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Bringing light in the discussion about GMOs? – A rather long reading list

These days I received an apparently easy request: “Do you have any recommendations for reading about the debate on GMOs? I think there is a lot of heat, but too little light in the discussion; I trust you can send me some…” To which I answered carelessly: “Sure, I will look into it, select a few references and post them…” 

 

I thought I’d have a quick look into my collection of bookmarks and references and post some of the links to satisfy the request. Obviously there would be too many individual studies and crop-specific or country-specific reports, but focusing only (i) on what was published over the last couple of years, (ii) on sources where all this information was already aggregated (literature reviews, meta-analyses, authoritative statements, FAQs, etc.), and (iii) on academic or publicly funded sources should produce a fairly concise list, I thought.

 

While not unmanageable, the list has become quite long. To get a rough idea of the current state of knowledge, it may be sufficient to peruse the first 1-2 (starred *) references under each heading, and to have a quick look at the abstracts and summaries of some of the others. (Given the controversy surrounding this topic I didn’t want to suggest just one or two sources, but to show a bit the width of the scientific consensus, and to offer some titbits of related information.) ... 

http://ajstein.tumblr.com/post/40504136918/ ;


Via Alexander J. Stein
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Jennifer Mach's comment, March 30, 2013 9:05 AM
I admit I haven't read this list... but for future reference, I'll definitely have a look.
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Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response: Developmental Cell

Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response: Developmental Cell | plant cell genetics | Scoop.it
Highlights

•tasiRNAs have an ancestral role in tuning the auxin response via repressor ARFs
•tasiRNAs promote sensitivity and robustness of the auxin response
•tasiRNAs allow for stochastic cell fate determination and environmental plasticity
•Network properties lent to the auxin response may underlie repeated tasiRNA cooption

Summary

Novel developmental programs often evolve via cooption of existing genetic networks. To understand this process, we explored cooption of the TAS3 tasiRNA pathway in the moss Physcomitrella patens. We find an ancestral function for this repeatedly redeployed pathway in the spatial regulation of a conserved set of Auxin Response Factors. In moss, this results in stochastic patterning of the filamentous protonemal tissue. Through modeling and experimentation, we demonstrate that tasiRNA regulation confers sensitivity and robustness onto the auxin response. Increased auxin sensitivity parallels increased developmental sensitivity to nitrogen, a key environmental signal. We propose that the properties lent to the auxin response network, along with the ability to stochastically modulate development in response to environmental cues, have contributed to repeated cooption of the tasiRNA-ARF module during evolution. The signaling properties of a genetic network, and not just its developmental output, are thus critical to understanding evolution of multicellular forms.
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Frontiers | Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus | Plant Biotechnology

Frontiers | Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus | Plant Biotechnology | plant cell genetics | Scoop.it
Betalains have high nutritional value and bioactivities. Red pulp pitaya (Hylocereus polyrhizus) is the only fruit containing abundant betalains for consumer. However, no information is available about genes involved in betalain biosynthesis in H. polyrhizus. Herein, two cDNA libraries of pitaya pulps with two different coloration stages (white and red pulp stages) of Guanhuahong (H. polyrhizus) were constructed. A total of about 12 Gb raw RNA-Seq data was generated and was de novo assembled into 122,677 transcripts with an average length of 1,183 bp and an N50 value of 2008. Approximately 99.99% of all transcripts were annotated based on seven public databases. A total of 8,871 transcripts were significantly regulated. Thirty-three candidate transcripts related to betalain biosynthesis were obtained from the transcriptome data. Transcripts encoding enzymes involved in betalain biosynthesis were analyzed using RT-qPCR at the whole pulp coloration stages of H. Polyrhizus (7-1) and H. Undatus (132-4). Nine key transcripts of betalain biosynthesis were identified. They were assigned to four kinds of genes in betalain biosynthetic pathway, including tyrosinase, 4, 5-DOPA dioxygenase extradiol, cytochrome P450 and glucosyltransferase. Ultimately, a preliminary betalain biosynthetic pathway for pitaya was proposed based on betalain analyses and gene expression profiles.
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PpASCL, the Physcomitrella patens Anther-Specific Chalcone Synthase-Like Enzyme Implicated in Sporopollenin Biosynthesis, Is Needed for Integrity of the Moss Spore Wall and Spore Viability

