Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Cytokinin Induces Cell Division in the Quiescent Center of the Arabidopsis Root Apical Meristem

Cytokinin Induces Cell Division in the Quiescent Center of the Arabidopsis Root Apical Meristem | Plant Gene Seeker -PGS | Scoop.it

SummaryBackground

In the root apical meristem, which contains the stem cells that feed into root development, the phytohormones auxin and cytokinin play opposing roles, with auxin promoting cell division and cytokinin promoting cell differentiation. Cytokinin acts in the root tip in part by modulating auxin transport through regulation of the level of the PIN auxin efflux carriers. Auxin plays a key role in the specification of the quiescent center (QC), which is essential for maintaining the stem cell fate of the surrounding cells.

Results

We demonstrate that cytokinin promotes cell division in the QC, which is generally mitotically inactive. Cytokinin downregulates the expression of several key regulatory genes in the root tip, including SCARECROW, WOX5, and the auxin influx carriers AUX1 and LAX2. The decrease in LAX2 expression in response to cytokinin requires ARR1 and ARR12, two type B ARRs that mediate the primary transcriptional response to cytokinin. ARR1 was found to bind directly to the LAX2 gene in vivo, which indicates that type B ARRs directly regulate genes that are repressed by cytokinin. Disruption of the LAX2 gene results in a phenotype similar to that observed in response to cytokinin, including increased division of the cells in the QC and decreased expression of WOX5 and the auxin response reporter DR5.

Conclusions

Cytokinin acts to regulate auxin distribution in the root apical meristem by regulating both the PINs and LAX2. This redistribution of auxin, potentially coupled with other auxin-independent effects of cytokinin, regulates the mitotic activity in the QC.

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Current Biology - Halotropism Is a Response of Plant Roots to Avoid a Saline Environment

Current Biology - Halotropism Is a Response of Plant Roots to Avoid a Saline Environment | Plant Gene Seeker -PGS | Scoop.it

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RAB5 Activation is Required for Multiple Steps in Arabidopsis thaliana Root Development

RAB5 Activation is Required for Multiple Steps in Arabidopsis thaliana Root Development | Plant Gene Seeker -PGS | Scoop.it
Plant and Cell Physiology
Andres Zurita's insight:

Rab GTPases regulate the tethering and fusion of transport vesicles to target membranes in membrane trafficking by acting as a molecular switch, cycling between GDP- and GTP-bound states. RAB5 is a member of the Rab GTPase family, the members of which have been shown to perform various functions in the endocytic pathway, including the regulation of endosomal fusion and motility in animal cells. RAB5-mediated endosomal trafficking has also been found to play important roles in various higher order plant functions, which include the regulation of the polar transport of auxin and responses to environmental conditions. The regulatory mechanisms and functions of plant RAB5 have also been investigated at the molecular and cellular levels. However, the significance of RAB5 activity at the tissue and organ levels has hardly been investigated thus far. In the present study, we examined the effect of a mutation inVPS9a, which encodes the sole guanine nucleotide exchange factor for all RAB5s in the vegetative stages of Arabidopsis thaliana. We found that multiple developmental processes were impaired in the mutant plants, including the growth and pattern formation of the roots and establishment of auxin maxima. Our results indicate that RAB5 plays distinctive pivotal roles in the development of plants.

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RHD3 Dynamin-Like GTPases Mediates Homotypic Endoplasmic Reticulum Fusion and Is Essential for Arabidopsis Development

