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Crop Diversity: An Unexploited Treasure Trove for Food Security: Trends in Plant Science

Crop Diversity: An Unexploited Treasure Trove for Food Security: Trends in Plant Science | postharvest central | Scoop.it
The prediction is that food supply must double by 2050 to cope with the impact of climate change and population pressure on global food systems. The diversification of staple crops and the systems in which they grow is essential to make future agriculture sustainable, resilient, and suitable for local environments and soils.

Via Andres Zurita
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The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

Drought is one of the major constraints in crop production and has an effect on a global scale. In order to improve crop production, it is necessary to understand how plants respond to stress. A good understanding of regulatory mechanisms involved in plant responses during drought will enable researchers to explore and manipulate key regulatory points in order to enhance stress tolerance in crops. Transcription factors (TFs) have played an important role in crop improvement from the dawn of agriculture. TFs are therefore good candidates for genetic engineering to improve crop tolerance to drought because of their role as master regulators of clusters of genes. Many families of TFs, such as CCAAT, homeodomain, bHLH, NAC, AP2/ERF, bZIP, and WRKY have members that may have the potential to be tools for improving crop tolerance to drought. In this review, the roles of TFs as tools to improve drought tolerance in crops are discussed. The review also focuses on current strategies in the use of TFs, with emphasis on several major TF families in improving drought tolerance of major crops. Finally, many promising transgenic lines that may have improved drought responses have been poorly characterized and consequently their usefulness in the field is uncertain. New advances in high-throughput phenotyping, both greenhouse and field based, should facilitate improved phenomics of transgenic lines. Systems biology approaches should then define the underlying changes that result in higher yields under water stress conditions. These new technologies should help show whether manipulating TFs can have effects on yield under field conditions.

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De novo sequencing and comparative analysis of holy and sweet basil transcriptomes

Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, July 18, 2014 12:03 PM
Abstract (provisional)Background

Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing.

Results

The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 +/- 1210.1 bp and 1363 +/- 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.

Conclusion

This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.

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Genetically modified crops could help improve the lives of millions

Genetically modiefied crops could help improve the lives of millions.
Julian Verdonk's insight:

"There is no mainstream scientific evidence showing that foods containing GMOs are any more or less harmful for people to consume than anything else in the supermarket, despite decades of development and use. If that doesn’t convince some people, they have the option of simply buying food bearing the “organic” label. There is no need for the government to stigmatize products with a label that suggests the potential for harm. Outright bans, meanwhile, are even worse than gratuitous labeling."

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microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development

microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development | postharvest central | Scoop.it

Fruit ripening in tomato (Solanum lycopersicum L.) is well understood at the molecular level. However, information regarding genetic pathways associated with tomato ovary and early fruit development is still lacking. Here, we investigate the possible role(s) of the microRNA156/SQUAMOSA promoter-binding protein-like (SPL or SBP box) module (miR156 node) in tomato ovary development. miR156-targeted S. lycopersicum SBP genes were dynamically expressed in developing flowers and ovaries, and miR156 was mainly expressed in meristematic tissues of the ovary, including placenta and ovules. Transgenic tomato cv. Micro-Tom plants over-expressing the AtMIR156b precursor exhibited abnormal flower and fruit morphology, with fruits characterized by growth of extra carpels and ectopic structures. Scanning electron microscopy and histological analyses showed the presence of meristem-like structures inside the ovaries, which are probably responsible for the ectopic organs. Interestingly, expression of genes associated with meristem maintenance and formation of new organs, such as LeT6/TKN2 (a KNOX-like class I gene) and GOBLET (a NAM/CUC-like gene), was induced in developing ovaries of transgenic plants as well as in the ovaries of the natural mutant Mouse ear (Me), which also displays fruits with extra carpels. Conversely, expression of the MADS box genes MACROCALYX (MC) and FUL1/TDR4, and the LEAFY ortholog FALSIFLORA, was repressed in the developing ovaries of miR156 over-expressors, suggesting similarities with Arabidopsis at this point of the miR156/SPL pathway but with distinct functional consequences in reproductive development. Altogether, these observations suggest that the miR156 node is involved in maintenance of the meristematic state of ovary tissues, thereby controlling initial steps of fleshy fruit development and determinacy.

