Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

Maize ZmLAZ1-3 gene negatively regulates drought tolerance in transgenic Arabidopsis

BACKGROUND

Molecular mechanisms in response to drought stress are important for the genetic improvement of maize. In our previous study, nine ZmLAZ1 members were identified in the maize genome, but the function of ZmLAZ1 was largely unknown.

RESULTS

The ZmLAZ1-3 gene was cloned from B73, and its drought-tolerant function was elucidated by expression analysis in transgenic Arabidopsis. The expression of ZmLAZ1-3 was upregulated by drought stress in different maize inbred lines. The driving activity of the ZmLAZ1-3 promoter was induced by drought stress and related to the abiotic stress-responsive elements such as MYB, MBS, and MYC. The results of subcellular localization indicated that the ZmLAZ1-3 protein localized on the plasma membrane and chloroplast. The ectopic expression of the ZmLAZ1-3 gene in Arabidopsis significantly reduced germination ratio and root length, decreased biomass, and relative water content, but increased relative electrical conductivity and malondialdehyde content under drought stress. Moreover, transcriptomics analysis showed that the differentially expressed genes between the transgenic lines and wild-type were mainly associated with response to abiotic stress and biotic stimulus, and related to pathways of hormone signal transduction, phenylpropanoid biosynthesis, mitogen-activated protein kinase signaling, and plant-pathogen interaction.

CONCLUSION

The study suggests that the ZmLAZ1-3 gene is a negative regulator in regulating drought tolerance and can be used to improve maize drought tolerance via its silencing or knockout.

Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice

The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.

A portable analog front-end system for label-free sensing of proteins using nanowell array impedance sensors

Proteins are useful biomarkers for a wide range of applications such as cancer detection, discovery of vaccines, and determining exposure to viruses and pathogens. Here, we present a low-noise front-end analog circuit interface towards development of a portable readout system for the label-free sensing of proteins using Nanowell array impedance sensing with a form factor of approximately 35cm². The electronic interface consists of a low-noise lock-in amplifier enabling reliable detection of changes in impedance as low as 0.1% and thus detection of proteins down to the picoMolar level. The sensitivity of our system is comparable to that of a commercial bench-top impedance spectroscope when using the same sensors. The aim of this work is to demonstrate the potential of using impedance sensing as a portable, low-cost, and reliable method of detecting proteins, thus inching us closer to a Point-of-Care (POC) personalized health monitoring system. We have demonstrated the utility of our system to detect antibodies at various concentrations and protein (45 pM IL-6) in PBS, however, our system has the capability to be used for assaying various biomarkers including proteins, cytokines, virus molecules and antibodies in a portable setting.

Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments

During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.

RNA Interference-Based Genetic Engineering Maize Resistant to Apolygus lucorum Does Not Manifest Unpredictable Unintended Effects Relative to Conventional Breeding: Short Interfering RNA, Transcriptome, and Metabolome Analysis

The use of omics techniques to analyze the differences between genetic engineering organisms and their parents can identify unintended effects and explore whether such unintended effects will have negative consequences. In order to evaluate whether genetic engineering will cause changes in crops beyond the changes introduced by conventional plant breeding, we compared the extent of transcriptome and metabolome modification in the leaves of three lines developed by RNA interference (RNAi)-based genetic engineering and three lines developed by conventional breeding. The results showed that both types of plant breeding methods can manifest changes at the short interfering RNA (siRNA), transcriptomic, and metabolic levels. Relative expression analysis of potential off-target gene revealed that there was no broad gene decline in the three RNAi-based genetic engineering lines. We found that the number of DEGs and DAMs between RNAi-based genetic engineering lines and the parental line was less than that between conventional breeding lines. These unique DEGs and DAMs between RNAi-based genetic engineering lines and the parental lines were not enriched in detrimental metabolic pathways. The results suggest that RNAi-based genetic engineering do not cause unintended effects beyond those found in conventional breeding in maize.

Efficacy of synbiotic interventions on blood pressure: a systematic review and meta-analysis of clinical trials

PURPOSE

The present systematic review and meta-analysis aimed to evaluate the effect of synbiotic interventions on blood pressure levels in adults.

METHODS

A systematic literature search was conducted in the databases of MEDLINE, Scopus, Web of Science, and Cochrane through March 2020 to identify all randomized control trials (RCTs) investigating the effects of synbiotic interventions on blood pressure parameter, including systolic (SBP) and diastolic blood pressure (DBP). Grading of Recommendations Assessment, Development and Evaluation (GRADE) scale was used to assess the certainty of evaluated outcomes and determine the strength of recommendations.

RESULTS

Eleven RCTs were included in the meta-analysis. Synbiotic interventions significantly reduced SBP (-3.02 mmHg; 95% CI: -4.84, -1.21; I² = 55%) without changing DBP levels (-0.57 mmHg; 95% CI: -1.78, 0.64; I² = 50%). Subgroup analyses revealed that the SBP-lowering effects of synbiotic interventions were more pronounced wherein trials were longer (≥12 weeks), synbiotic interventions were administrated as a supplement, and participants were younger (<50 years old). Also, a significant improvement in both SBP and DBP levels was evident in subgroups with a lower (<30 kg/m²) body mass index.

CONCLUSIONS

Synbiotic interventions may significantly improve SBP levels in adults.

Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics

Genetic engineering (GM) has great potential to improve maize productivity, but rises some concerns on unintended effects, and equivalent as their comparators. There are some limitations through targeted analysis to detect the UE in genetically modified organisms in many previous studies. We here reported a case-study on the effects of introducing herbicides and insect resistance (HIR) gene cassette on molecular profiling (transcripts and metabolites) in a popular maize variety Zhengdan958 (ZD958) in China. We found that introducing HIR gene cassette bring a limited numbers of differential abundant genes (DAGs) or differential abundant metabolites (DAMs) between transgenic events and non-transgenic control. In contrast, averaged 10 times more DAGs and DAMs were observed when performed comparison under different growing environments in three different ecological regions of China than the numbers induced by gene effects. Major biological pathways relating to stress response or signaling transduction could explain somehow the effects of growing environments. We further compared two transgenic events mediated ZD958 (GM-ZD958) with either transgenic parent GM-Z58, and other genetic background nonGM-Z58, nonGM-ZD958, and Chang7-2. We found that the numbers of DAGs and DAMs between GM-ZD958 and its one parent maize variety, Z58 or GM-Z58 is equivalent, but not Chang7-2. These findings suggest that greater effects due to different genetic background on altered molecular profiling than gene modification itself. This study provides a case evidence indicating marginal effects of gene pleiotropic effects, and environmental effects should be emphasized.

Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding

Advancements in -omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and high-performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross-breeding in rice.

Sequencing of two transgenic early-flowering poplar lines confirmed vector-free single-locus T-DNA integration

Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus tremula lines, T193-2 and T195-1, both carrying the FLOWERING LOCUS T gene from Arabidopsis thaliana under control of a heat-inducible promoter (pHSP::AtFT) and the non-transgenic control clone W52, were further characterised by NGS and third-generation sequencing. The results support previous findings that the T-DNA was hemizygously inserted in one genomic locus of each line. However, the T-DNA insertions consist of conglomerations of one or two T-DNA copies together with a small T-DNA fragment without AtFT parts. Based on NGS data, no additional T-DNA splinters or vector backbone sequences could be identified in the genome of the two transgenic lines. Seedlings derived from crosses between the pHSP::AtFT transgenic male parents and female wild type plants are therefore expected to be T-DNA splinter or vector backbone free. Thus, PCR analyses amplifying a partial T-DNA fragment with AtFT-specific primers are sufficient to determine whether the seedlings are transgenic or not. An analysis of 72 second generation-seedlings clearly showed that about 50% of them still reveal the presence of the T-DNA, confirming data already published. To prove if unanticipated genomic changes were induced by T-DNA integration, extended future studies using long-range sequencing technologies are required once a suitable chromosome-level P. tremula reference genome sequence is available.

Familiarity in the Context of Risk Assessment of Transgenic Crops: Focus on Some Countries in the Americas

Problem formulation is the formal opening stage of a risk assessment that determines its purpose and scope and hence guides the gathering of information data. The concepts of familiarity and history of safe use are an integral part of problem formulation. These concepts do not replace the case-by-case approach and are not taken as safety standards but are valuable components of the process that shape the generation of plausible, testable risk hypotheses. The International Life Sciences Institutes in Brazil and Argentina have facilitated numerous discussions on the scientific principles for risk assessment of transgenic crops in the Latin American region in the past 5–6 years. The session held at ISBR 15th elaborated on the familiarity concept and derived tools and their role in the evolution of risk evaluation criteria. Examples of how different countries in the Americas interpret and apply these conceptual tools show that familiarity is a valuable concept, although terms are very often confused and vaguely defined. Formalizing these terms with clear definitions and scope of application in guidelines and regulatory documents would reduce ambiguity, enhance predictability, and add transparency to the evaluation processes.

Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food?

Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement

CRISPR-Cas9 enabled genome engineering has great potential for improving agriculture productivity, but the possibility of unintended off-target edits has evoked some concerns. Here we employ a three-step strategy to investigate Cas9 nuclease specificity in a complex plant genome. Our approach pairs computational prediction with genome-wide biochemical off-target detection followed by validation in maize plants. Our results reveal high frequency (up to 90%) on-target editing with no evidence of off-target cleavage activity when guide RNAs were bioinformatically predicted to be specific. Predictable off-target edits were observed but only with a promiscuous guide RNA intentionally designed to validate our approach. Off-target editing can be minimized by designing guide RNAs that are different from other genomic locations by at least three mismatches in combination with at least one mismatch occurring in the PAM proximal region. With well-designed guides, genetic variation from Cas9 off-target cleavage in plants is negligible, and much less than inherent variation.

Unintended effects of transgenic rice revealed by transcriptome and metabolism

Genetically modified (GM) organisms have been developed for decades. However, unintended effects are the main concerns of safety assessment that needs to be carefully investigated. Here, eight varieties of GM rice that were developed in China were selected to assess the unintended effects through transcriptome and metabolism. There are 2892-8758 differentially expressed genes (DEGs) and 7-50 metabolites at significant level between GM varieties and their isogenic counterparts, which were far fewer than that between traditional rice varieties. The function enrichment analysis showed altered transcription in stress-related pathway and starch and sucrose metabolism. DEGs shared among eight GM samples constitute less than 1% of the genes in the genome, and none of them is reported more than four times. The insertion effect on the nearby gene expression and the associated metabolism is only restricted to 50 genes. All the results provide a comprehensive analysis of unintended effects and indication of difference in Chinese transgenic rice based on their backgrounds, transformation, and insertion elements.

