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Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two Oryza species

Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression (DGE) technology and the paired-end RNA sequencing (RNA-Seq) method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, ~8% (1717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5’flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.


Via Pierre-Marc Delaux, Francis Martin
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Added gene can make rice more climate-friendly | Tim Radford | Climate News Network

Added gene can make rice more climate-friendly | Tim Radford | Climate News Network | plant research | Scoop.it

An international team of scientists has found a way to make rice more productive, more nutritious and less of a greenhouse gas producer – simply by adding just one gene from the cereal, barley.

The single gene SUSIBA 2 – the acronym stands for sugar signalling in barley – makes all the difference. And the importance of the breakthrough is that rice feeds half the world – but, as it grows, is one of the great sources of the greenhouse gas, methane.

The world’s rice paddy fields release up to 100 million tonnes each year of methane − possibly 17% of the global total.

And although methane emissions are small compared with carbon dioxide, each molecule of methane is far more potent a global warmer. The gas is 34 times more potent than CO2 over a century, but 84 times more so over a much shorter timespan – just 20 years.

 

Click headline to read more and access hot links--


Via Chuck Sherwood, Senior Associate, TeleDimensions, Inc
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Simple cooking methods flush arsenic out of rice ("more hot water washing can flush out arsenic")

Simple cooking methods flush arsenic out of rice ("more hot water washing can flush out arsenic") | plant research | Scoop.it
Preparing rice in a coffee machine can halve levels of the naturally occurring substance.

Cooking rice by repeatedly flushing it through with fresh hot water can remove much of the grain’s stored arsenic, researchers have found — a tip that could lessen levels of the toxic substance in one of the world’s most popular foods.

Billions of people eat rice daily, but it contributes more arsenic to the human diet than any other food. Conventionally grown in flooded paddies, rice takes up more arsenic (which occurs naturally in water and soil as part of an inorganic compound) than do other grains. High levels of arsenic in food have been linked to different types of cancer, and other health problems.

Andrew Meharg, a plant and soil scientist at Queen’s University Belfast, UK, wondered whether cooking the grain in a different way might help to lessen the health risk. The standard method for making rice — boiling it in a pot until it soaks up all the liquid — binds into place any arsenic contained in the rice and the cooking water.

Meharg and colleagues found that using this method with increasing proportions of water removed progressively more arsenic — up to a 57% reduction with a ratio of 12 parts water to one part rice. That result confirmed that the arsenic is 'mobile' in liquid water, and thus can be removed.

 


Via Bert Guevara
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Bert Guevara's curator insight, July 23, 2015 10:01 PM

You are probably eating commercial rice with certain levels of arsenic. Here is how to flush out the arsenic in a simple kitchen procedure. Read and learn.


"Cooking rice by repeatedly flushing it through with fresh hot water can remove much of the grain’s stored arsenic, researchers have found — a tip that could lessen levels of the toxic substance in one of the world’s most popular foods."

DebbyBruck's comment, July 24, 2015 4:54 AM
That's super information... Thank you Bert!
Eric Larson's curator insight, July 28, 2015 7:50 PM

Arsenic in rice flushed.

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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 | plant research | 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, Dorian Q Fuller
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Seeds of Freedom

A landmark film narrated by Jeremy Irons. Find out more at www.seedsoffreedom.info The story of seed has become one of loss, control, dependence and debt. It’s…
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Nature: 30 years of GMOs

Nature: 30 years of GMOs | plant research | Scoop.it

There are several good articles in this week's Nature, celebrating 30 years since the first transgenic plants were produced.

Don't miss the analyses of agricultural biotech in Africa (http://www.nature.com/nature/journal/v497/n7447/full/497031a.html) and China (http://www.nature.com/nature/journal/v497/n7447/full/497033a.html), and a good perspectie on "Using membrane transporters to improve crops for sustainable food production" (http://www.nature.com/nature/journal/v497/n7447/full/nature11909.html).


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Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation - Springer

Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation - Springer | plant research | Scoop.it

During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world. The association of the Hd5 genotype with heading date and genetical analysis clearly showed that the loss-of-function Hd5 has an important role in exhibiting earlier heading among a local population in Hokkaido. Distinct distribution of the loss-of-function Hd5 revealed that this mutation event of the 19-bp deletion occurred in a local landrace Bouzu and that this mutation may have been selected as an early-heading variety in rice breeding programs in Hokkaido in the early 1900s. The loss-of-function Hd5 was then introduced into the rice variety Fanny from France and contributed to its extremely early heading under the presence of functional Ghd7. These results demonstrated that Hd5 plays roles not only in generating early heading in variations of heading date among a local population in Hokkaido, but also in extremely early heading for adaptation to northern limits of rice cultivation


Via Dorian Q Fuller
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Dorian Q Fuller's curator insight, March 8, 2013 7:20 AM

Although the particular heading date mutation this paper focuses on it perhaps just over 100 years old, as an adaptation to growing rice in Hokkaido, it illustrated the more general principle the northward spread of rice required geneitc adaptations to shorter growing seasons.  (See also the DTH2 paper scooped a few weeks ago).