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A Conserved Network of Transcriptional Activators and Repressors Regulates Anthocyanin Pigmentation in Eudicots

A Conserved Network of Transcriptional Activators and Repressors Regulates Anthocyanin Pigmentation in Eudicots | postharvest central | Scoop.it

Plants require sophisticated regulatory mechanisms to ensure the degree of anthocyanin pigmentation is appropriate to myriad developmental and environmental signals. Central to this process are the activity of MYB-bHLH-WD repeat (MBW) complexes that regulate the transcription of anthocyanin genes. In this study, the gene regulatory network that regulates anthocyanin synthesis in petunia (Petunia hybrida) has been characterized. Genetic and molecular evidence show that the R2R3-MYB, MYB27, is an anthocyanin repressor that functions as part of the MBW complex and represses transcription through its C-terminal EAR motif. MYB27 targets both the anthocyanin pathway genes and basic-helix-loop-helix (bHLH) ANTHOCYANIN1 (AN1), itself an essential component of the MBW activation complex for pigmentation. Other features of the regulatory network identified include inhibition of AN1 activity by the competitive R3-MYB repressor MYBx and the activation of AN1, MYB27, and MYBx by the MBW activation complex, providing for both reinforcement and feedback regulation. We also demonstrate the intercellular movement of the WDR protein (AN11) and R3-repressor (MYBx), which may facilitate anthocyanin pigment pattern formation. The fundamental features of this regulatory network in the Asterid model of petunia are similar to those in the Rosid model ofArabidopsis thaliana and are thus likely to be widespread in the Eudicots.

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Isoprene production in transgenic tobacco alters isoprenoids, non-structural carbohydrates and phenylpropanoids metabolism, and protects photosynthesis from drought stress

Isoprene production in transgenic tobacco alters isoprenoids, non-structural carbohydrates and phenylpropanoids metabolism, and protects photosynthesis from drought stress | postharvest central | Scoop.it

Isoprene exerts important functions in plant defense. In the present study we show that photosynthesis of transgenic tobacco plants in which isoprene biosynthesis was made possible, is less affected by drought, and that isoprene production is associated to increased biosynthesis of secondary metabolites during and after drought.

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Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing

Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing | postharvest central | Scoop.it

Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.

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These Beautiful Graphics Reveal The Chemistry Of Everyday Foods

These Beautiful Graphics Reveal The Chemistry Of Everyday Foods | postharvest central | Scoop.it
From lemons to coffee to cilantro.
Julian Verdonk's insight:

Plant Secondary Metabolites, this is beautiful. Love it!!

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Herbivory and floral signaling: phenotypic plasticity and tradeoffs between reproduction and indirect defense

Herbivory and floral signaling: phenotypic plasticity and tradeoffs between reproduction and indirect defense | postharvest central | Scoop.it

SummaryPlant defense against herbivores may compromise attraction of mutualists, yet information remains limited about the mechanisms underlying such signaling tradeoffs.Here, we investigated the effects of foliar herbivory by two herbivore species on defense compounds, floral signaling, pollinator and parasitoid attraction, and seed production.Herbivory generally reduced the quantity of many floral volatile organic compounds VOCs) in Brassica rapa. By contrast, floral color, flower diameter, and plant height remained unaffected. The decreased amounts of floral volatiles led to reduced attractiveness of flowers to pollinators, but increased the attractiveness of herbivore-infested plants to parasitoids. Plants infested with the native butterfly Pieris brassicae produced more flowers during early flowering, effectively compensating for the lower olfactory attractiveness. Herbivory by the invasive Spodoptera littoralis increased the amounts of glucobrassicanapin, and led to delayed flowering. These plants tended to attract fewer pollinators and to produce fewer seeds.Our study indicates a tradeoff between pollinator attraction and indirect defense (parasitoid attraction), which can be mitigated by reduced floral VOC emission and production of more early flowers. We suggest that this compensatory mechanism is specific to plant–herbivore associations with a coevolutionary history.