The evolving EU regulatory framework for precision breeding

Plant breeding has always relied on progress in various scientific disciplines to generate and enable access to genetic variation. Until the 1970s, available techniques generated mostly random genetic alterations that were subject to a selection procedure in the plant material. Recombinant nucleic acid technology, however, started a new era of targeted genetic alterations, or precision breeding, enabling a much more targeted approach to trait management. More recently, developments in genome editing are now providing yet more control by enabling alterations at exact locations in the genome. The potential of recombinant nucleic acid technology fueled discussions about potentially new associated risks and, starting in the late 1980s, biosafety legislation for genetically modified organisms (GMOs) has developed in the European Union. However, the last decade has witnessed a lot of discussions as to whether or not genome editing and other precision breeding techniques should be encompassed by the EU GMO legislation. A recent ruling from the Court of Justice of the European Union indicated that directed mutagenesis techniques should be subject to the provisions of the GMO Directive, essentially putting many precision breeding techniques in the same regulatory basket. This review outlines the evolving EU regulatory framework for GMOs and discusses some potential routes that the EU may take for the regulation of precision breeding.

Elevated carotenoids in staple crops: The biosynthesis, challenges and measures for target delivery

Poverty eradication and global food security are among the targets of world leaders, most especially combating the scourge of hidden hunger. Provitamin A carotenoids cannot be synthesized de novo by human and so it must be taken as part of the diet. The deficiency of which is causing almost 6000 sights to be lost daily in most developing countries because of the monotonous starchy diets lacking substantial amount of carotenoid. Conventional breeding as well as genetic engineering have been used to increase the level of carotenoid in many staples including rice, potato, maize and cassava. While products from genetic engineering are still been subjected to strict regulatory measures preventing the delivery of the products to target consumers, some of the products from conventional breeding are already on the table of consumers. Interestingly, both technologies are crucial to tackling micronutrient deficiencies. This review discusses the role of carotenoid in human, the biosynthesis in plant and some of the staple crops that have been modified for increased carotenoid. Some measures expected of the leaders of the countries in need of these products for safe delivery to the target population after two decades is also highlighted.

Responses of PYR/PYL/RCAR ABA Receptors to Contrasting stresses, Heat and Cold in Arabidopsis

Plants growing in natural habitats have evolved a wide range of mechanisms to copy with environmental challenging, including biotic and abiotic stresses. Abiotic stresses-induced increases in Abscisic acid (ABA) levels in plants suffering from stresses, including drought, cold or heat stress. To explore the function of the core components in ABA signaling, we used the overexpression of RCARs transgenic plants to expose in heat or cold stress. In this study, overexpression of RCAR12 or RCAR13 (R12-OE or R13-OE) transgenic plants had higher germination and survival rate than the wild-type (WT) Arabidopsis, indicating that they are both positively responsive to the high temperature. And the heat shock genes HSP18.2 and HSP70 were significantly induced by RCAR12 or RCAR13. Further, the results inferred that the over-expression of RCAR12 or RCAR13 could tolerance the cold stress, through induction CBFs expressions, the cold-responsive genes when plants were challenged the cold tress. And when complementation of RCAR12 to the 1124 mutant (R12:1124), the results indicated that RCAR12 could recover the insensitivity of 1124 to heat and cold stresses. Hence, we propose that RCAR12 and RCAR13, the ABA receptors, may play the positive roles in regulating the extreme temperature, including cold and high temperature in Arabidopsis.

Scientific mistakes from the agri-food biotech critics

Critics of the use of advanced biotechnologies in the agri-food sector ("New Breeding Techniques", comprising CRISPR) demand a strict regulation of any such method, even more severe than rules applied to so-called "Genetically Modified Organisms" (i.e. recombinant DNA processes and products). But their position is unwarranted, since it relies on faulty arguments.While most life scientists have always explained that the trigger for regulation should be the single product and its phenotypic traits, opponents insist that the target should be certain biotech processes.The antagonists maintain that NBTs are inherently risky: this belief is exactly the opposite of a long-standing, overwhelming scientific consensus. NBTs involve unpredictable effects, but it is the same for the results of any other technique. The critics wrongly equate "unintended" with "harmful" and misunderstand two meanings of "risk": the "risk" of not achieving satisfactory results does not automatically translate into health or environment "risks". Generic claims that allergenic or toxic properties are a hidden danger of outcomes from NBTs are unsubstantiated - as they would be for traditional techniques.Among several errors, we criticize the misuse of the Precautionary principle, a misplaced alarm about "uncontrolled spreading" of genetically engineered cultivars and the groundless comparison of (hypothetical) agricultural products from NBTs with known toxic substances.In order to "save" traditional techniques from "GMO"-like regulations, while calling for the enforcement of similar sectarian rules for the NBTs, the dissenters engage in baseless, unscientific distinctions.Important and necessary socio-economic, ethical and legal considerations related to the use of agri-food biotechnologies (older and newer) are outside the scope of this paper, which mostly deals with arguments from genetics, biology, and evolutionary theory that are provided by those who are suspicious of NBTs. Yet, we will provide some hints on two additional facets of the debate: the possible motivations for certain groups to embrace views which are utterly anti-scientific, and the shaky regulatory destiny of NBTs in the European Union.