PpASCL, the Physcomitrella patens Anther-Specific Chalcone Synthase-Like Enzyme Implicated in Sporopollenin Biosynthesis, Is Needed for Integrity of the Moss Spore Wall and Spore Viability | plant cell genetics | Scoop.it
Sporopollenin is the main constituent of the exine layer of spore and pollen walls. The anther-specific chalcone synthase-like (ASCL) enzyme of Physcomitrella patens, PpASCL, has previously been implicated in the biosynthesis of sporopollenin, the main ...
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Determination of some minerals and β-carotene contents in aromatic indica rice (Oryza sativa L.) germplasm

Determination of some minerals and β-carotene contents in aromatic indica rice (Oryza sativa L.) germplasm | plant cell genetics | Scoop.it
39 aromatic indica rice (Oryza sativa L.) cultivars were characterized for Iron, Zinc, Calcium, Magnesium, Copper and β-carotene contents. The β-carotene contents were ranging from 1.23 to 9.9 μg/g in brown and 0.08 to 1.99 μg/g in milled rice. Among the mineral contents, Magnesium was found ranging from 855 μg/g (Gham) to maximum of 1636 μg/g (Badshahbhog) followed by Iron in 32 μg/g (Jirga) to 218 μg/g (Kalsal), Copper content from 2 μg/g (Girga) to 1004 μg/g (Gham), Zinc content from 25 (Gham) to 165 μg/g (Ambemohar-157) and Calcium ranged from 14 μg/g (Ambemohar pandhara) to 67 μg/g (Kate chinoor). The study showed that the germplasm assessed is a good source of micronutrients and can be further exploited in breeding programme.
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Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew | plant cell genetics | Scoop.it
Sequence-specific nucleases have been applied to engineer targeted modifications in polyploid genomes1, but simultaneous modification of multiple homoeoalleles has not been reported. Here we use transcription activator–like effector nuclease (TALEN)2, 3 and clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (refs. 4,5) technologies in hexaploid bread wheat to introduce targeted mutations in the three homoeoalleles that encode MILDEW-RESISTANCE LOCUS (MLO) proteins6. Genetic redundancy has prevented evaluation of whether mutation of all three MLO alleles in bread wheat might confer resistance to powdery mildew, a trait not found in natural populations7. We show that TALEN-induced mutation of all three TaMLO homoeologs in the same plant confers heritable broad-spectrum resistance to powdery mildew. We further use CRISPR-Cas9 technology to generate transgenic wheat plants that carry mutations in the TaMLO-A1 allele. We also demonstrate the feasibility of engineering targeted DNA insertion in bread wheat through nonhomologous end joining of the double-strand breaks caused by TALENs. Our findings provide a methodological framework to improve polyploid crops.
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Long-term toxicity study on genetically modified corn with cry1Ac gene in a Wuzhishan miniature pig model - Chen &al (2016) - J Sci Food Ag

Long-term toxicity study on genetically modified corn with cry1Ac gene in a Wuzhishan miniature pig model - Chen &al (2016) - J Sci Food Ag | plant cell genetics | Scoop.it

The objective of the present study was to investigate the chronic effect of transgenic maize lines by the insertion of the cry1Ac gene from Bacillus thuringiensis (Bt) on the growth performance, immune response and health using a Wuzhishan miniature pig model through a 196-day feeding study... 

Pigs were randomly assigned one of the diets containing 65% non-transgenic isogenic corn or Bt corn at three stages of growth (day 0~69, 70~134 and 135~196). The potential toxicological effects of transgenic corn on pigs were explored... 


Long-term feeding Bt corn carrying cry1Ac genes to Wuzhishan miniature pigs did not indicate adverse effects on the growth, immune response and health indicators at any stages of growth. 

 

http://dx.doi.org/10.1002/jsfa.7624

 


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Fatty acids from GM oilseed crops could replace fish oil - UEA (2016)

Fatty acids from GM oilseed crops could replace fish oil - UEA (2016) | plant cell genetics | Scoop.it
Oil from genetically modified (GM) oil seed crops could replace fish oil as a primary source of the beneficial Omega 3 fatty acid EPA... 
 