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Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative | postharvest central | Scoop.it

In plants, continuous formation of lateral roots (LRs) facilitates efficient exploration of the soil environment. Roots can maximize developmental capacity in variable environmental conditions through establishment of sites competent to form LRs. This LR prepattern is established by a periodic oscillation in gene expression near the root tip. The spatial distribution of competent (prebranch) sites results from the interplay between this periodic process and primary root growth; yet, much about this oscillatory process and the formation of prebranch sites remains unknown. We find that disruption of carotenoid biosynthesis results in seedlings with very few LRs. Carotenoids are further required for the output of the LR clock because inhibition of carotenoid synthesis also results in fewer sites competent to form LRs. Genetic analyses and a carotenoid cleavage inhibitor indicate that an apocarotenoid, distinct from abscisic acid or strigolactone, is specifically required for LR formation. Expression of a key carotenoid biosynthesis gene occurs in a spatially specific pattern along the root’s axis, suggesting spatial regulation of carotenoid synthesis. These results indicate that developmental prepatterning of LRs requires an uncharacterized carotenoid-derived molecule. We propose that this molecule functions non–cell-autonomously in establishment of the LR prepattern.

 
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Sugar and acid interconversion in tomato fruits based on biopsy sampling of locule gel and pericarp tissue

Sugar and acid interconversion in tomato fruits based on biopsy sampling of locule gel and pericarp tissue | postharvest central | Scoop.it
Highlights 
• A medical biopsy needle is introduced to sample pericarp and gel tissue of tomato. 
• Sugar and acid interconversions within individual tomatoes are measured. 
• A sugar acid model is proposed and calibrated on data from several cultivars. 
• More hexose turnover was found in locular gel than in pericarp tissue. 
• Acid to sugar conversion is more important in the cherry type cultivar. 

Abstract 
This study deals with quantifying sugar and acids levels important for the perceived taste of tomatoes (Solanum lycopersicum). Sugar and acids levels were measured repeatedly on the same tomato using tissue samples obtained with a biopsy needle in combination with HPLC protocols. Biopsies of pericarp and locular gel tissue from tomatoes differing in position in the truss, from mature green to ripe red, were taken from a beef- (‘Licorossa’), a cocktail- (‘Lucino’) and a cherry type (‘Petit Sweet’) cultivar. Tomatoes were stored up to three weeks at three temperatures (12, 19 and 24.5 °C) and biopsy samples were taken every few days. A model regarding the most important processes that interconvert sugars and acids (glycolysis, TCA cycle and gluconeogenesis (GNG)) is proposed. Results of the model calibration showed more breakdown of hexoses in red tomatoes and more conversion of malate into hexoses in green tomatoes. More hexose turnover was found in locular gel than in pericarp tissue. GNG was more important in the cherry type cultivar due to faster hexose and malate breakdown. In the round type cultivar malate levels were higher due to faster citrate breakdown and slower malate breakdown. Starch and sucrose levels did not significantly affect postharvest sugar and acid development. Molecular markers that quantify the kinetic parameters of the model might be important to develop genotypes with better taste performance. Keywords Biopsy; HPLC; OptiPa; Glycolysis; Citric acid cycle; Gluconeogenesis
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Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato : Nature Communications : Nature Publishing Group

Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato : Nature Communications : Nature Publishing Group | postharvest central | Scoop.it
Experimental evidence for compositional syntax in bird calls Nature Communications 08 March 2016
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An integrated genomic and metabolomic framework for cell wall biology in rice

Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, July 18, 2014 12:01 PM
Abstract (provisional)Background

Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences.

Results

In this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification.

Conclusions

Here, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice.

