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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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The Archaeobotanist: A genome map that is not a map of origins (Rice Genetic Watch returns)

The Archaeobotanist: A genome map that is not a map of origins (Rice Genetic Watch returns) | Rice origins and cultural history | Scoop.it

Last week Nature ran an article (Huang et al) with the headline that " A map of rice genome variation reveals the origin of cultivated rice." I here to report that this paper does not do what is says. There is nothing obviously relevant to locating where rice was first brought into cultivation, and the claims in the article are misleading and misguided. This is apparently one of most read Nature papers at the moment, so no doubt we will have to face lots of additional confusion over rice domestication-- and I thought there was already enough confused and misguided info out there. I have had several queries on this over the past week, so below is my quick response.

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New study finds many rice varieties are low-to-medium GI | Australian Food News

New study finds many rice varieties are low-to-medium GI | Australian Food News | Rice origins and cultural history | Scoop.it

New research from Australia’s Commonwealth Scientific Industrial Research Organisation (CSIRO) and the International Rice Research Institute (IRRI) has found that rice can help maintain a healthy, low glycemic index (GI) diet, even for diabetes sufferers.

 

The study found that most varieties of rice have a low-to-medium GI score. Researcher analysed 235 types of rice from around the world and discovered that the GI of rice ranges from a low of 48 to a high of 92, with an average of 64. Low-GI foods are those measured at 55 or less. Foods with a score between 58 and 69 are considered medium GI, while high-GI foods measure 70 and above.


Via Frank Kusters
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Population structure of the primary gene pool of Oryza sativa in Thailand

Population structure of the primary gene pool of Oryza sativa in Thailand | Rice origins and cultural history | Scoop.it

Genetic Resources and Crop Evolution, Online First™ - SpringerLink.

The gene pool of cultivated Asian rice consists of wild rice (Oryza rufipogon Griff.), cultivated rice (O. sativa L.) and a weedy form (O. sativa f. spontanea). All three components are widespread in Thailand, frequently co-occurring within fields and providing the opportunity for gene flow and introgression. The purpose to this study is to understand the on-going evolutionary processes that affect the gene pool of rice by analysis of microsatellite variation. Results indicate that O. rufipogon, the wild ancestor of rice, has high levels of genetic variation both within and among populations. Moreover, the variation is structured predominantly by annual and perennial life history. High levels of variation are detected among cultivars indicating Thai cultivated rice has a broad genetic base with only a 20 % reduction in diversity from its wild ancestor. The weedy rice populations reveal varying levels of genetic variation, from nearly as high as wild rice to near zero. Weedy rice is genetically structured into 2 groups. Some populations of invasive weedy rice are the result of hybridization and gene flow between local wild rice and local cultivated rice in the regions of co-occurrence. Other populations of weedy rice are genetically nearly identical to the local cultivated rice. The diversity analysis indicates that the rice gene pool in Thailand is a dynamic genetic system. Gene flow is ongoing among its three main components, first between cultivated and wild rice resulting in weedy rice. Weedy rice in turn crosses with both cultivated varieties and wild rice.

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PLoS ONE: Recent and Projected Increases in Atmospheric CO2 Concentration Can Enhance Gene Flow between Wild and Genetically Altered Rice (Oryza sativa)

PLoS ONE: Recent and Projected Increases in Atmospheric CO2 Concentration Can Enhance Gene Flow between Wild and Genetically Altered Rice (Oryza sativa) | Rice origins and cultural history | Scoop.it

Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO2 from an early 20th century concentration (300 µmol mol−1) to current (400 µmol mol−1) and projected, mid-21st century (600 µmol mol−1) values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 µmol mol−1. The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO2 also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.

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Paddy production: Bihar panchayat breaks China’s record

Paddy production: Bihar panchayat breaks China’s record | Rice origins and cultural history | Scoop.it

NEW DELHI, MAR 20:
A gram panchayat in Nalanda district of Bihar has surpassed the Chinese record of paddy production, the Union Agriculture Minister Mr Sharad Pawar informed Parliament today.

“As per the reports received from the state government, the yield of wet paddy has been recorded at 22.4 tonnes per hectare and that of dry paddy at 20.16 tonnes a hectare in the district of Nalanda, Bihar...,” Mr Pawar said in a written reply to Lok Sabha.

The record yield was achieved under demonstration on System of Rice Intensification (SRI) which was organised at farmer’s field during kharif 2011, he added.