Researchers studied the effect in mice of consuming feed enriched with oil from... genetically engineered Camelina sativa, developed at the agricultural science centre Rothamsted Research. The goal of the research was to discover whether mammals... can absorb and accumulate EPA from this novel source of omega-3s... The results show that the benefits were similar to those derived from fish oils.

 

The long chain omega-3 polyunsaturated fatty acids EPA and DHA are beneficial for cardiovascular and cognitive health, as well as for foetal development in pregnancy. The recommended minimum dietary intake can be achieved by eating one to two portions of oily fish per week. But for everyone in the world to achieve their minimum dietary intake, you would need around 1.3 million metric tonnes of fish oil per year... there is a large deficit between supply and demand. There is a great need to identify alternative and sustainable sources of these beneficial fatty acids... 

 

The mice were fed with a control diet similar to a Westernised human diet, supplemented with EPA from genetically engineered Camelina sativa or fish oil, for ten weeks – enough time for any beneficial results to be seen. We found that the genetically engineered oil is a bioavailable source of EPA, with comparable benefits for the liver to eating oily fish. 

 

https://www.uea.ac.uk/about/-/fatty-acids-from-gm-oilseed-crops-could-replace-fish-oil

 

Original article:  http://jn.nutrition.org/content/early/2016/01/20/jn.115.223941

 


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Alexander J. Stein's curator insight, January 21, 1:44 PM

Also good news for vegetarians. 

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A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction

A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction | plant cell genetics | Scoop.it
In the moss Physcomitrella patens, a single gene called BELL1 can trigger the gametophyte-to-sporophyte transition, and induce embryogenesis and asexual reproduction without fertilization.
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Pierre-Marc Delaux's curator insight, January 19, 4:21 AM

Really amazing oO

Jennifer Mach's curator insight, January 20, 9:37 AM

I wanted a bit more in the title... maybe 

"A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction in Physcomitrella patens "

#title

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Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice : Nature : Nature Publishing Group

Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice : Nature : Nature Publishing Group | plant cell genetics | Scoop.it
Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times1, 2. Rice paddies are the largest anthropogenic methane source and produce 7–17% of atmospheric methane2, 3. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25–100-million tonnes3, 4. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades4. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement5. Despite proposed strategies to increase rice productivity and reduce methane emissions4, 6, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies
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Plants and climate change: complexities and surprises

Plants and climate change: complexities and surprises | plant cell genetics | Scoop.it
We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime's C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made.
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PLOS Pathogens: Worse Comes to Worst: Bananas and Panama Disease—When Plant and Pathogen Clones Meet

PLOS Pathogens: Worse Comes to Worst: Bananas and Panama Disease—When Plant and Pathogen Clones Meet | plant cell genetics | Scoop.it
RT @hyphaltip: Plant pathology & plant breeding matter! Fusarium oxysporum f.sp. cubense & loss of bananas https://t.co/z2BQMjKfSN https://…
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Genome-wide expression analysis offers new insights into the origin and evolution of
Physcomitrella patens stress response

Genome-wide expression analysis offers new insights into the origin and evolution of<br/>                Physcomitrella patens stress response | plant cell genetics | Scoop.it
Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants, and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought, and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.
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Opportunities for Products of New Plant Breeding Techniques

Opportunities for Products of New Plant Breeding Techniques | plant cell genetics | Scoop.it
Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.
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Betalains, Phenols and Antioxidant Capacity in Cactus Pear [Opuntia ficus-indica (L.) Mill.] Fruits from Apulia (South Italy) Genotypes

Betalains, Phenols and Antioxidant Capacity in Cactus Pear [Opuntia ficus-indica (L.) Mill.] Fruits from Apulia  (South Italy) Genotypes | plant cell genetics | Scoop.it
Betacyanin (betanin), total phenolics, vitamin C and antioxidant capacity (by Trolox-equivalent antioxidant capacity (TEAC) and oxygen radical absorbance capacity (ORAC) assays) were investigated in two differently colored cactus pear (Opuntia ficus-indica (L.) Mill.) genotypes, one with purple fruit and the other with orange fruit, from the Salento area, in Apulia (South Italy). In order to quantitate betanin in cactus pear fruit extracts (which is difficult by HPLC because of the presence of two isomers, betanin and isobetanin, and the lack of commercial standard with high purity), betanin was purified from Amaranthus retroflexus inflorescence, characterized by the presence of a single isomer. The purple cactus pear variety showed very high betanin content, with higher levels of phenolics, vitamin C, and antioxidant capacity (TEAC) than the orange variety. These findings confirm the potential for exploiting the autochthonous biodiversity of cactus pear fruits. In particular, the purple variety could be an interesting source of colored bioactive compounds which not only have coloring potential, but are also an excellent source of dietary antioxidant components which may have beneficial effects on consumers’ health.
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Life at the boundary: photosynthesis at the soil–fluid interface. A synthesis focusing on mosses