 
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Key Applications of Plant Metabolic Engineering

Key Applications of Plant Metabolic Engineering | postharvest central | Scoop.it

A remarkable 180 million tons of nitrogen fertilizer is used every year in industrial farming [12], and it has played such an enabling role that fertilizer use is estimated to meet the nutritional needs of one-third of the human population [13]. However, the use of nitrogen fertilizers has serious disadvantages, including substantial cost and deleterious effects on the soil and surrounding environment, and neighboring waterways. Plants that could satisfy some or all of their own nitrogen requirement would transform agriculture by reducing or eliminating this enormous dependence on fertilizer.

There are two conceivable ways in which a plant could be engineered to satisfy its own nitrogen requirement. The first takes advantage of the fact that some bacteria carry out their own version of the Haber-Bosch process—reducing atmospheric N2 into a more bioavailable form, NH3—using the enzyme nitrogenase [14]. This complex enzyme contains multiple metalloclusters and requires a large quantity of biochemical energy to transfer the electrons needed to activate the exceptionally stable N2 triple bond. By expressing nitrogenase, plants would be able to fix their own nitrogen. The primary advantage of this approach is that it is direct: nitrogen fixed by a plant could be used immediately to generate amino acid and nucleic acid monomers and transport them to neighboring cells. Although the process would incur a metabolic cost, it could be regulated by the endogenous level of nitrogen to maximize its efficiency.

Immense technological challenges stand in the way of accomplishing this goal [15]. Eighteen gene products (in Klebsiella oxytoca) are necessary and sufficient for the production of nitrogenase and its complex iron-molybdenum cofactor. By an impressive feat of microbial engineering, the biosynthetic gene cluster for nitrogenase has been refactored—taken apart, re-coded, and put back together using known components—and shown to be active in its new host [16]. The successful transfer of other large gene clusters from one microbe to another, such as the one encoding the magnetosome, suggests that the process of functionalizing microbes is undergoing a dramatic improvement [17].

But new challenges must be overcome for the expression of similar elements in plants. First, all 18 components of the nitrogenase biosynthetic apparatus would need to be expressed simultaneously in plants and function in concert, a considerable barrier given that the largest number of genes expressed in an engineered plant to date is eight in the establishment of a photorespiratory bypass in Arabidopsis [18]. Second, since plants are eukaryotic and multicellular, where in the plant cell should the genes be expressed and in which cell types of the plant? This question is especially relevant for nitrogenase, which is poisoned by oxygen and must therefore be expressed under anaerobic conditions. Tools that enable organelle- and cell-type specific expression will be of great utility here and in other plant engineering efforts.

The second way to reduce or eliminate the need for nitrogen fertilizer would be to engineer a rhizosphere symbiosis between a nitrogen-fixing microorganism and a plant host. Although this approach is less direct than expressing nitrogenase in plants, it has two primary advantages: (1) It uncouples the difficulties of utilizing nitrogenase (e.g., sequestering the enzyme in an anaerobic compartment) from the biology of the plant host, and outsources the demanding chemistry involved to a bacterial strain better suited to the task. (2) The well-studied symbioses between legumes and their nitrogen-fixing, root-nodulating bacterial symbionts prove that a bacterial mutualist can satisfy the nitrogen needs of a plant host [19]. Even though root-nodulating bacteria appear to be specific to legumes, the presence of nitrogen-fixing bacteria in the rhizosphere opens the possibility that symbioses of this sort are a much more widely distributed phenomenon [20]. If so, then the feasibility of making this mode of nitrogen exchange more efficient—rather than engineering it from scratch—would appear high. However, there remain two primary challenges in engineering a stable and practical rhizosphere symbiosis: enabling efficient nutrient exchange and maintaining specificity of the host-microbe pair. Both could take years to develop and are likely to require not just plant but also microbial metabolic engineering. In the meantime, advanced molecular breeding tools that enable access to natural variation in a plant's wild ancestors [21] are a promising alternative approach to increasing crop plant yields [22].


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Why asparagus makes your urine smell and onions make your cry

Why asparagus makes your urine smell and onions make your cry | postharvest central | Scoop.it
An anonymous chemistry teacher based in the UK created the infographics to demystify the chemistry of everyday foods and show that chemicals are in everything.