RHD3 Dynamin-Like GTPases Mediates Homotypic Endoplasmic Reticulum Fusion and Is Essential for Arabidopsis Development | Plant Gene Seeker -PGS | Scoop.it
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In all eukaryotic cells, the endoplasmic reticulum (ER) forms a tubular network whose generation requires the fusion of ER membranes. In Arabidopsis (Arabidopsis thaliana), the membrane-bound GTPase ROOT HAIR DEFECTIVE3 (RHD3) is a potential candidate to mediate ER fusion. In addition, Arabidopsis has two tissue-specific isoforms of RHD3, namely RHD3-like (RL) proteins, and their function is not clear. Here, we show that a null allele of RHD3, rhd3-8, causes growth defects and shortened root hairs. A point mutant, rhd3-1, exhibits a more severe growth phenotype than the null mutant, likely because it exerts a dominant-negative effect on the RL proteins. Genetic analysis reveals that the double deletion of RHD3 and RL1 is lethal and that the rhd3 rl2 plants produce no viable pollen, suggesting that the RL proteins are redundant to RHD3. RHD3 family proteins can replace Sey1p, the homolog of RHD3 in yeast (Saccharomyces cerevisiae), in the maintenance of ER morphology, and they are able to fuse membranes both in vivo and in vitro. Our results suggest that RHD3 proteins mediate ER fusion and are essential for plant development and that the formation of the tubular ER network is of general physiological significance.

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Gray whale dies bringing us a message — with stomach full of plastic trash

Gray whale dies bringing us a message — with stomach full of plastic trash | Plant Gene Seeker -PGS | Scoop.it

Via Olgy Gary
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Jatropha curcas, a biofuel crop: Functional genomics for understanding metabolic pathways and genetic improvement - Maghuly - 2013 - Biotechnology Journal - Wiley Online Library

Jatropha curcas, a biofuel crop: Functional genomics for understanding metabolic pathways and genetic improvement - Maghuly - 2013 - Biotechnology Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Jatropha curcas is currently attracting much attention as an oilseed crop for biofuel, as Jatropha can grow under climate and soil conditions that are unsuitable for food production. However, little is known about Jatropha, and there are a number of challenges to be overcome. In fact, Jatropha has not really been domesticated; most of the Jatropha accessions are toxic, which renders the seedcake unsuitable for use as animal feed. The seeds of Jatropha contain high levels of polyunsaturated fatty acids, which negatively impact the biofuel quality. Fruiting of Jatropha is fairly continuous, thus increasing costs of harvesting. Therefore, before starting any improvement program using conventional or molecular breeding techniques, understanding gene function and the genome scale of Jatropha are prerequisites. This review presents currently available and relevant information on the latest technologies (genomics, transcriptomics, proteomics and metabolomics) to decipher important metabolic pathways within Jatropha, such as oil and toxin synthesis. Further, it discusses future directions for biotechnological approaches in Jatropha breeding and improvement.

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A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis - McHale - 2013 - The Plant Journal - Wiley Online Library

A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis - McHale - 2013 - The Plant Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

It is known that 22-nucleotide (nt) microRNAs (miRNAs) derived from asymmetric duplexes trigger phased small-interfering RNA (phasiRNA) production from complementary targets. Here we investigate the efficacy of 22-nt artificial miRNA (amiRNA)-mediated RNA silencing relative to conventional hairpin RNA (hpRNA) and 21-nt amiRNA-mediated RNA silencing. CHALCONE SYNTHASE (CHS) was selected as a target in Arabidopsis thaliana due to the obvious and non-lethal loss of anthocyanin accumulation upon widespread RNA silencing. Over-expression of CHS in the pap1-D background facilitated visual detection of both local and systemic RNA silencing. RNA silencing was initiated in leaf tissues from hpRNA and amiRNA plant expression vectors under the control of an Arabidopsis RuBisCo small subunit 1A promoter (SSU). In this system, hpRNA expression triggered CHS silencing in most leaf tissues but not in roots or seed coats. Similarly, 21-nt amiRNA expression from symmetric miRNA/miRNA* duplexes triggered CHS silencing in all leaf tissues but not in roots or seed coats. However, 22-nt amiRNA expression from an asymmetric duplex triggered CHS silencing in all tissues, including roots and seed coats, in the majority of plant lines. This widespread CHS silencing required RNA-DEPENDENT RNA POLYMERASE6-mediated accumulation of phasiRNAs from the endogenous CHS transcript. These results demonstrate the efficacy of asymmetric 22-nt amiRNA-directed RNA silencing and associated phasiRNA production and activity, in mediating widespread RNA silencing of an endogenous target gene. Asymmetric 22-nt amiRNA-directed RNA silencing requires little modification of existing amiRNA technology and is expected to be effective in suppressing other genes and/or members of gene families.