Life at the boundary: photosynthesis at the soil–fluid interface. A synthesis focusing on mosses | plant cell genetics | Scoop.it
Mosses are among the earliest branching embryophytes and probably originated not later than the early Ordovician when atmospheric CO2 was higher and O2 was lower than today. The C3 biochemistry and physiology of their photosynthesis suggests, by analogy with tracheophytes, that growth of extant bryophytes in high CO2 approximating Ordovician values would increase the growth rate. This occurs for many mosses, including Physcomitrella patens in suspension culture, although recently published transcriptomic data on this species at high CO2 and present-day CO2 show down-regulation of the transcription of several genes related to photosynthesis. It would be useful if transcriptomic (and proteomic) data comparing growth conditions are linked to measurements of growth and physiology on the same, or parallel, cultures. Mosses (like later-originating embryophytes) have been subject to changes in bulk atmospheric CO2 and O2 throughout their existence, with evidence, albeit limited, for positive selection of moss Rubisco. Extant mosses are subject to a large range of CO2 and O2 concentrations in their immediate environments, especially aquatic mosses, and mosses are particularly influenced by CO2 generated by, and O2 consumed by, soil chemoorganotrophy from organic C produced by tracheophytes (if present) and bryophytes.
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Development of a novel-type transgenic cotton plant for control of cotton bollworm - Yue &al (2016) - Plant Biotechnol J

Development of a novel-type transgenic cotton plant for control of cotton bollworm - Yue &al (2016) - Plant Biotechnol J | plant cell genetics | Scoop.it

Transgenic Bt cotton... has been widely planted throughout the world for the control of cotton budworm (Helicoverpa armigera). However, a shift towards insect tolerance of Bt cotton is now apparent. In this study, the gene encoding neuropeptide F (NPF) was cloned from cotton budworm... The npf gene produces two splicing mRNA variants – npf1 and npf2. These are predicted to form the mature NPF1 and NPF2 peptides, and they were found to regulate feeding behaviour.

 

Knock down of larval npf with dsNPF in vitro resulted in decreases of food consumption and body weight, and dsNPF also caused a decrease of glycogen and an increase of trehalose... We produced... transgenic cotton plants with stably expressed dsNPF. Results showed that H. armigera larvae fed on these transgenic plants or leaves had lower food consumption, body size and body weight compared to controls. These results indicate that NPF is important in the control of feeding of H. armigera and valuable for production of potential transgenic cotton. 

 

http://dx.doi.org/10.1111/pbi.12534

 


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How can higher-yield farming help to spare nature?

How can higher-yield farming help to spare nature? | plant cell genetics | Scoop.it
Expansion of land area used for agriculture is a leading cause of biodiversity loss and greenhouse gas emissions, particularly in the tropics. One potential way to reduce these impacts is to increase food production per unit area (yield) on existing farmland, so as to minimize farmland area and to spare land for habitat conservation or restoration. There is now widespread evidence that such a strategy could benefit a large proportion of wild species, provided that spared land is conserved as natural habitat (1). However, the scope for yield growth to spare land by lowering food prices and, hence, incentives for clearance (“passive” land sparing) can be undermined if lower prices stimulate demand and if higher yields raise profits, encouraging agricultural expansion and increasing the opportunity cost of conservation (2, 3). We offer a first description of four categories of “active” land-sparing mechanisms that could overcome these rebound effects by linking yield increases with habitat protection or restoration (table S1). The effectiveness, limitations, and potential for unintended consequences of these mechanisms have yet to be systematically tested, but in each case, we describe real-world interventions that illustrate how intentional links between yield increases and land sparing might be developed.
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A proposed regulatory framework for genome-edited crops : Nature Genetics : Nature Publishing Group

