days has become the darling of gourmets seeking superior nutrition. Now geneticists have traced where this rare rice came from.
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Black rice represents a post-domestication selection pathway from wild-type red to a deep dark purple, distinct from the better known selection to white (or light brown). Now we have some clear genetic indicators for the causation of this change-- even it it remains to challenge to determined when and where (and why) this took place.

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PLOS ONE: Modelling the Geographical Origin of Rice Cultivation in Asia Using the Rice Archaeological Database

PLOS ONE: Modelling the Geographical Origin of Rice Cultivation in Asia Using the Rice Archaeological Database | Rice origins and cultural history | Scoop.it
We have compiled an extensive database of archaeological evidence for rice across Asia, including 400 sites from mainland East Asia, Southeast Asia and South Asia. This dataset is used to compare several models for the geographical origins of rice cultivation and infer the most likely region(s) for its origins and subsequent outward diffusion. The approach is based on regression modelling wherein goodness of fit is obtained from power law quantile regressions of the archaeologically inferred age versus a least-cost distance from the putative origin(s). The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. The origin region that best fits the archaeobotanical data is also compared to other hypothetical geographical origins derived from the literature, including from genetics, archaeology and historical linguistics. The model that best fits all available archaeological evidence is a dual origin model with two centres for the cultivation and dispersal of rice focused on the Middle Yangtze and the Lower Yangtze valleys.
Dorian Q Fuller's insight:

The rice projects latest modelling effort: this is the first in a series of new models of rice's dispersal history, based on the RAD 2 (rice archaeological database), which can be explored in googleearth through the supplementary information.

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Dorian Q Fuller's curator insight, October 12, 2015 10:04 AM

The full dataset of archaeological rice across Asia supports two Yangtze foci of early cultivation from which rice spread.

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Cover Photo — April 29, 2014, 111 (17)

Cover Photo — April 29, 2014, 111 (17) | Rice origins and cultural history | Scoop.it

29 April 2014. Cover of PNAS. The issue with the special feature on the "Modern View of Domestication". Cover image: Pictured are the Gamo-Gofa highlands of southern Ethiopia, a traditional agricultural landscape dotted with domesticated plants and animals such as hybrid cattle. Domesticated plants of diverse geographical origins include maize, sorghum, barley, Ethiopian banana, palm kale, and castor oil plant. The Modern View of Domestication Special Feature, appearing in this issue, presents recent genetic and archaeological evidence regarding the origin and spread of domesticated plants and animals, and addresses questions including those concerning the speed and intentionality of early domestication. See the Introduction to the Special Feature by Greger Larson et al. on pages 6139–6146. Image courtesy of Dorian Fuller.

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Dorian Q Fuller's curator insight, April 29, 2014 7:02 PM
have to show off my photo a little...
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Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record | Rice origins and cultural history | Scoop.it
Agriculture was a transformative development in the history of human societies and natural environments and drove the evolution of new domesticated species. Crop plants are the predominant domesticated species in most agricultural systems and are an essential component in all the food production systems that underpinned the development of urban societies. Archaeological plant remains provide a range of insights into the processes by which plants were domesticated in different parts of the world. The present paper provides a unique synthesis of evidence, including quantitative evidence on the trajectory and rate of domestication in seed crops and patterns in the development of tropical vegetatively propagated crops
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This paper includes the most upto date data on archaeologically documented domestication traits in rice, include non-shattering spikelet bases from China, and grain size change in both China and India.
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Dorian Q Fuller's curator insight, April 24, 2014 4:34 AM
This is one of the papers in a Special Feature on domestication in the PNAS issue out next week. This one represents two of the key work packages in the ERC-funded ComPAg project -- quantifying rates of change in domestication and comparing different regional pathways to agriculture in terms of settlement systems and economic styles. On ComPAg, see http://www.ucl.ac.uk/archaeology/research/directory/compag-fuller ) This paper emerged from a meeting held on NESCENT on domestication (http://www.nescent.org/science/awards_summary.php?id=218)
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QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice - Springer

QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice - Springer | Rice origins and cultural history | Scoop.it

In this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of theO. rufipogon allele at qSPP5 was 10–15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%.

Based on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica andindica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5.
Dorian Q Fuller's insight:

So linked alleles for grain number and grain size! This really does mean that unintentional selection for larger grain, parts of the domestication syndrome, would lead to early gains for cultivators potentially offsetting the added labour of cultivation over foraging. This fits the model on entanglement put forward in World Archaeology 42(1) (http://dx.doi.org/10.1080/00438240903429680) but even more dramatically so. It is also worth noting that this may be a specifically japonica rice domestication entanglement and one that was no readily available in early proto-indica, but was introgressed from japonica.