 
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NatRevMicrobiol: Microbial ecology of rhizosphere

NatRevMicrobiol: Microbial ecology of rhizosphere | Plant Gene Seeker -PGS | Scoop.it

Via Mary Williams, Jennifer Mach
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PNAS: Electron transfer precedes ATP hydrolysis during nitrogenase catalysis

PNAS: Electron transfer precedes ATP hydrolysis during nitrogenase catalysis | Plant Gene Seeker -PGS | Scoop.it

Chemistry's so useful for understanding biology...

Two PNAS papers dissecting the chemistry of this exciting enzyme, here; http://www.pnas.org/content/early/2013/09/18/1311218110.abstract

and here: http://www.pnas.org/content/early/2013/09/20/1315852110.abstract

and a press release here: http://www.usu.edu/ust/index.cfm?article=52663

 

 


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Auxin: special! Journal of Experimental Botany

Auxin: special! Journal of Experimental Botany | Plant Gene Seeker -PGS | Scoop.it
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Auxin: special!

We are delighted that the Journal of Experimental Botany has provided this podium to summarize recent advances in the field of auxin biology. Highlights including the simplified view of the main biosynthetic pathway for indole acetic acid (IAA; Mashiguchi et al., 2011; Dai et al., 2013) and the growing insights into non-transcriptional auxin signalling (Chen et al., 2012; Lin et al., 2012) are reflected in these reviews leading to a state-of-the-art account of this vivacious part of plant biology. Several of the reviews address a particular developmental pathway to integrate the known aspects of auxin biology – synthesis, metabolism, transport, and signalling – into a developmental context. The research article by Peer et al. emphasizes the renewed interest in reactive oxygen species (ROS) as a regulator of auxin signalling.

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Integration of epigenetic and genetic controls of seed size by cytokinin in Arabidopsis

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The development of seeds in flowering plants is placed under complex interactions between maternal tissues, the embryo, and the endosperm. The endosperm plays a major role in the regulation of seed size. In Arabidopsis thaliana, endosperm size depends on the coordination of the genetic pathway HAIKU (IKU) with epigenetic controls comprising genome dosage, DNA methylation, and trimethylated lysine 27 on histone H3 (H3K27me3) deposition. However, the effectors that integrate these pathways have remained unknown. Here, we identify a target of the IKU pathway, the cytokinin oxidase CKX2, that affects cytokinin signaling. CKX2 expression is activated by the IKU transcription factor WRKY10 directly and promotes endosperm growth. CKX2 expression also depends on H3K27me3 deposition, which fluctuates in response to maternal genome dosage imbalance and DNA demethylation of male gametes. Hence, the control of endosperm growth by CKX2 integrates genetic and epigenetic regulations. In angiosperms, cytokinins are highly active in endosperm, and we propose that IKU effectors coordinate environmental and physiological factors, resulting in modulation of seed size.

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Soybeans, Poverty and Inequality in the Brazilian Amazon - Weinhold &al (2013) - World Development

Soybeans, Poverty and Inequality in the Brazilian Amazon - Weinhold &al (2013) - World Development | Plant Gene Seeker -PGS | Scoop.it

Using a mixed-method approach of econometric and ethnographic field research, this article examines the social and economic costs and benefits of increases in soybean production in the Brazilian Amazon. Statistical analysis suggests that increased soy production both reduces poverty indicators and raises median rural incomes, but is also associated with increased measures of inequality.