A proposed regulatory framework for genome-edited crops : Nature Genetics : Nature Publishing Group | plant cell genetics | Scoop.it
Crop breeding is being revolutionized by rapid progress in DNA sequencing and targeted alteration of DNA sequences by genome editing. Here we propose a regulatory framework for precision breeding with 'genome-edited crops' (GECs) so that society can fully benefit from the latest advances in plant genetics and genomics.
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Identification of a Catalase-Phenol Oxidase in Betalain Biosynthesis in Red Amaranth (Amaranthus cruentus)

Identification of a Catalase-Phenol Oxidase in Betalain Biosynthesis in Red Amaranth (Amaranthus cruentus) | plant cell genetics | Scoop.it
Betalains are a group of nitrogen-containing pigments that color plants in most families of Caryophyllales. Their biosynthesis has long been proposed to begin with hydroxylation of L-tyrosine to L-DOPA through monophenolase activity of tyrosinase, but biochemical evidence in vivo remains lacking. Here we report that a Group 4 catalase, catalase-phenol oxidase (named as AcCATPO), was identified, purified and characterized from leaves of Amaranthus cruentus, a betalain plant. The purified enzyme appeared to be a homotrimeric protein composed of subunits of about 58 kDa, and demonstrated not only the catalase activity toward H2O2, but also the monophenolase activity toward L-tyrosine and diphenolase activity toward L-DOPA. Its catalase and phenol oxidase activities were inhibited by common classic catalase and tyrosinase inhibitors, respectively. All its peptide fragments identified by nano-LC-MS/MS were targeted to catalases, and matched with a cDNA-encoded polypeptide which contains both classic catalase and phenol oxidase active sites. These sites were also present in catalases of non-betalain plants analyzed. AcCATPO transcript abundance was positively correlated with the ratio of betaxanthin to betacyanin in both green and red leaf sectors of A. tricolor. These data shows that the fourth group catalase, catalase-phenol oxidase, is present in plant, and might be involved in betaxanthin biosynthesis.
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Mobile small RNAs regulate genome-wide DNA methylation

Mobile small RNAs regulate genome-wide DNA methylation | plant cell genetics | Scoop.it

Small RNAs (sRNAs) of 24 nt are associated with transcriptional gene silencing by targeting DNA methylation to complementary sequences. We demonstrated previously that sRNAs move from shoot to root, where they regulate DNA methylation of three endogenous transposable elements (TEs). However, the full extent of root DNA methylation dependent on mobile sRNAs was unknown. We demonstrate that DNA methylation at thousands of sites depends upon mobile sRNAs. These sites are associated with TE superfamilies found in gene-rich regions of the genome, which lose methylation selectively in an sRNA-deficient mutant. If the TEs were able to reactivate, they could cause genome instability and altered gene expression patterns, with negative effects on the plant. Consequently, mobile sRNAs may defend against these TEs.

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Three ancient hormonal cues co-ordinate shoot branching in a moss

Three ancient hormonal cues co-ordinate shoot branching in a moss | plant cell genetics | Scoop.it
Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.
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Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants - Polturak - 2015 - New Phytologist - Wiley Online Library

Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants - Polturak - 2015 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Betalains are tyrosine-derived red-violet and yellow pigments, found in plants only of the Caryophyllales order. Although much progress has been made in recent years in the understanding of the betalain biosynthetic process, many questions remain open with regards to several of the proposed steps in the pathway. Most conspicuous by its absence is the characterization of the first committed step in the pathway, namely the 3-hydroxylation of tyrosine to form l-3,4-dihydroxyphenylalanine (l-DOPA).
We used transcriptome analysis of the betalain-producing plants red beet (Beta vulgaris) and four o'clocks (Mirabilis jalapa) to identify a novel, betalain-related cytochrome P450-type gene, CYP76AD6, and carried out gene silencing and recombinant expression assays in Nicotiana benthamiana and yeast cells to examine its functionality.
l-DOPA formation in red beet was found to be redundantly catalyzed by CYP76AD6 together with a known betalain-related enzyme, CYP76AD1, which was previously thought to only catalyze a succeeding step in the pathway. While CYP76AD1 catalyzes both l-DOPA formation and its subsequent conversion to cyclo-DOPA, CYP76AD6 uniquely exhibits only tyrosine hydroxylase activity.
The new findings enabled us to metabolically engineer entirely red-pigmented tobacco plants through heterologous expression of three genes taking part in the fully decoded betalain biosynthetic pathway.
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Detecting long-term metabolic shifts using isotopomers: CO2-driven suppression of photorespiration in C3 plants over the 20th century