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PLOS ONE: Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

PLOS ONE: Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa | plant research | Scoop.it

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.


Via Dorian Q Fuller
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Intercropping 'boosts maize yields by 50 per cent' - SciDev.Net

Intercropping 'boosts maize yields by 50 per cent' - SciDev.Net | plant research | Scoop.it
A 12-year study in Southern Africa has found that intercropping has a long-term positive effect on rain-fed maize yields.
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When did groundnuts become perennials?

When did groundnuts become perennials? | plant research | Scoop.it
Dear IFPRI Have you managed to turn groundnuts (Arachis hypogea) into a perennial? Or are you confused perhaps by the difference between perennials and nitrogen-fixing legumes, some of which are indeed perennial?
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Wild rice gene gives yield boost

Wild rice gene gives yield boost | plant research | Scoop.it
A gene from wild Indian rice plants can significantly raise the yield of common varieties in nutrient-poor soils by boosting root growth.
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A Guide to Mass Shootings in America

A Guide to Mass Shootings in America | plant research | Scoop.it
There have been at least 57 in the last 30 years—and most of the killers got their guns legally.

 

Still not sure if I'm prepared to explain what this all means, but it would be worth discussing in class. 


Via Seth Dixon
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OsLG1 regulates a closed panicle trait in domesticated rice

OsLG1 regulates a closed panicle trait in domesticated rice | plant research | Scoop.it

Reduction in seed shattering was an important phenotypic change during cereal domestication. Here we show that a simple morphological change in rice panicle shape, controlled by the SPR3 locus, has a large impact on seed-shedding and pollinating behaviors. In the wild genetic background of rice, we found that plants with a cultivated-like type of closed panicle had significantly reduced seed shedding through seed retention. In addition, the long awns in closed panicles disturbed the free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. We localized the SPR3 locus to a 9.3-kb genomic region, and our complementation tests suggest that this region regulates the liguleless gene (OsLG1). Sequencing analysis identified reduced nucleotide diversity and a selective sweep at theSPR3 locus in cultivated rice. Our results suggest that a closed panicle was a selected trait during rice domestication.


Via Dorian Q Fuller
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Dorian Q Fuller's curator insight, March 8, 2013 6:55 AM

This is further important work from the Kobe University rice research group (Ishii, Ishikawa, and colleagues) which derives from careful experimental growing on wild rice and breeding of crop traits in wild rices. A few years ago they showed that sh4 alone was not apparently an effective mutation for non-shattering, as normally inferred, but required additional interacting mutations. They have identified a key trait (if not the key trait), SPR3, which delays shattering, and together with sh4 essentially leads to the key domestication trait of non-shattering. Of particular interest it is has the side effect of decreasing cross pollination, and thus pushing rice towards selfing, another key change with domestication. The main feaure of SPR3 seems to be towards a closed (and less branching) panicle, which we would expect to have the effect of making it easier to gather a larger proportion of grains when harvesting using hunter-gatherer methods like basket beating. Ethnographically wild rice gathering (including of Zizania amongst the Ojibwa) often features tieing panicles into a knot after flowering when grains are green so as to catch early shattering grains. Essentially this mutation achieves a similar end and we might therefore see this as likely quite early in the domestication process. I suspect this goes some way towards helping explain how rice domesticiation worked in the absence of sickles (which are 3rd Millennium BC in the Yangtze), a clear contrast from wheat and barley. It is also worth noting that long awns play a role in retaining mature grains, which goes some way to explain why selection for awnlessness is so clearly an incomplete and post-domestication development.

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Activation of Big Grain1 significantly improves grain size by regulating auxin transport in rice

Activation of Big Grain1 significantly improves grain size by regulating auxin transport in rice | plant research | Scoop.it

Here's an interesting OPEN paper in PNAS. The gene was identified by activation tagging, meaning that the mutant overexpresses a normal protein, resulting in big rice grains. The overexpressed gene encodes an uncharacterized membrane-localized protein that affects auxin transport. Lots more work to do, but an interesting and potentially useful phenotype!


Via Mary Williams
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Triple-grained rice news

Triple-grained rice news | plant research | Scoop.it
What it is to have friends, especially knowledgeable friends. Bhuwon Sthapit, local rice wallah extraordinaire,1 responded quickly and in depth when asked what he knew about triple-grained rice.