 

Since the 1960s, Brazil’s national and regional governments have invested large sums in the development of soybean production… Soybean products are currently one of Brazil’s most valuable agricultural exports, and a key component of the nation’s continued economic development… Observers, however, remain divided about the social and environmental effects of this development. On one side many researchers fear that the large scale of this plantation crop will both increase deforestation and displace small farmers, increasing inequality and poverty… Other researchers, however, argue that most new soybean production takes place on land converted from pasture, rather than from forest, and that the growth of supporting enterprises that accompany large soybean production creates jobs and reduces poverty…

 

While all interlocutors are aware that any decisions concerning Brazil’s economic and developmental future and its land use involve trade-offs between economic, social, political, and environmental outcomes, the debate at all levels of society can be extremely impassioned. These arguments are often played out in public forums both in the areas most directly affected by soybean expansion as well as at the governmental level and in the national and international media, and this domestic political debate has had real consequences in the pattern of Brazilian agricultural expansion.

 

Thus an understanding of the economic consequences of particular agricultural land use patterns is incomplete without a complementary understanding of how that land use pattern impacts the political discourse. This article contributes to this debate by focussing on the socio-economic impacts of soy cultivation in the Amazon… This article thus presents new empirical evidence on the relationship between soy expansion and poverty.

 

However, we seek not only to measure the impact of the introduction of soy production on socio-economic outcomes, but also to better understand the political impact of this new development and the sources of some of the bitter local debates that surround the issue. In the process we attempt to reconcile the results of the statistical work with the political debate on the ground; to the extent that we find robust evidence that soy production does not increase poverty… how can we explain the continuing strong local political resistance to soy cultivation on the grounds of its socio-economic impact? Thus we combine an econometric analysis of the data with qualitative fieldwork to identify how the economic impacts of soy link to the continued political debates over its impact…

 

The need for such work is particularly important given the numerous criticisms of the soybean industry made by many researchers, activists, and local populations. The main emphasis here has been on the argument that the large scale of this plantation displaces small farmers, increasing inequality and poverty and, in turn, pushes such individuals to claim new land, often through deforestation…

 

The basic premise of this argument is that large-scale mechanized agriculture uses less labor per hectare than small-scale farming techniques… However others have argued that this kind of reasoning misses the dynamic argument that, in the long run, large scale mechanized agriculture increases overall productivity and avoids vicious cycles of rural poverty and population growth associated with low productivity smallholdings and deforestation.

 

In addition, wealth generated by large-scale soybean farms adds not only to both regional economies and government revenues but also to the growth of supporting enterprises that, in turn, creates jobs and reduces poverty all over the nation. It can also be argued that the associated increased investment in infrastructure also contributes to general, local welfare. It has also been suggested that the expansion of agriculture, the use of modern technology and the resulting productivity gains, result in the diversification of local economies…

 

The important point for the current article is that although there is a widespread belief among the public and NGOs about the negative effects of soy, empirical analysis is lacking on both sides of the debate. Here we make use of a large panel data set on agricultural and economic variables to address the question of the socio-economic impact of soy. We further complement and augment our econometric analysis with ethnographic fieldwork in a region which has recently undergone a large increase in soy production, interviewing local residents, policy makers, and other relevant actors about their views on the impact of soy cultivation. These qualitative findings shed light on why and how changing local land use patterns shape perceptions and drive significant political debates in ways that may seem at odds with the statistical results…

 

Given the relatively robust econometric finding of significant economic growth effects of soy, the existence of relatively strong local political resistance… in some areas raises some interesting questions… from both an econometric as well as a policy perspective, it would be useful to better understand the source of the beliefs and political debates surrounding the soy boom in the Amazon. To that end, in parallel with our quantitative research, we conducted qualitative fieldwork in areas of soy production in the Brazilian Amazon…

 