“It has surpassed the yield of 19 tonnes per hectare which was recorded earlier in China,” Mr Pawar said.

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A chance in the wild

A chance in the wild | Rice origins and cultural history | Scoop.it
Scientists are scouring the deep and “wild” end of the rice gene pool to help find hidden traits and genes that can help breed new rice varieties better at thriving and producing food in difficult environments.

Via Luigi Guarino
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The Archaeobotanist: Weed evolution by de-domestication: the case of rice

The Archaeobotanist: Weed evolution by de-domestication: the case of rice | Rice origins and cultural history | Scoop.it

The study of weed origins and evolutionary history is the poor cousin of the archaeobotany of crop domestication. Archaeobotanists can potentially do much more on this, and undoubtedly should. To provide some inspiration it is worth considering some recent insights from genetics, to do with weedy rice. While it is surely the case that rice's wild progenitors may act as weeds in the crop, it now appears that much weedy rice is descended from the crop and not directly from the wild progenitor.

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Chinese Archaeology Conference | Stanford Archaeology Center

Chinese Archaeology Conference | Stanford Archaeology Center | Rice origins and cultural history | Scoop.it

The origins of Sedentism and agriculture in early China

Sedentari­zation and the appearance of agriculture are two of the most momentous evolutionary steps towards the emergence of complex societies in human history. These two developments, together with pottery and polished stone tools, have been generally regarded as part of Neolithization. However, recent studies from many regions in the world have shown that the beginnings of sedentariness and the emergence of food production did not always coincide. On the one hand, sedentism could be practiced in non-agricultural societies; on the other hand, the progress from low-level food production to agriculture may have taken many millennia, during which domesticates did not play an important role in subsistence strategies. In Chinese archaeological research, the origins of cereal and animal domestication have long been emphasized, but much less attention has been paid to sedentism. In this workshop we intend to investigate the evidence from interdisciplinary perspectives for understanding the initial transition from mobile hunter-gatherer lifeways to sedentism, the development and various formulations of sedentism, the emergence of plant/animal domestication, and the relationships between sedentarization and food production in China.

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Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.)

Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.) | Rice origins and cultural history | Scoop.it

Apparent amylose content (AAC) is a key determinant of eating and cooking quality in rice and it is mainly controlled by the Wx gene which encodes a granule-bound starch synthase (GBSS). In this study, sixteen single-segment substitution lines harboring the Wx gene from 16 different donors and their recipient HJX74 were used to detect the naturally occurring allelic variation at the Wx locus. The AAC in the materials varied widely and could be grouped into glutinous, low, intermediate, and two high AAC sub-classes, high I (24.36–25.20%) and high II (25.81–26.19%), under different experimental environments, which showed a positive correlation with the enzymatic activity of GBSS. One insertion/deletion (InDel) and three single nucleotide polymorphisms in the Wx gene were detected and their combinations resulted in the variation of five classes of AAC. Based on the results of AAC phenotypes, GBSS activities and cDNA sequences, five Wx alleles, wx, Wx t, Wx g1, Wx g2, and Wx g3, were identified, two of which, Wx g2 and Wx g3, are separated for the first time in this study. Under different cropping seasons, the AAC differed significantly for the Wx t and Wx g1 alleles, with higher AAC in the fall season than in the spring season, but did not differ significantly for the wx, Wx g2, and Wx g3 alleles. In conclusion, the present results might contribute to our understanding of the naturally occurring allelic variation at the Wx locus and will facilitate the improvement of rice quality by marker-assisted selection.

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Genetics of black rice.

Genetics of black rice. | Rice origins and cultural history | Scoop.it

Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.).

 

Image from: http://www.chinese-black-rice.com/

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Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice

Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice | Rice origins and cultural history | Scoop.it

Seed dormancy—the temporary failure of a viable seed to germinate under favorable conditions—is a complex characteristic influenced by many genes and environmental factors. To detect the genetic factors associated with seed dormancy in rice, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (strong dormancy) and Koshihikari (weak dormancy). Comparison of the levels of seed dormancy of the CSSLs and their recurrent parent Koshihikari revealed that two chromosomal regions—on the short arms of chromosomes 1 and 6—were involved in the variation in seed dormancy. Further genetic analyses using an F2 population derived from crosses between the CSSLs and Koshihikari confirmed the allelic differences and the chromosomal locations of three putative QTLs: Sdr6 on chromosome 1 and Sdr9 and Sdr10 on chromosome 6. The Nona Bokra alleles of the three QTLs were associated with decreased germination rate. We discuss the physiological features of the CSSLs and speculate on the possible mechanisms of dormancy in light of the newly detected QTLs.