Via Luigi Guarino, Dorian Q Fuller, Frank Kusters
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A domestication gene in rice that affects cytokinin synthesis and awn formation

A domestication gene in rice that affects cytokinin synthesis and awn formation | plant research | Scoop.it

Nice study. "LABA1, a domestication gene associated with long, barbed awns in wild rice".
LABA1 is a homolog of rice LONELY GUY (LOG), which encodes a cytokinin riboside 5'-monophosphate phosphoribohydrolase that directly converts inactive cytokinin nucleotide 5'-monophosphate (iPRMP and tZRMP) to the biologically active free-base form (iP and tZ) in the final step of bioactive cytokinin biosynthesis.
www.plantcell.org/content/…/2015/06/16/tpc.15.00260.abstract
Summary here http://www.plantcell.org/conte…/early/2015/…/16/tpc.15.00504


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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 | plant research | 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.


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

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

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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Functional genomics based understanding of rice endosperm development

Functional genomics based understanding of rice endosperm development | plant research | Scoop.it

Seed development, especially the relevant regulatory mechanism and genetic network are of fundamental scientific interest. Seed development consists of the development of embryo and endosperm; and endosperm development of rice (model species of monocots) is closely related to grain yield and quality. Recent genetic studies, together with other approaches, including transcriptome and proteomics analysis, high-throughput sequencing (RNA-seq, ChIP-seq), revealed the crucial roles of genetic and epigenetic controls in rice endosperm development. Here we summarize and update the genetic networks involved in the regulation of endosperm initiation, cell cycle regulation, aleurone layer specification, starch synthesis, storage protein accumulation and endosperm size, and the interactions between embryo and endosperm.


Via Dorian Q Fuller
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Dorian Q Fuller's curator insight, May 6, 2013 11:29 AM

Looks like a very useful review of the various genes affecting rice grain development, from waxy starch to grain width. Many of these could be selected during various stages in domestication history.

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Specific patterns of genetic diversity among aromatic rice varieties in Myanmar - Springer

Specific patterns of genetic diversity among aromatic rice varieties in Myanmar - Springer | plant research | Scoop.it

Microsatellites were able to retrieve the well-established classification into Indica (isozyme group 1), Japonica (group 6, comprising temperate and tropical forms) and specific groups from the Himalayan foothills including some Aus varieties (group 2) and some aromatic varieties (group 5). They revealed a new cluster of accessions close to, but distinct from, non-Myanmar varieties in group 5. With reference to earlier terminology, we propose to distinguish a group “5A” including group 5 varieties from the Indian subcontinent (South and West Asia) and a group “5B” including most group 5 varieties from Myanmar. In Myanmar varieties, aroma was distributed in group 1 (Indica) and in group 5B. New BADH2 variants were found. Some accessions carried a 43 bp deletion in the 3’ UTR that was not completely associated with aroma. Other accessions, all of group 5B, displayed a particularBADH2 allele with a 3 bp insertion and 100% association with aroma. With the new group and the new alleles found in Myanmar varieties, our study shows that the Himalayan foothills contain series of non-Indica and non-Japonica varietal types with novel variations for useful traits.


Via Dorian Q Fuller
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Dorian Q Fuller's curator insight, March 20, 2013 8:55 AM

yet more convergent lineages of fragrant rice...

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Africa, an agricultural powerhouse?

Africa, an agricultural powerhouse? | plant research | Scoop.it
Analysis: By defying the World Bank, Malawi's president showed that Africa's dormant fields have vast export potential.
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Sacramental varieties

Sacramental varieties | plant research | Scoop.it
The CIMMYT genebank holds about 13,000 wheat lines (from a couple hundred populations) from Mexico that they call “sacramental wheats.” This collection was put together by the late Bent Skovmand, who established the CIMMYT genebank back in the 1970s.
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July 2012 Hottest Month Ever in U.S.

July 2012 Hottest Month Ever in U.S. | plant research | Scoop.it
By Climate Central's Michael D. Lemonick: July 2012 was officially not only the warmest July on record, but also the warmest month ever recorded for the lower 48 states, according to a report released Wednesday by scientists at the National Oceanic...

 

The drought footprint cover 63% of the contiguous states during the hottest month in American history.  It's the hottest 12 month stretch (August 2011-July 2012) on record for the lower 48, making it the fourth consecutive month to set a new record (i.e. old record was July 2011-June 2012).The biggest difference from other hot months is the nighttime temperature have been exceptionally high.  The most current drought monitor map can be found at:  http://droughtmonitor.unl.edu


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