Robust label-free microRNA detection using one million ISFET array

Detection of nucleic acid molecules is one of the most pervasive assays in biology, medicine, and agriculture applications. Currently, most comely used DNA/RNA detection platforms use fluorescence labeling and require lab-scale setting for performing the assay. There is a need for developing less expensive, label-free, and rapid detection of biomolecules with minimal utilization of resources. Use of electrical approaches for detection of biomolecules by utilizing their inherent charge is a promising direction for biosensing assays. Here, we report a 1024 × 1024 array of Ion Sensitive Field Effect Transistors (ISFET) as label free sensors for detection of nucleic acid molecules. Using PNA probe functionalized on these ISFET array, we robustly detected miRNA Let-7b by measuring changes in drain current after hybridization of target molecules with concentration as low as 1 nM. We demonstrate that mismatched or non-complementary target molecules resulted in statistically smaller changes. Most importantly, the high-density sensor array shows unprecedented reliability and robustness with P values <0.0001 for all experiments. Practical implementation of this platform could have a wide range of applications in high-throughput nucleic acid genotyping, detection of amplified pathogenic nucleic acid, detection of cell-free DNA, and electrical readouts for current hybridization-based DNA biomolecular assays.

Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq

Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches. Although these GM lines have different types of integration sites, copy numbers, and levels of gene expression, 21 differentially expressed miRNAs have been found compared to wild type. There is no correlation between transgenic protein expression level and the quantity of differentially expressed miRNAs. This study provides useful data about the miRNA composition of GM plants, and it might be helpful for future risk assessments of miRNA-based GM plants.

Use of Foodomics for Control of Food Processing and Assessing of Food Safety

Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.

Molecular and genetic characterization of barley mutants and genetic mapping of mutant rpr2 required for Rpg1-mediated resistance against stem rust

This study describes the generation, screening, genetic and molecular characterization, and high-resolution mapping of barley mutants susceptible to stem rust ( Puccinia graminis f. sp. tritici ) races MCCF and HKHJ. A single gene, Rpg1, has protected barley cultivars against many races of stem rust pathogen (Puccinia graminis f. sp. tritici) for the last 70 years in the United States and Canada. To identify signaling components of protein product RPG1, we employed a mutagenesis approach. Using this approach, six mutants exhibiting susceptibility to Puccinia graminis f. sp. tritici races MCCF and HKHJ were identified in the gamma irradiated M2 population of resistant cultivar Morex, which carries Rpg1 on chromosome 7H. The mutants retained a functional Rpg1 gene and an apparently functional protein, suggesting that the mutated genes were required for downstream or upstream signaling. Selected mutants were non-allelic, hence each mutant represents a unique gene. Low and high-resolution genetic mapping of the rpr2 mutant identified chromosome 6H (bin 6) as the location of the mutated gene. The target region was reduced to 0.6 cM and gene content analyzed. Based on the published barley genomic sequence, the target region contains approximately 157 genes, including a set that encodes putative leucine-rich receptor-like protein kinases, which may be strong candidates for the gene of interest. Overall, this study presents a strong platform for future map-based cloning of genes identified in this mutant screen.

Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

Development of a construct-based risk assessment framework for genetic engineered crops

Experience gained in the risk assessment (RA) of genetically engineered (GE) crops since their first experimental introductions in the early nineties, has increased the level of familiarity with these breeding methodologies and has motivated several agencies and expert groups worldwide to revisit the scientific criteria underlying the RA process. Along these lines, the need to engage in a scientific discussion for the case of GE crops transformed with similar constructs was recently identified in Argentina. In response to this need, the Argentine branch of the International Life Sciences Institute (ILSI Argentina) convened a tripartite working group to discuss a science-based evaluation approach for transformation events developed with genetic constructs which are identical or similar to those used in previously evaluated or approved GE crops. This discussion considered new transformation events within the same or different species and covered both environmental and food safety aspects. A construct similarity concept was defined, considering the biological function of the introduced genes. Factors like environmental and dietary exposure, familiarity with both the crop and the trait as well as the crop biology, were identified as key to inform a construct-based RA process.

Functional and transcriptional characterization of a barley mutant with impaired photosynthesis

Chemical mutagenesis induces variations that may assist in the identification of targets for adaptation to growth under atmospheric CO2 enrichment. The aim of this work was to characterize the limitations causing reduced photosynthetic capacity in G132 mutagenized barley (Hordeum vulgare L. cv. Graphic) grown in a glasshouse. Compared to the wild type (WT) G132 showed increased transcript levels for the PSII light harvesting complex, but lower levels of chlorophyll, transcripts for protochlorophyllide oxidoreductase A and psbQ, and PSII quantum efficiency in young leaves. Rubisco limitation had an overriding influence on G132 photosynthesis, and was due to strong and selective decreases in Rubisco protein and activity. These reductions were accompanied by enhanced Rubisco transcripts, but increased levels of a Rubisco degradation product. G132 showed lower levels of carbohydrates, amino acids and corresponding transcripts, and proteins, but not of nitrate. Many of the measured parameters recovered in the mutant as development progressed, or decreased less than in the WT, indicating that senescence was delayed. G132 had a longer growth period than the WT and similar final plant dry matter. The reduced resource investment in Rubisco of G132 may prove useful for studies on barley adaptation to elevated CO2 and climate change.