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From wild grass to golden grain

From wild grass to golden grain | Rice origins and cultural history | Scoop.it

Believe it or not, rice, our staple crop, was not introduced to our island by Aryan migrants from Eastern India around the 5th century BC as had been previously supposed. Rather its cultivation seems to go back to pre-historic times, in all probability to Sri Lanka’s Stone Age

Dorian Q Fuller's insight:

So the claim is made that there was a period of indigenous rice cultivation in the early Holocene of Sri Lanka, that was in the middle Holocene. Not implausible, perhaps, but certainly not proven. (1) Sri Lanka has a rich range of wild rices, both progenitor and non-progenitor species; (2) the evidence of phytoliths cannot easily or relaibly differentiate morphologixall wild versus domesticated rices, although phytoliths assemablges can be useful for determining ecology and this inferred cultivated versus wild ecologies (as we are finding in early China), but such evidence has (not yet) be made available in this case. As happens all too often journalistic headlines trump real science, which is a pity, but core sequences of pollen and phytoliths from Sri Lanka will indeed prove to be important for reconsturcting the prehistory of the island. So too will be rejecting predjudices, expressed by this journalist, that hunter-gatherers (like Veddahs) should be assumed to be "stupid" (and by implication only farmers are "intelligent"). All humans are intelligent have expressed this in many different ways-- adapting to the tropical rainforests through microlithihc tools and hunting of arboreal game some 40,000 years ago-- which is evidence in Sri Lanka-- is one means by which they have done so.(see, e.g. http://www.sciencedirect.com/science/article/pii/S0047248411000881 ;)

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Dorian Q Fuller's curator insight, January 10, 2014 7:48 AM

Some journalist hyperbole that masks what could be an important dataset.

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Evolution of crop species: genetics of domestication and diversification : Nature Reviews Genetics : Nature Publishing Group

Evolution of crop species: genetics of domestication and diversification : Nature Reviews Genetics : Nature Publishing Group | Rice origins and cultural history | Scoop.it

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

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Dorian Q Fuller's curator insight, November 20, 2013 4:40 AM

A nice review on the current genetics of parallel and convergent evolution of domestication traits.

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Dynamics of decadal changes in the distribution of double-cropping rice cultivation in China - Springer

Dynamics of decadal changes in the distribution of double-cropping rice cultivation in China - Springer | Rice origins and cultural history | Scoop.it

Quantitative description of changes in the distribution of paddy rice cultivation in response to recent climate change provides a reference for rice cultivation patterns and formulation of countermeasures to cope with future climate change in China. This study analyzes the dynamics of decadal changes in distribution of double-cropping rice in China during 1961–2010 in relation to climate change based on the maximum entropy method. Decadal changes in the double-cropping rice cultivation area and climatic suitability in China were apparent. The total area of climatically suitable regions was highest in the 1960s, and subsequently showed an increasing trend at first and then a decreasing trend from the 1970s to 2000s. However, the low climatic suitability area decreased, which implied that the moderate and high climatic suitability areas increased. Among the latter, the high climatic suitability area showed the highest increase in extent to 4.4 times that of the 1990s and four times that of the 1960s. The areas of double-cropping rice cultivation most sensitive to climate change are mainly located in central Jiangsu, central Anhui, the eastern Sichuan Basin, southern Henan and central Guizhou. Transformation of areas between low and moderate climatic suitability was observed in northern Zhejiang, southern Anhui and Hubei, and northern Guangxi. Transformation of areas between moderate and high climatic suitability was observed in central Jiangxi and Leizhou Peninsula. The northern boundary of double-cropping rice cultivation in China shifted southwards and contracted eastwards in the 1970s, and extended northwards in the 1980s. However, the northern boundary did not shift northwards in response to climate warming in the 2000s.

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ScienceDirect.com - Agricultural Water Management - Genotypic trade-offs between water productivity and weed competition under the System of Rice Intensification in the Sahel

ScienceDirect.com - Agricultural Water Management - Genotypic trade-offs between water productivity and weed competition under the System of Rice Intensification in the Sahel | Rice origins and cultural history | Scoop.it

Yield, water productivity and weed-inflicted Relative Yield Losses (RYL) under Recommended Management Practices (RMP) were compared with the System of Rice Intensification (SRI) under double-cropping for two seasons and at two locations in the Senegal River Valley. Seven genotypes from Oryza sativa and Oryza glaberrima species and their interspecific crosses, were grown under weed-free conditions and in competition with weeds. Weed-free grain yields in SRI were never significantly different than those obtained with RMP. An average of 27% (range 18–46%) less water was applied to SRI than required for continuous flooding in RMP, resulting in consistently higher water productivity with SRI. However, when subjected to weed competition, mean SRI yields were significantly lower than RMP in three of four experimental iterations (an average of 28% less). Across experiments, weed-inflicted RYL was greater in SRI than RMP in 81% of observed cases. Weeds reduced the water productivity enhancing benefits of SRI by an average of 38% compared to weed-free treatments, resulting in significantly lower water productivity with SRI in three of four experiments. Rice genotypes Jaya and Sahel-202 were identified as relatively weed-competitive under each crop management system, however both have intermediate-length cycles and required more irrigation than shorter-duration genotypes. When weeds are carefully controlled, good yields and significant water savings can be achieved with SRI. However, this specific requirement of careful weed control might be difficult to meet by farmers coping with high weed infestations or with limited access to tools, inputs or labor to address them. Weed-competitive genotypes could help reduce weed-inflicted yield losses associated with SRI and other water-saving rice production systems, though future breeding efforts should address the trade-offs between weed competitive traits, water productivity and crop duration to meet the needs of farmers practicing double rice cropping.

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PLOS ONE: Comparative Genomic and Transcriptomic Analysis of Tandemly and Segmentally Duplicated Genes in Rice

PLOS ONE: Comparative Genomic and Transcriptomic Analysis of Tandemly and Segmentally Duplicated Genes in Rice | Rice origins and cultural history | Scoop.it

Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution

Dorian Q Fuller's insight:

Shows there are quite alot of duplicated genes in the rice genome. Unfortunately, the number that were involved in the domestication process remains speculative-- and needs to be investigated!

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