Differences are noted and often commented on by members of both groups in the region. More than physical distinctions, individuals tend to emphasize the cultural differences that exist in the working and social practices of the two groups. One focus is on the distinctions between homes and living styles. While local populations tend to have smaller houses and spend more time sitting outside them in their surrounding grounds, immigrants from the south bring a particular style of large house, with surrounding verandas that provide privacy from the outside. Members of older local populations portray themselves as very sociable in comparison to the more recent arrivals from Brazil’s southern states. However people from the South tend to portray such sociability as a form of laziness that they contrast with their own work ethic…

 

As our quantitative analysis shows the rise of median incomes and local GDP associated with soybean production and, most importantly, a lowering of poverty levels, it also supports the view that increased soy production increases inequality. This result is consistent with our qualitative observations that soybean production in Legal Amazonia is mostly controlled by wealthy landowners on large farms. Thus, even as all levels of local populations benefit economically from the growth of soybean production, large landowners accrue, or are perceived to accrue, relatively more gains… it appears that it is local perceptions of this growing inequality that fuel much of the long term opposition to the increase in large-scale soy farming… the emphasis on inequality is linked to other social and political factors, and in particular the fact that most large-scale farmers are immigrants to the region.. these tensions help to explain some of the continued animosity felt toward soybean cultivation even as its appears to have the effect of lowering poverty levels…

 

In this article we have provided both quantitative and qualitative evidence rejecting the hypothesis that the introduction of soy into the Amazon has increased poverty. On the contrary, our evidence is suggestive of poverty reducing effects, and strongly indicative of positive income gains. We… find that increases in soy cultivation are associated with strong increases in rural median household income and rural and urban GDP per capita. Both the quantitative evidence as well as ethnographic fieldwork also point to an association between increased soy production and inequality… to ethnic differences between large soy farmers and local populations that raise long standing prejudices and tensions… A significant portion of the negative publicity and local beliefs about soy held by a subset of the population can be traced to this perceived (and actual) unequal gains of soy expansion between different ethnic groups with historical rivalries…

 

http://dx.doi.org/10.1016/j.worlddev.2012.11.016


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Alexander J. Stein's curator insight, September 15, 2013 7:55 PM

An interesting article, not least because of its contribution to the ongoing discussion on how smallholder farming and large-scale agriculture can contribute to poverty alleviation. It is well worth to be read in its entirety. (Unfortunately it is behind a pay-wall.) 

 

What is also interesting is that the study confirms that absolute poverty (or income growth) only matters to some extent for people's overal satisfaction and contentment and that inequality (or income distribution) is also an important determinant of social welfare and social peace. 

 

I found it a bit surprising, though, that the authors did not mention that most soybeans in Brazil are genetically modified and that this is probably one of the motivations why there was a "demonstration organized by Greenpeace against soybean farming" or that this may have been a driver behind the "publicity generating tactics of confrontation used by the international environmental NGO Greenpeace". Therefore, while the authors very nicely analyse the cultural differences between ethnic groups and their historical rivalries, perhaps they could have done more to elaborate on the influence of such global interest groups and their role in social conflicts. 

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Cell - The Regulation of Cell Size

Cell - The Regulation of Cell Size | Plant Gene Seeker -PGS | Scoop.it
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An adult animal consists of cells of vastly different size and activity, but the regulation of cell size remains poorly understood. Recent studies uncovering some of the signaling pathways important for size/growth control, together with the identification of diseases resulting from aberrations in these pathways, have renewed interest in this field. This Review will discuss our current understanding of how a cell sets its size, how it can adapt its size to a changing environment, and how these processes are relevant to human disease.