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq

BACKGROUND

Soybean (Glycine max) has been bred for thousands of years to produce seeds rich in protein for human and animal consumption, making them an appealing bioreactor for producing valuable recombinant proteins at high levels. However, the effects of expressing recombinant protein at high levels on bean physiology are not well understood. To address this, we investigated whether gene expression within transgenic soybean seed tissue is altered when large amounts of recombinant proteins are being produced and stored exclusively in the seeds. We used RNA-Seq to survey gene expression in three transgenic soybean lines expressing recombinant protein at levels representing up to 1.61 % of total protein in seed tissues. The three lines included: ST77, expressing human thyroglobulin protein (hTG), ST111, expressing human myelin basic protein (hMBP), and 764, expressing a mutant, nontoxic form of a staphylococcal subunit vaccine protein (mSEB). All lines selected for analysis were homozygous and contained a single copy of the transgene.

METHODS

Each transgenic soybean seed was screened for transgene presence and recombinant protein expression via PCR and western blotting.  Whole seed mRNA was extracted and cDNA libraries constructed for Illumina sequencing.  Following alignment to the soybean reference genome, differential gene expression analysis was conducted using edgeR and cufflinks.  Functional analysis of differentially expressed genes was carried out using the gene ontology analysis tool AgriGO.

RESULTS

The transcriptomes of nine seeds from each transgenic line were sequenced and compared with wild type seeds. Native soybean gene expression was significantly altered in line 764 (mSEB) with more than 3000 genes being upregulated or downregulated. ST77 (hTG) and ST111 (hMBP) had significantly less differences with 52 and 307 differentially expressed genes respectively. Gene ontology enrichment analysis found that the upregulated genes in the 764 line were annotated with functions related to endopeptidase inhibitors and protein synthesis, but suppressed expression of genes annotated to the nuclear pore and to protein transport. No significant gene ontology terms were detected in ST77, and only a few genes involved in photosynthesis and thylakoid functions were downregulated in ST111. Despite these differences, transgenic plants and seeds appeared phenotypically similar to non-transgenic controls. There was no correlation between recombinant protein expression level and the quantity of differentially expressed genes detected.

CONCLUSIONS

Measurable unscripted gene expression changes were detected in the seed transcriptomes of all three transgenic soybean lines analyzed, with line 764 being substantially altered. Differences detected at the transcript level may be due to T-DNA insert locations, random mutations following transformation or direct effects of the recombinant protein itself, or a combination of these. The physiological consequences of such changes remain unknown.

Label and Label-Free Detection Techniques for Protein Microarrays

Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano-biological events.

Comparison of the physiological characteristics of transgenic insect-resistant cotton and conventional lines

The introduction of transgenic insect-resistant cotton into agricultural ecosystems has raised concerns regarding its ecological effects. Many studies have been conducted to compare the differences in characteristics between transgenic cotton and conventional counterparts. However, few studies have focused on the different responses of transgenic cotton to stress conditions, especially to the challenges of pathogens. The aim of this work is to determine the extent of variation in physiological characteristics between transgenic insect-resistant cotton and the conventional counterpart infected by cotton soil-borne pathogens. The results showed that the difference in genetic backgrounds is the main factor responsible for the effects on biochemical characteristics of transgenic cotton when incubating with cotton Fusarium oxysporum. However, genetic modification had a significantly greater influence on the stomatal structure of transgenic cotton than the effects of cotton genotypes. Our results highlight that the differences in genetic background and/or genetic modifications may introduce variations in physiological characteristics and should be considered to explore the potential unexpected ecological effects of transgenic cotton.

A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments

During genetic engineering, DNA is inserted into a plant’s genome, and such insertions are often accompanied by the insertion of additional DNA, deletions and/or rearrangements. These genetic changes are collectively known as insertional effects, and they have the potential to give rise to unintended traits in plants. In addition, there are many other genetic changes that occur in plants both spontaneously and as a result of conventional breeding practices. Genetic changes similar to insertional effects occur in plants, namely as a result of the movement of transposable elements, the repair of double-strand breaks by non-homologous end-joining, and the intracellular transfer of organelle DNA. Based on this similarity, insertional effects should present a similar level of risk as these other genetic changes in plants, and it is within the context of these genetic changes that insertional effects must be considered. Increased familiarity with genetic engineering techniques and advances in molecular analysis techniques have provided us with a greater understanding of the nature and impact of genetic changes in plants, and this can be used to refine pre-market assessments of genetically engineered plants and food and feeds derived from genetically engineered plants.

Successful crossings with early flowering transgenic poplar: interspecific crossings, but not transgenesis, promoted aberrant phenotypes in offspring

In forest tree species, the reproductive phase is reached only after many years or even decades of juvenile growth. Different early flowering systems based on the genetic transfer of heat-shock promoter driven flowering-time genes have been proposed for poplar; however, no fertile flowers were reported until now. Here, we studied flower and pollen development in both HSP::AtFT and wild-type male poplar in detail and developed an optimized heat treatment protocol to obtain fertile HSP::AtFT flowers. Anthers from HSP::AtFT poplar flowers containing fertile pollen grains showed arrested development in stage 12 instead of reaching phase 13 as do wild-type flowers. Pollen grains could be isolated under the binocular microscope and were used for intra- and interspecific crossings with wild-type poplar. F1-seedlings segregating the HSP::AtFT gene construct according to Mendelian laws were obtained. A comparison between intra- and interspecific crossings revealed that genetic transformation had no detrimental effects on F1-seedlings. However, interspecific crossings, a broadly accepted breeding method, produced 47% seedlings with an aberrant phenotype. The early flowering system presented in this study opens new possibilities for accelerating breeding of poplar and other forest tree species. Fast breeding and the selection of transgene-free plants, once the breeding process is concluded, can represent an attractive alternative even under very restrictive regulations.