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Antiquity Vol 86:331, 2012: Later hunter-gatherers in southern China, 18 000-3000 BC

Antiquity Vol 86:331, 2012: Later hunter-gatherers in southern China, 18 000-3000 BC | Rice origins and cultural history | Scoop.it

The authors present new research on social and economic developments in southern China in the Early Holocene, ninth to fifth millennia BC. The ‘Neolithic package’ doesn't really work for this fascinating chapter of the human experience, where pottery, social aggregation, animal domestication and rice cultivation all arrive at different places and times. The authors define the role of the ‘pottery-using foragers’, sophisticated hunter-gatherers who left shell or fish middens in caves and dunes. These colonising non-farmers shared numerous cultural attributes with rice cultivators on the Yangtze, their parallel contemporaries over more than 5000 years. Some agriculturalists became hunter-foragers in turn when they expanded onto less fertile soils. No simple linear transition then, but the practice of ingenious strategies, adaptations and links in a big varied land

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A map of rice genome variation reveals the origin of cultivated rice : Nature : Nature Publishing Group

A map of rice genome variation reveals the origin of cultivated rice : Nature : Nature Publishing Group | Rice origins and cultural history | Scoop.it

[or does it?]

 

published abstract: Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

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Evidence for a Neolithic Age fire-irrigation paddy cultivation system in the lower Yangtze River Delta, China

Evidence for a Neolithic Age fire-irrigation paddy cultivation system in the lower Yangtze River Delta, China | Rice origins and cultural history | Scoop.it

ScienceDirect.com - Journal of Archaeological Science -

Highlights
► Long-term use of fires was found in ancient paddy production in the Neolithic age. ► Ancient people removed weed by fire in the Neolithic age. ► Fire-using left more black carbon in the soil of ancient paddy fields.

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Dorian Q Fuller's curator insight, December 15, 2012 11:58 AM

The extent to which early burning was merely for rice cultivation and not part of older traditions of landscape (including forest) management remains unclear. That rice fields after harvest, when dry, were burned seems highly likely based on the palaeosol evidence there is, which would make early cultivated rice soils nice examples of anthropogenic soils that are enhanced in nutrients in part through burning.

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Parallel domestication of the Shattering1 genes in cereals : Nature Genetics : Nature Publishing Group

Parallel domestication of the Shattering1 genes in cereals : Nature Genetics : Nature Publishing Group | Rice origins and cultural history | Scoop.it

"A key step in domestication of cereals was loss of seed shattering. Jianming Yu and colleagues show that seed shattering is controlled by alleles at Sh1 in sorghum."

 

(although Sh1 is not realy central to rice domestication, in which Sh4 is universal, and Sh1 is restricted to some japonica varieties only -- ed.)

 

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Improving agriculture through rice production - DR Congo - a set on Flickr

As part of the GCP-040 project, farmers near the village of Kamangu, Katanga province, in the Democratic Republic of Congo have received improved-variety seeds, tools, and technical training to increase the yield of their crops.
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Analysis: Why rice intensification matters in Asia

Analysis: Why rice intensification matters in Asia | Rice origins and cultural history | Scoop.it
The system of rice intensification (SRI) is gaining ground across Asia as more and more governments come to rely on it for food security.
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Did alder (Alnus) fires trigger rice cultivation in the lower reaches of the Yangtze River, East China?

Did alder (Alnus) fires trigger rice cultivation in the lower reaches of the Yangtze River, East China? | Rice origins and cultural history | Scoop.it

ScienceDirect.com - Palaeoworld -Abstract
It remains debatable as to how the prehistoric human communities managed the environment to enable the initial cultivation of rice during the early Neolithic in the coastal lower reaches of the Yangtze River, East China. Previous studies proposed an environmental context for the first rice cultivation at Kuahuqiao, Hangzhou, based on an archaeological sedimentary microfossil record that had been well-dated using radiocarbon methods. Those studies suggested that early humans began burning the predominantly alder scrub in a local swampy wetland, starting about 7750 cal. yr BP, which permitted the start of dedicated rice (Oryza) cultivation. Here we present a new, finer-detailed pollen-phytolith-microscopic charcoal record from the same locality. Our result reveals that local woods dominated by oak (Quercus) and pine (Pinus) were targeted for burning by early cultivators before the start of rice agriculture.