Via Meristemi
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Marco Fulvio Barozzi's curator insight, May 17, 2014 4:35 PM

La chimica è dovunque, ragazzo mio: devi fartene una ragione.

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Tempest in a Tea Pot: How did the Public Conversation on Genetically Modified Crops Drift so far from the Facts? - Goldstein (2014) - J Med Toxicol

Tempest in a Tea Pot: How did the Public Conversation on Genetically Modified Crops Drift so far from the Facts? - Goldstein (2014) - J Med Toxicol | postharvest central | Scoop.it

The debate over genetically modified (GM) crops has raged in Europe since 1996, but had barely risen above a whisper in the USA until recent labeling debates raised public attention. This article will explain GM crops and traits discuss safety assessment provide a view on safety from authoritative organizations discuss selected issues of current debate, and provide the author’s perspective as to why the public debate has drifted so far from scientific reality.

 

The economic and environmental benefits of GM crops are beyond scope, but references are provided. GM food and feed undergo comprehensive assessments using recognized approaches to assure they are as safe as the conventional congener. Issues of food safety and nutrition, unrelated to the GM process, may arise when GM foods display novel components or composition. Unanticipated genetic effects in GM crops appear to be limited in contrast to existing variations among conventional varieties resulting from breeding, mutation, and natural mobile genetic elements.

 

Allergenic potential is assessed when selecting genes for introduction into GM crops and remains a theoretical risk to date. Emerging weed and insect resistance is not unique to GM technology and will require the use of integrated pest management/best practices for pest control. Gene flow from GM crops to wild relatives is limited by existing biological barriers but can at time be a relevant consideration in gene selection and planting practices.Insect-resistant GM crops have significantly reduced use of chemical insecticides and appear to have reduced the incidence of pesticide poisoning in areas where small scale farming and hand application are common. Changes in herbicide patterns are more complex and are evolving over time in response to weed resistance management needs. 

 

Recent public debate is driven by a combination of unfounded allegations about the technology and purveyors, pseudoscience, and attempts to apply a strict precautionary principle... Authoritative organizations such as the FDA, World Health Organization, AAAS, the Royal Society of Medicine, and the National Academy of Science have affirmed the safety of GM crops. So, how did the public conversation on GM crops become so negative? Opponents of GM have used three approaches to drive negative public opinion. The first approach has been to create negative impressions about the developers and purveyors of this technology... A second approach is to question the science underlying GM safety, often via misinterpretation of data obtained in inappropriate test systems... 

 A third approach is to invoke the “precautionary principle.” As originally proposed, the principle stated that risk assessors and policy makers should take account of uncertainties... to provide adequate margins of safety. The absolute version employed by some suggests that in the presence of any uncertainty, we should not move forward. This is of course a “black hole”—one can never prove a negative and hence one can never move forward when employing the absolute precautionary principle. The latter ignores both the risks of existing technology and the benefits of innovation and leaves decision making in the hands of anyone who chooses to raise doubts.  GM crops have a more than 20-year track record of being grown and used commercially without a single human illness known to be caused by GM food or feed. Moreover, billions of animals have been fed predominantly GM diets for consecutive generations with no evidence that animal health and productivity were affected. The safety assessment paradigm for GM crops is robust and well established, and the approach has been confirmed by authoritative regulatory agencies and scientific organizations around the globe. These are, by far, the most thoroughly assessed foods and feeds in human history, and the National Academies of Science concluded that risk or unintended effects of GM technologies falls within the range of risks for conventional breeding technologies—which include forced inter-species crosses and radiation-induced mutagenesis. We can move forward with high confidence that GM food and feed are as safe and nutritious as their conventional congeners and perhaps look forward to rationalizing food safety assessment across conventional, GM, and other new breeding technologies to achieve a more focused and resource-efficient safety assessment process.