Tempest in a tea pot: How did the public conversation on genetically modified crops drift so far from the facts?

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.

Analytical method evaluation and discovery of variation within maize varieties in the context of food safety: transcript profiling and metabolomics

Profiling techniques such as microarrays, proteomics, and metabolomics are used widely to assess the overall effects of genetic background, environmental stimuli, growth stage, or transgene expression in plants. To assess the potential regulatory use of these techniques in agricultural biotechnology, we carried out microarray and metabolomic studies of 3 different tissues from 11 conventional maize varieties. We measured technical variations for both microarrays and metabolomics, compared results from individual plants and corresponding pooled samples, and documented variations detected among different varieties with individual plants or pooled samples. Both microarray and metabolomic technologies are reproducible and can be used to detect plant-to-plant and variety-to-variety differences. A pooling strategy lowered sample variations for both microarray and metabolomics while capturing variety-to-variety variation. However, unknown genomic sequences differing between maize varieties might hinder the application of microarrays. High-throughput metabolomics could be useful as a tool for the characterization of transgenic crops. However, researchers will have to take into consideration the impact on the detection and quantitation of a wide range of metabolites on experimental design as well as validation and interpretation of results.

Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA)

Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.

Transcriptional variation in response to salt stress in commonly used Arabidopsis thaliana accessions

Transcriptional variation is increasingly recognized as a component of genetic diversity and environmental adaptation. It can also provide insights into stress responsive determinants and underlying adaptive mechanisms. Prior studies showed phenotypic differences in response to salinity stress for two widely used Arabidopsis thaliana accessions, Wassilewskija-2 (Ws) and Columbia-0 (Col). This study examined changes in global gene expression in relation to differences in response to salt stress among Ws, Col, and the glabrous mutant of Col [Col(gl)]. Transcripts most highly affected by accession and salt stress were related to abiotic or biotic stress responses. Approximately 60% of salt-induced changes in Ws overlapped with changes in Col, suggesting common salt stress responses. However, a markedly greater number of genes was altered in the highly salt sensitive Col, likely reflecting both adaptive responses and salt injury. The Col(gl) transcriptome was least affected by salt. Many salt-responsive transcripts observed in Col were altered in Col(gl) prior to salt stress, indicating that even without salt, the gl1-1 mutation induced a suite of stress responsive genes. Regardless of salt stress, there were greater transcriptomic differences between Col and Col(gl) than between Col and Ws. The transcript expression differences between [Ws vs. Col] and [Col(gl) vs. Col] formed largely non-overlapping sets. Thus, although Ws, Col and Col(gl) are commonly and sometimes interchangeably used, here they displayed distinct responses. Collectively, their observed expression differences likely reflect a combination of adaptive traits, response to injury, or phenotypic buffering of mutational effects.

GMOs in animal agriculture: time to consider both costs and benefits in regulatory evaluations

In 2012, genetically engineered (GE) crops were grown by 17.3 million farmers on over 170 million hectares. Over 70% of harvested GE biomass is fed to food producing animals, making them the major consumers of GE crops for the past 15 plus years. Prior to commercialization, GE crops go through an extensive regulatory evaluation. Over one hundred regulatory submissions have shown compositional equivalence, and comparable levels of safety, between GE crops and their conventional counterparts. One component of regulatory compliance is whole GE food/feed animal feeding studies. Both regulatory studies and independent peer-reviewed studies have shown that GE crops can be safely used in animal feed, and rDNA fragments have never been detected in products (e.g. milk, meat, eggs) derived from animals that consumed GE feed. Despite the fact that the scientific weight of evidence from these hundreds of studies have not revealed unique risks associated with GE feed, some groups are calling for more animal feeding studies, including long-term rodent studies and studies in target livestock species for the approval of GE crops. It is an opportune time to review the results of such studies as have been done to date to evaluate the value of the additional information obtained. Requiring long-term and target animal feeding studies would sharply increase regulatory compliance costs and prolong the regulatory process associated with the commercialization of GE crops. Such costs may impede the development of feed crops with enhanced nutritional characteristics and durability, particularly in the local varieties in small and poor developing countries. More generally it is time for regulatory evaluations to more explicitly consider both the reasonable and unique risks and benefits associated with the use of both GE plants and animals in agricultural systems, and weigh them against those associated with existing systems, and those of regulatory inaction. This would represent a shift away from a GE evaluation process that currently focuses only on risk assessment and identifying ever diminishing marginal hazards, to a regulatory approach that more objectively evaluates and communicates the likely impact of approving a new GE plant or animal on agricultural production systems.

A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy

Genetic modification (GM) by Agrobacterium-mediated transformation is a robust and widely employed method to confer new traits to crops. In this process, a transfer DNA is delivered into the host genome, but it is still unclear how the host genome is altered by this event at single-base resolution. To decipher genomic discrepancy between GM crops and their host, we conducted whole-genome sequencing of a transgenic rice line OSCR11. This rice line expresses a seed-based edible vaccine containing two major pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis. We revealed that genetic differences between OSCR11 and its host a123 were significantly less than those between a123 and its precedent cultivar Koshihikari. The pattern of nucleotide base substitution in OSCR11, relative to a123, was consistent with somaclonal variation. Mutations in OSCR11 probably occurred during the cell culture steps. In addition, strand-specific mRNA-Seq revealed similar transcriptomes of a123 and OSCR11, supporting genomic integrity between them.