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Genetic diversity and origin of Japonica- and Indica-like rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China

Genetic diversity and origin of Japonica- and Indica-like rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China | Rice origins and cultural history | Scoop.it

Weedy rice has been becoming a notorious weed in the paddy field of China in recent decades due to its increasing damage to rice yield and rice quality. In this study, a microsatellite technique with 21 pairs of SSR markers was utilized to estimate the genetic structure of two biotypes of weedy rice with Japonica and Indica rice characteristics, collected from Liaoning and Guangdong provinces, respectively. The genetic diversity of the weedy rice in the two provinces was relatively low (Liaoning h = 0.086; Guangdong h = 0.160), and distinctly large genetic differences existed between these two provinces (Gcs = 0.623). The genetic diversity was found primarily within populations, and genetic differentiation was relatively low within the same province. Both cluster analysis (UPGMA) and principle component analysis (PCA) showed that weedy rice had a closer relationship with the cultivated rice collected from the sample field than with other cultivated rice and common wild rice varieties in China. Thus, the results of this study on samples from the Liaoning and Guangdong provinces in China support the de-domestication hypothesis that weedy rice most probably originated from local cultivated rice.

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Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice

Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice | Rice origins and cultural history | Scoop.it

Seed size is an important trait in determinant of rice seed quality and yield. In this study, we report a novel semi-dominant mutant S mall and r ound s eed 5 (Srs5) that encodes alpha-tubulin protein. Lemma cell length was reduced in Srs5 compared with that of the wild-type. Mutants defective in the G-protein alpha subunit (d1-1) and brassinosteroid receptor, BRI1 (d61-2) also exhibited short seed phenotypes, the former due to impaired cell numbers and the latter due to impaired cell length. Seeds of the double mutant of Srs5 and d61-2 were smaller than those of Srs5 or d61-2. Furthermore, SRS5 and BRI1 genes were highly expressed in Srs5 and d61-2 mutants. These data indicate that SRS5 independently regulates cell elongation of the brassinosteroid signal transduction pathway

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Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1

Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1 | Rice origins and cultural history | Scoop.it

Heading date in rice is an important agronomic trait controlled by several genes. In this study, flowering time of variety Dianjingyou 1 (DJY1) was earlier than a near-isogenic line (named NIL) carried chromosome segment from African rice on chromosome 3S, when grown in both long-day (LD) and short-day (SD) conditions. By analyzing a large F2 population from NIL × DJY1, the locus DTH3 (QTL for days to heading on chromosome 3) controlling early heading date in DJY1 was fine mapped to a 64-kb segment which contained only one annotated gene, a MIKC-type MADS-box protein. We detected a 6-bp deletion and a single base substitution in the C-domain by sequencing DTH3 in DJY1 compared with dth3 in NIL, and overexpression of DTH3 caused early flowering in callus. Quantitative real-time PCR revealed that the transcript level of dth3 in NIL was lower than that DTH3 in DJY1 in both LD and SD conditions. The Early heading date 1 (Ehd1) which promotes the RFT1, was up-regulated by DTH3 in both LD and SD conditions. Based on Indel and dCAPs marker analysis, the dth3 allele was only present in African rice accessions. A phylogenetic analysis based on microsatellite genotyping suggested that African rice had a close genetic relationship to O. rufipogon and O. latifolia, and was similar to japonica cultivars. DTH3 affected flowering time and had no significant effect on the main agronomic traits.

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Forbidden black rice could be next superfood - Indian Express

Forbidden black rice could be next superfood - Indian Express | Rice origins and cultural history | Scoop.it
Forbidden black rice could be next superfood - Black rice, regularly used in China but uncommon in the West, could be one of the healthiest foods, say experts.
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India Emerges as a Top Rice Exporter

India Emerges as a Top Rice Exporter | Rice origins and cultural history | Scoop.it

Five months after lifting a ban on exports of cheaper varieties of rice, India has emerged as one of the world's top rice exporters.


Via Luigi Guarino
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Early millet use in northern China

It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5–11.0 cal kyBP) and Donghulin (11.0–9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.

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Dorian Q Fuller's curator insight, December 15, 2012 11:53 AM

Whether we can really judge domestication and domestiction process from starch grains require more work, but the patterns here are suggestive both of intensive use of Setaria italica (sensu lato) and possible some morphometric change in foxtail millet, all prior to the accepted 6000 BC start date for millet-based Neolithic farming.