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Accumulation of anthocyanins in tomato skin extends shelf life - Bassolino - 2013 - New Phytologist - Wiley Online Library

Accumulation of anthocyanins in tomato skin extends shelf life - Bassolino - 2013 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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SummaryShelf life is one of the most important traits for the tomato (Solanum lycopersicum) industry. Two key factors, post-harvest over-ripening and susceptibility to post-harvest pathogen infection, determine tomato shelf life.Anthocyanins accumulate in the skin of Aft/Aft atv/atv tomatoes, the result of introgressing alleles affecting anthocyanin biosynthesis in fruit from two wild relatives of tomato, which results in extended fruit shelf life. Compared with ordinary, anthocyanin-less tomatoes, the fruits of Aft/Aft atv/atv keep longer during storage and are less susceptible to Botrytis cinerea, a major tomato pathogen, post-harvest.Using genetically modified tomatoes over-producing anthocyanins, we confirmed that skin-specific accumulation of anthocyanins in tomato is sufficient to reduce the susceptibility of fruit to Botrytis cinerea.Our data indicate that accumulation of anthocyanins in tomato fruit, achieved either by traditional breeding or genetic engineering can be an effective way to extend tomato shelf life.
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Violet/Blue Chrysanthemums—Metabolic Engineering of the Anthocyanin Biosynthetic Pathway Results in Novel Petal Colors

Violet/Blue Chrysanthemums—Metabolic Engineering of the Anthocyanin Biosynthetic Pathway Results in Novel Petal Colors | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Chrysanthemums (Chrysanthemum×morifolium Ramat.) are an important cut-flower and potted plant crop in the horticultural industry world wide. Chrysanthemums express the flavonoid 3′-hydroxylase (F3′H) gene and thus accumulate anthocyanins derived from cyanidin in their inflorescences which appear pink/red. Delphinidin-based anthocyanins are lacking due to the deficiency of a flavonoid 3′, 5′-hydroxylase (F3′5′H), and so violet/blue chrysanthemum flower colors are not found. In this study, together with optimization of transgene expression and selection of the host cultivars and gene source, F3′5′H genes have been successfully utilized to produce transgenic bluish chrysanthemums that accumulate delphinidin-based anthocyanins. HPLC analysis and feeding experiments with a delphinidin precursor identified 16 cultivars of chrysanthemums out of 75 that were predicted to turn bluish upon delphinidin accumulation. A selection of eight cultivars were successfully transformed with F3′5′H genes under the control of different promoters. A pansy F3′5′H gene under the control of a chalcone synthase promoter fragment from rose resulted in the effective diversion of the anthocyanin pathway to produce delphinidin in transgenic chrysanthemum flower petals. The resultant petal color was bluish, with 40% of total anthocyanidins attributed to delphinidin. Increased delphinidin levels (up to 80%) were further achieved by hairpin RNA interference-mediated silencing of the endogenous F3′H gene. The resulting petal colors were novel bluish hues, not possible by hybridization breeding. This is the first report of the production of anthocyanins derived from delphinidin in chrysanthemum petals leading to novel flower color.


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Andres Zurita's comment, October 12, 2013 10:24 AM
U welcome!
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Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach - Falchi - 2013 - The Plant Journal - Wiley Online Library

Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach - Falchi - 2013 - The Plant Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Peach flesh color (white or yellow) is among the most popular commercial criteria for peach classification, and has implications for consumer acceptance and fruit nutritional quality. Despite the increasing interest in improving cultivars of both flesh types, little is known about the genetic basis for the carotenoid content diversity in peach. Here we describe the association between genotypes at a locus encoding the carotenoid cleavage dioxygenase 4 (PpCCD4), localized in pseudomolecule 1 of the Prunus persica reference genome sequence, and the flesh color for 37 peach varieties, including two somatic revertants, and three ancestral relatives of peach, providing definitive evidence that this locus is responsible for flesh color phenotype. We show that yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions, and that these mutations, despite being located within the transcribed portion of the gene, also result in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a gene for which humans, in their quest to diversify phenotypic appearance and qualitative characteristics of a fruit, have been able to select and exploit multiple mutations resulting from a variety of mechanisms.