Genomic misconception: a fresh look at the biosafety of transgenic and conventional crops. A plea for a process agnostic regulation

The regulation of genetically engineered crops, in Europe and within the legislation of the Cartagena biosafety protocol is built on false premises: The claim was (and unfortunately still is) that there is a basic difference between conventional and transgenic crops, this despite the fact that this has been rejected on scientifically solid grounds since many years. This contribution collects some major arguments for a fresh look at regulation of transgenic crops, they are in their molecular processes of creation not basically different from conventional crops, which are based in their breeding methods on natural, sometimes enhanced mutation. But the fascination and euphoria of the discoveries in molecular biology and the new perspectives in plant breeding in the sixties and seventies led to the wrong focus on transgenic plants alone. In a collective framing process the initial biosafety debates focused on the novelty of the process of transgenesis. When early debates on the risk assessment merged into legislative decisions, this wrong focus on transgenesis alone seemed uncontested. The process-focused view was also fostered by a conglomerate of concerned scientists and biotechnology companies, both with a vested interest to at least tolerate the rise of the safety threshold to secure research money and to discourage competitors of all kinds. Policy minded people and opponent activists without deeper insight in the molecular science agreed to those efforts without much resistance. It is interesting to realize, that the focus on processes was uncontested by a majority of regulators, this despite of serious early warnings from important authorities in science, mainly of US origin. It is time to change the regulation of genetically modified (GM) crops toward a more science based process-agnostic legislation. Although this article concentrates on the critique of the process-oriented regulation, including some details about the history behind, there should be no misunderstanding that there are other important factors responsible for the failure of this kind of process-oriented regulation, most importantly: the predominance of politics in the decision making processes combined with the lack of serious scientific debates on regulatory matters within the European Union and also in the Cartagena system, the obscure and much too complex decision making structures within the EU, and the active, professional, negative and intimidating role of fundamental opposition against GM crops on all levels dealing with flawed science, often declared as better parallel science published by 'independent' scientists.

Assessment of GE food safety using '-omics' techniques and long-term animal feeding studies

Despite the fact that a thorough, lengthy and costly evaluation of genetically engineered (GE) crop plants (including compositional analysis and toxicological tests) is imposed before marketing some European citizens remain sceptical of the safety of GE food and feed. In this context, are additional tests necessary? If so, what can we learn from them? To address these questions, we examined data from 60 recent high-throughput '-omics' comparisons between GE and non-GE crop lines and 17 recent long-term animal feeding studies (longer than the classical 90-day subchronic toxicological tests), as well as 16 multigenerational studies on animals. The '-omics' comparisons revealed that the genetic modification has less impact on plant gene expression and composition than that of conventional plant breeding. Moreover, environmental factors (such as field location, sampling time, or agricultural practices) have a greater impact than transgenesis. None of these '-omics' profiling studies has raised new safety concerns about GE varieties; neither did the long-term and multigenerational studies on animals. Therefore, there is no need to perform such long-term studies in a case-by-case approach, unless reasonable doubt still exists after conducting a 90-day feeding test. In addition, plant compositional analysis and '-omics' profiling do not indicate that toxicological tests should be mandatory. We discuss what complementary fundamental studies should be performed and how to choose the most efficient experimental design to assess risks associated with new GE traits. The possible need to update the current regulatory framework is discussed.

Genetic modification; the development of transgenic ornamental plant varieties

Plant transformation technology (hereafter abbreviated to GM, or genetic modification) has been used to develop many varieties of crop plants, but only a few varieties of ornamental plants. This disparity in the rate and extent of commercialisation, which has been noted for more than a decade, is not because there are no useful traits that can be engineered into ornamentals, is not due to market potential and is not due to a lack of research and development activity. The GM ornamental varieties which have been released commercially have been accepted in the marketplace. In this article, progress in the development of transgenic ornamentals is reviewed and traits useful to both consumers and producers are identified. In considering possible factors limiting the release of genetically modified ornamental products it is concluded that the most significant barrier to market is the difficulty of managing, and the high cost of obtaining, regulatory approval.

Differentially expressed genes distributed over chromosomes and implicated in certain biological processes for site insertion genetically modified rice Kemingdao

Release of genetically modified (GM) plants has sparked off intensive debates worldwide partly because of concerns about potential adverse unintended effects of GM plants to the agro system and the safety of foods. In this study, with the aim of revealing the molecular basis for unintended effects of a single site insertion GM Kemingdao (KMD) rice transformed with a synthetic cry1Ab gene, and bridging unintended effects of KMD rice through clues of differentially expressed genes, comparative transcriptome analyses were performed for GM KMD rice and its parent rice of Xiushui11 (XS11). The results showed that 680 differentially expressed transcripts were identified from 30-day old seedlings of GM KMD rice. The absolute majority of these changed expression transcripts dispersed and located over all rice chromosomes, and existed physical distance on chromosome from the insertion site, while only two transcripts were found to be differentially expressed within the 21 genes located within 100 kb up and down-stream of the insertion site. Pathway and biology function analyses further revealed that differentially expressed transcripts of KMD rice were involved in certain biological processes, and mainly implicated in two types of pathways. One type was pathways implicated in plant stress/defense responses, which were considerably in coordination with the reported unintended effects of KMD rice, which were more susceptible to rice diseases compared to its parent rice XS11; the other type was pathways associated with amino acids metabolism. With this clue, new unintended effects for changes in amino acids synthesis of KMD rice leaves were successfully revealed. Such that an actual case was firstly provided for identification of unintended effects in GM plants by comparative transciptome analysis.