 

http://dx.doi.org/10.1007/s13181-014-0402-7

 


Via Alexander J. Stein, Andres Zurita
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Plant Genome -An Assessment of the Relative Influences of Genetic Background, Functional Diversity at Major Regulatory Genes, and Transgenic Constructs on the Tomato Fruit Metabolome

Plant Genome -An Assessment of the Relative Influences of Genetic Background, Functional Diversity at Major Regulatory Genes, and Transgenic Constructs on the Tomato Fruit Metabolome | postharvest central | Scoop.it

While the greatest strength of systems biology may be to measure tens of thousands of variables across different genotypes, this simultaneously presents an enormous challenge to statistical analysis that cannot be completely solved with conventional approaches that identify and rank differences. Here we examine a diverse panel of conventional and transgenic, field-grown tomato fruits (Solanum lycopersicum L.) by liquid chromatography–mass spectrometry (LC-MS) metabolic fingerprinting. We used a progression of statistics to examine phenotypic variation observed. While clear trends were found by principal component analysis (PCA) related to genetic background and ripeness, it could not detect differences between transgenic genotypes and their nontransgenic parent variety. Partial least squares discriminant analysis (PLS-DA), a supervised method, identified 15 metabolic features of potential interest, but only five were significantly different between the transgenic lines and their nontransgenic parent. Weighted correlation network analysis (WGCNA) recognized relationships among these features and others, suggesting that a small suite of highly correlated compounds accumulated to significantly lower levels in the transgenic genotypes. We assert that metabolic fingerprinting with a series of statistical methods is an efficient and powerful approach to examine both large and small genetic effects on phenotypes of high value or interest.


Via Andres Zurita
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Andres Zurita's curator insight, May 5, 2014 10:35 PM

While the greatest strength of systems biology may be to measure tens of thousands of variables across different genotypes, this simultaneously presents an enormous challenge to statistical analysis that cannot be completely solved with conventional approaches that identify and rank differences. Here we examine a diverse panel of conventional and transgenic, field-grown tomato fruits (Solanum lycopersicum L.) by liquid chromatography–mass spectrometry (LC-MS) metabolic fingerprinting. We used a progression of statistics to examine phenotypic variation observed. While clear trends were found by principal component analysis (PCA) related to genetic background and ripeness, it could not detect differences between transgenic genotypes and their nontransgenic parent variety. Partial least squares discriminant analysis (PLS-DA), a supervised method, identified 15 metabolic features of potential interest, but only five were significantly different between the transgenic lines and their nontransgenic parent. Weighted correlation network analysis (WGCNA) recognized relationships among these features and others, suggesting that a small suite of highly correlated compounds accumulated to significantly lower levels in the transgenic genotypes. We assert that metabolic fingerprinting with a series of statistical methods is an efficient and powerful approach to examine both large and small genetic effects on phenotypes of high value or interest.

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An improved genome release (version Mt4.0) for the model legume Medicago truncatula

Background

Medicago truncatula, a close relative of alfalfa, is a preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The Medicago sequencing project began in 2003 with the goal to decipher sequences originated from the euchromatic portion of the genome. The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011.

Results

Here we describe a further improved and refined version of the M. truncatula genome (Mt4.0) based on de novo whole genome shotgun assembly of a majority of Illumina and 454 reads using ALLPATHS-LG. The ALLPATHS-LG scaffolds were anchored onto the pseudomolecules on the basis of alignments to both the optical map and the genotyping-by-sequencing (GBS) map. The Mt4.0 pseudomolecules encompass ~360 Mb of actual sequences spanning 390 Mb of which ~330 Mb align perfectly with the optical map, presenting a drastic improvement over the BAC-based Mt3.5 which only contained 70% sequences (~250 Mb) of the current version. Most of the sequences and genes that previously resided on the unanchored portion of Mt3.5 have now been incorporated into the Mt4.0 pseudomolecules, with the exception of ~28 Mb of unplaced sequences. With regard to gene annotation, the genome has been re-annotated through our gene prediction pipeline, which integrates EST, RNA-seq, protein and gene prediction evidences. A total of 50,894 genes (31,661 high confidence and 19,233 low confidence) are included in Mt4.0 which overlapped with ~82% of the gene loci annotated in Mt3.5. Of the remaining genes, 14% of the Mt3.5 genes have been deprecated to an "unsupported" status and 4% are absent from the Mt4.0 predictions.