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Plant Physiol. Focus Issue: Calcium signaling

Plant Physiol. Focus Issue: Calcium signaling | Plant Gene Seeker -PGS | Scoop.it

Want to talk about calcium signaling? Of course you do! It's important in the regulation of stomatal aperture, stress response, interactions with microbes etc.

Check out the focus issue of Plant Physiology on calcium signalling - lots of uptakes, reviews and new research, with an overview by Alex Webb here: www.plantphysiol.org/content/163/2/457.full.html


Via Mary Williams
Andres Zurita's insight:

Great Issue with several interesting topics, and free acce$$

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The academic jungle: ecosystem modelling reveals why women are driven out of research - O’Brien - 2012 - Oikos - Wiley Online Library

The academic jungle: ecosystem modelling reveals why women are driven out of research - O’Brien - 2012 - Oikos - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The number of women studying science and engineering at undergraduate and postgraduate levels has increased markedly in recent decades. However females have lower retention rates than males in these fields, and perform worse on average than men in terms of promotion and common research metrics. Two key differences between men and women are the larger role that women play in childcare and house work in most families, and the narrower window for female fertility. Here we explore how these two factors affect research output by applying a common ecological model to research performance, incorporating part-time work and the duration of career prior to the onset of part-time work. The model parameterizes the positive feedback between historical research output (i.e. track record) and current output, and the minimum threshold below which research output declines. We use the model to provide insight into how women (and men) can pursue a career in academia while working part-time and devoting substantial time to their family. The model suggests that researchers entering a tenure track (teaching and research) role part-time without an established track record in research will spend longer in the early career phase compared to full-time academics, researchers without teaching commitments, and those who were beyond the early career phase prior to working part-time. The results explain some of the mechanisms behind the observed difference between male and female performance in common metrics and the higher participation of women in teaching-focussed roles. Based on this analysis, we provide strategies for researchers (particularly women) who want to devote substantial time to raising their families while still remaining engaged with their profession. We also identify how university leaders can enable part-time academics to flourish rather than flounder. In particular, we demonstrate that careless application of metrics is likely to further reduce female participation in research, and so reduce the pool of talent available.

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Comparative Transcriptomic Analysis of Salt Adaptation in Roots of Contrasting Medicago truncatula Genotypes

Comparative Transcriptomic Analysis of Salt Adaptation in Roots of Contrasting Medicago truncatula Genotypes | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Evolutionary diversity can be driven by the interaction of plants with different environments. Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools. Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants. We analyzed in the Medicago truncatula legume the root transcriptome of two genotypes having contrasting responses to salt stress: TN1.11, sampled in a salty Tunisian soil, and the reference Jemalong A17 genotype. TN1.11 plants show increased root growth under salt stress as well as a differential accumulation of sodium ions when compared to A17. Transcriptomic analysis revealed specific gene clusters preferentially regulated by salt in root apices of TN1.11, notably those related to the auxin pathway and to changes in histone variant isoforms. Many genes encoding transcription factors (TFs) were also differentially regulated between the two genotypes in response to salt. Among those selected for functional studies, overexpression in roots of the A17 genotype of the bHLH-type TF most differentially regulated between genotypes improved significantly root growth under salt stress. Despite the global complexity of the differential transcriptional responses, we propose that an increase in this bHLH TF expression may be linked to the adaptation of M. truncatula to saline soil environments.

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PNAS: Leaf-galling phylloxera on grapes reprograms host metabolism and morphology (2013)

PNAS: Leaf-galling phylloxera on grapes reprograms host metabolism and morphology (2013) | Plant Gene Seeker -PGS | Scoop.it

Some herbivorous insects induce galls, abnormal structures, in their host plants, benefiting the gall-forming parasite by providing nutritive tissue. The gall-forming insect phylloxera induces stomata, openings through which plants regulate water and CO2, on the upper surface of grape leaves where they typically do not occur. Carbon uptake and transpiration by induced stomata facilitate nutrient acquisition by gall tissue and phylloxera. Moreover, gall formation reprograms the host-leaf transcriptome to increase transcripts associated with sucrose mobilization and glycolysis and decrease defense-related transcripts. Thus, stomata induction by phylloxera reconfigures leaves to increase carbon gain, to partially offset negative impacts of gall formation.