Comparison of salt stress resistance genes in transgenic Arabidopsis thaliana indicates that extent of transcriptomic change may not predict secondary phenotypic or fitness effects

Engineered abiotic stress resistance is an important target for increasing agricultural productivity. There are concerns, however, regarding possible ecological impacts of transgenic crops. In contrast to the first wave of transgenic crops, many abiotic stress resistance genes can initiate complex downstream changes. Transcriptome profiling has been suggested as a comprehensive non-targeted approach to examine the secondary effects. We compared phenotypic and transcriptomic effects of constitutive expression of genes intended to confer salt stress tolerance by three different mechanisms: a transcription factor, CBF3/DREB1a; a metabolic gene, M6PR, for mannitol biosynthesis; and the Na⁺/H⁺ antiporter, SOS1. Transgenic CBF3, M6PR and SOS1 Arabidopsis thaliana were grown together in the growth chamber, greenhouse and field. In the absence of salt, M6PR and SOS1 lines performed comparably with wild type; CBF3 lines exhibited dwarfing as reported previously. All three transgenes conferred fitness advantage when subjected to 100 mm NaCl in the growth chamber. CBF3 and M6PR affected transcription of numerous abiotic stress-related genes as measured by Affymetrix microarray analysis. M6PR additionally modified expression of biotic stress and oxidative stress genes. Transcriptional effects of SOS1 in the absence of salt were smaller and primarily limited to redox-related genes. The extent of transcriptome change, however, did not correlate with the effects on growth and reproduction. Thus, the magnitude of global transcriptome differences may not predict phenotypic differences upon which environment and selection act to influence fitness. These observations have implications for interpretation of transcriptome analyses in the context of risk assessment and emphasize the importance of evaluation within a phenotypic context.

Comparability of imazapyr-resistant Arabidopsis created by transgenesis and mutagenesis

The Arabidopsis CSR1 gene codes for the enzyme acetohydroxyacid synthase (AHAS, EC 2.2.1.6), also known as acetolactate synthase, which catalyzes the first step in branched-chain amino acid biosynthesis. It is inhibited by several classes of herbicides, including the imidazolinone herbicides, such as imazapyr; however, a substitution mutation in csr1-2 (Ser-653-Asn) confers selective resistance to the imidazolinones. The transcriptome of csr1-2 seedlings grown in the presence of imazapyr has been shown in a previous study (Manabe in Plant Cell Physiol 48:1340-1358, 2007) to be identical to that of wild-type seedlings indicating that AHAS is the sole target of imazapyr and that the mutation is not associated with pleiotropic effects detectable by transcriptome analysis. In this study, a lethal null mutant, csr1-7, created by a T-DNA insertion into the CSR1 gene was complemented with a randomly-inserted 35S/CSR1-2/NOS transgene in a subsequent genetic transformation event. A comparison of the csr1-2 substitution mutant with the transgenic lines revealed that all were resistant to imazapyr; however, the transgenic lines yielded significantly higher levels of resistance and greater biomass accumulation in the presence of imazapyr. Microarray analysis revealed few differences in their transcriptomes. The most notable was a sevenfold to tenfold elevation in the CSR1-2 transcript level. The data indicate that transgenesis did not create significant unintended pleiotropic effects on gene expression and that the mutant and transgenic lines were highly similar, except for the level of herbicide resistance.

The identification and interpretation of differences in the transcriptomes of organically and conventionally grown potato tubers

In the European integrated research project SAFEFOODS, one of the aims was to further establish the potential of transcriptomics for the assessment of differences between plant varieties grown under different environmental conditions. Making use of the knowledge of cellular processes and interactions is one of the ways to obtain a better understanding of the differences found with transcriptomics. For the present study the potato genotype Santé was grown under both organic and conventional fertilizer, and each combined with either organic or conventional crop protection, giving four different treatments. Samples were derived from the European project QualityLowInputFood (QLIF). Microarray data were analyzed using different statistical tools (multivariate, principal components analysis (PCA); univariate, analysis of variance (ANOVA)) and with pathway analysis (hypergeometric distribution (HGD) and gene set enrichment analysis (GSEA)). Several biological processes were implicated as a result of the different treatments of the plants. Most obvious were the lipoxygenase pathway, with higher expression in organic fertilizer and lower expression in organic crop protection; the starch synthase pathway, with higher expression in both organic crop protection and fertilizer; and the biotic stress pathway, with higher expression in organic fertilizer. This study confirmed that gene expression profiling in combination with pathway analysis can identify and characterize differences between plants grown under different environmental conditions.

Unsupervised principal component analysis of NMR metabolic profiles for the assessment of substantial equivalence of transgenic grapes (Vitis vinifera)

Substantial equivalence is a key concept in the evaluation of unintended and potentially harmful metabolic impact consequent to a genetic modification of food. The application of unsupervised multivariate data analysis to the metabolic profiles is expected to improve the effectiveness of such evaluation. The present study uses NMR spectra of hydroalcoholic extracts, as holistic representations of the metabolic profiles of grapes, to evaluate the effect of the insertion of one or three copies of the DefH9-iaaM construct in plants of Silcora and Thompson Seedless cultivars. The comparison of the metabolic profiles of transgenic derivatives with respect to their corresponding natural lines pointed out that the overall metabolic changes occur in the same direction, independent of the host genotype, although the two cultivars are modified to different extents. A higher number of copies not only produces a larger effect but also modifies the whole pattern of perturbed metabolites.