Detecting long-term metabolic shifts using isotopomers: CO2-driven suppression of photorespiration in C3 plants over the 20th century | plant cell genetics | Scoop.it
Terrestrial vegetation currently absorbs approximately a third of anthropogenic CO2 emissions, mitigating the rise of atmospheric CO2. However, terrestrial net primary production is highly sensitive to atmospheric CO2 levels and associated climatic changes. In C3 plants, which dominate terrestrial vegetation, net photosynthesis depends on the ratio between photorespiration and gross photosynthesis. This metabolic flux ratio depends strongly on CO2 levels, but changes in this ratio over the past CO2 rise have not been analyzed experimentally. Combining CO2 manipulation experiments and deuterium NMR, we first establish that the intramolecular deuterium distribution (deuterium isotopomers) of photosynthetic C3 glucose contains a signal of the photorespiration/photosynthesis ratio. By tracing this isotopomer signal in herbarium samples of natural C3 vascular plant species, crops, and a Sphagnum moss species, we detect a consistent reduction in the photorespiration/photosynthesis ratio in response to the ∼100-ppm CO2 increase between ∼1900 and 2013. No difference was detected in the isotopomer trends between beet sugar samples covering the 20th century and CO2 manipulation experiments, suggesting that photosynthetic metabolism in sugar beet has not acclimated to increasing CO2 over >100 y. This provides observational evidence that the reduction of the photorespiration/photosynthesis ratio was ca. 25%. The Sphagnum results are consistent with the observed positive correlations between peat accumulation rates and photosynthetic rates over the Northern Hemisphere. Our results establish that isotopomers of plant archives contain metabolic information covering centuries. Our data provide direct quantitative information on the “CO2 fertilization” effect over decades, thus addressing a major uncertainty in Earth system models.
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ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy - Springer

ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy - Springer | plant cell genetics | Scoop.it
ARABIDILLO proteins regulate multicellular root development in Arabidopsis thaliana. Conserved ARABIDILLO homologues are present throughout land plants, even in early-evolving plants that do not possess complex root architecture, suggesting that ARABIDILLO genes have additional functions. Here, we have cloned and characterised ARABIDILLO gene homologues from two early-evolving land plants, the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii. We show that two of the PHYSCODILLO genes (PHYSCODILLO1A and -1B) exist as a tail-to-tail tandem array of two almost identical 12 kb sequences, while a third related gene (PHYSCODILLO2) is located elsewhere in the Physcomitrella genome. Physcomitrella possesses a very low percentage of tandemly arrayed genes compared with the later-evolving plants whose genomes have been sequenced to date. Thus, PHYSCODILLO1A and -1B genes represent a relatively unusual gene arrangement. PHYSCODILLO promoters are active largely in the haploid gametophyte, with additional activity at the foot of the sporophyte. The pattern of promoter activity is uniform in filamentous and leafy tissues, suggesting pleiotropic gene functions and likely functional redundancy: the latter possibility is confirmed by the lack of discernible phenotype in a physcodillo2 deletion mutant. Interestingly, the pattern of PHYSCODILLO promoter activity in female reproductive organs is strikingly similar to that of an Arabidopsis homologue, suggesting co-option of some PHYSCODILLO functions or regulation into both the sporophyte and gametophyte. In conclusion, our work identifies and characterises some of the earliest-evolving land plant ARABIDILLO homologues. We confirm that all land plant ARABIDILLO genes arose from a single common ancestor and suggest that PHYSCODILLO proteins have novel and pleiotropic functions, some of which may be conserved in later-evolving plants.
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Ferns: the missing link in shoot evolution and development

Ferns: the missing link in shoot evolution and development | plant cell genetics | Scoop.it
Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.
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