Via Kamoun Lab @ TSL, Jennifer Mach
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Plant Cell: An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium Homeostasis

Plant Cell: An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium Homeostasis | Plant Gene Seeker -PGS | Scoop.it

The soil salinity tolerance of an Arabidopsis mutant is shown to be caused by a mutation in the ETO1 gene that results in ethylene overproduction. Increased ethylene causes root stele reactive oxygen species (ROS)–dependent reductions in root Na influx and xylem loading and stelar ROS-independent enhancement of root K status, thus improving plant Na/K homeostasis and salinity tolerance.

 

See also the In Brief about this article: www.plantcell.org/content/early/2013/09/22/tpc.113.250911.full.pdf


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Nature Outlook : Agriculture and Drought

Nature Outlook : Agriculture and Drought | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Climate change means the coming decades are likely to bring more frequent episodes of severe drought, with potentially devastating impact on the world's ability to feed a growing population. We therefore need a sustainable agricultural system that makes the most efficient use of water and reduces expensive and environmentally challenging inputs such as fertilizer and pesticides.

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Role of NINJA in root jasmonate signaling

Andres Zurita's insight:

Plant growth, the basis of agricultural production, is compromised when plants defend themselves against herbivores.Wound-induced growth reduction is coordinated between organs by hormones termed “jasmonates.” We developed a sensitive assay that marks tissues where wounding activates jasmonate function in seedlings. This assay showed that a key repressor of jasmonate responses is active mainly in roots where it permits normal growth. A deeper understanding of cell-size control is crucial in successfully engineering plants that display reduced growth restriction under stress.

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A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis

A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.

 

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Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013)

Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013) | Plant Gene Seeker -PGS | Scoop.it

Do you think only 'Monsanto' (or any multi-national seed company) has the capacity to develop transgenic crops? The answer is a clear 'no'. Indian scientists, working with public sector research institutions and universities, too have developed many genetically engineered varieties which, in fact, could not move beyond lab or 'restricted' trials... 

Indian scientists have over the years developed more than 200 genetically modified (GM) varieties of as many as 15 crops including cotton, brinjal, castor, groundnut, mustard, papaya, potato, rice, rubber, sugarcane, wheat and tomato. These varieties... have all the traits — resistance to insect, fungal, drought and virus — which may bring them in the league of Bt cotton by increasing productivity and export earnings. 

Indigenous transgenic varieties include a high salt-tolerant rice which can grow in salty water near coast. This variety is developed using genes of mangrove. Similarly, Indian scientists have developed a tomato variety having shelf life of over 50 days. The farmers will, however, reap the benefit of these findings only when government allows the scientists to go for extensive field trials and eventually for commercial production... 

 

A green signal to commercial production of such crops will affect the Indian farmers due to monopolistic control of seed business by multi-national companies (MNCs). "The solution to this problem is to encourage competition among the GM seed companies and even more importantly to have mission-mode programmes for the development of genetically modified seeds in the public sector", said N K Singh, professor at National Research Centre on Plant Biotechnology... "The Seed Act and the Monopoly and Restrictive Trade Practices Act should be used effectively to ensure competition and control of seed prices in addition to the bio-safety". 

It is true that the MNCs are far ahead in the development of GM crop varieties due to heavy investment and focused attempts by the companies. But, Indian research data show that the public sector transgenic crops can compete if allowed to grow. Expressing his confidence over what the Indian scientists have developed over the years, Asis Datta, former vice-chancellor of Jawaharlal Nehru University, said, "GM crop is going to be an essential part of our life today or tomorrow. If we don't realize it now, it will only push the country back. It will be difficult to recover later due to intense global competition"... 


Via Alexander J. Stein
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