Conclusions

Mt4.0 and its associated resources, such as genome browsers, BLAST-able datasets and gene information pages, can be found on the JCVI Medicago web site (http://www.jcvi.org/medicago). The assembly and annotation has been deposited in GenBank (BioProject: PRJNA10791). The heavily curated chromosomal sequences and associated gene models of Medicago will serve as a better reference for legume biology and comparative genomics.


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Induced transcriptional profiling of phenylpropanoid pathway genes increased flavonoid and lignin content in Arabidopsis leaves in response to microbial products

The production and use of biologically derived soil additives is one of the fastest growing sectors of the fertilizer industry. These products have been shown to improve crop yields while at the same time reducing fertilizer inputs to and nutrient loss from cropland. The mechanisms driving the changes in primary productivity and soil processes are poorly understood and little is known about changes in secondary productivity associated with the use of microbial products. Here we investigate secondary metabolic responses to a biologically derived soil additive by monitoring changes in the phenlypropanoid (PP) pathway in Arabidopsis thaliana.
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After trip to space, cherry trees mysteriously blossom years ahead of schedule

After trip to space, cherry trees mysteriously blossom years ahead of schedule | postharvest central | Scoop.it
It's that time of year when cherry blossoms draw crowds across the world, but a few cherry trees this year have sprouted a mystery. Four cherry tree saplings across Japan blossomed this spring, as...
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Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks

Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks | postharvest central | Scoop.it

Plant metabolomics is increasingly used for pathway discovery and to elucidate gene function. However, the main bottleneck is the identification of the detected compounds. This is more pronounced for secondary metabolites as many of their pathways are still underexplored. Here, an algorithm is presented in which liquid chromatography–mass spectrometry profiles are searched for pairs of peaks that have mass and retention time differences corresponding with those of substrates and products from well-known enzymatic reactions. Concatenating the latter peak pairs, called candidate substrate-product pairs (CSPP), into a network displays tentative (bio)synthetic routes. Starting from known peaks, propagating the network along these routes allows the characterization of adjacent peaks leading to their structure prediction. As a proof-of-principle, this high-throughput cheminformatics procedure was applied to the Arabidopsis thaliana leaf metabolome where it allowed the characterization of the structures of 60% of the profiled compounds. Moreover, based on searches in the Chemical Abstract Service database, the algorithm led to the characterization of 61 compounds that had never been described in plants before. The CSPP-based annotation was confirmed by independent MSn experiments. In addition to being high throughput, this method allows the annotation of low-abundance compounds that are otherwise not amenable to isolation and purification. This method will greatly advance the value of metabolomics in systems biology.

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Enhanced levels of S-linalool by metabolic engineering of the terpenoid pathway in spike lavender leaves

Enhanced levels of S-linalool by metabolic engineering of the terpenoid pathway in spike lavender leaves | postharvest central | Scoop.it

Transgenic Lavandula latifolia plants overexpressing the linalool synthase (LIS) gene from Clarkia breweri, encoding the LIS enzyme that catalyzes the synthesis of linalool were generated. Most of these plants increased significantly their linalool content as compared to controls, especially in the youngest leaves, where a linalool increase up to a 1000% was observed. The phenotype of increased linalool content observed in young leaves was maintained in those T1 progenies that inherit the LIS transgene, although this phenotype was less evident in the flower essential oil. Cross-pollination of transgenic spike lavender plants allowed the generation of double transgenic plants containing the DXS (1-deoxy-d-xylulose-5-P synthase), coding for the first enzyme of the methyl-d-erythritol-4-phosphate pathway, and LIS genes. Both essential oil yield and linalool content in double DXS-LIS transgenic plants were lower than that of their parentals, which could be due to co-suppression effects linked to the structures of the constructs used.

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