Using Metabolomics To Estimate Unintended Effects in Transgenic Crop Plants: Problems, Promises, and Opportunities

Transgenic crops are widespread in some countries and sectors of the agro-economy, but are also highly contentious. Proponents of transgenic crop improvement often cite the “substantial equivalence” of transgenic crops to the their nontransgenic parents and sibling varieties. Opponents of transgenic crop improvement dismiss the substantial equivalence standard as being without statistical basis and emphasize the possible unintended effects to food quality and composition due to genetic transformation. Systems biology approaches should help consumers, regulators, and other stakeholders make better decisions regarding transgenic crop improvement by characterizing the composition of conventional and transgenically improved crop species and products. In particular, metabolomic profiling via mass spectrometry and nuclear magnetic resonance can make broad and deep assessments of food quality and content. The metabolome observed in a transgenic variety can then be assessed relative to the consumer and regulator accepted phenotypic range observed among conventional varieties. I briefly discuss both targeted (closed architecture) and nontargeted (open architecture) metabolomics with respect to the transgenic crop debate and highlight several challenges to the field. While most experimental examples come from tomato (Solanum lycoperiscum), analytical methods from all of systems biology are discussed.     

Safe composition levels of transgenic crops assessed via a clinical medicine model

Substantial equivalence has become established as a foundation concept in the safety evaluation of transgenic crops. In the case of a food and feed crop, no single variety is considered the standard for safety or nutrition, so the substantial equivalence of transgenic crops is investigated relative to the array of commercial crop varieties with a history of safe consumption. Although used extensively in clinical medicine to compare new generic drugs with brand-name drugs, equivalence limits are shown to be a poor model for comparing transgenic crops with an array of reference crop varieties. We suggest an alternate model, also analogous to that used in clinical medicine, where reference intervals are constructed for a healthy heterogeneous population. Specifically, we advocate the use of distribution-free tolerance intervals calculated across a large amount of publicly available compositional data such as is found in the International Life Sciences Institute Crop Composition Database.     

Assays of the production of harmful substances by genetically modified oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.) plants in accordance with regulations for evaluating the impact on biodiversity in Japan

Environmental risk assessment of transgenic crops is implemented under the Cartagena Protocol domestic law in accordance with guidelines for implementing the assessment established by the Ministry of Agriculture, Forestry and Fisheries (MAFF) and the Ministry of Environment (MOE) in Japan. Environmental risk assessments of transgenic crops are implemented based on the concept of ‘substantial equivalence’ to conventional crops. A unique requirement in Japan to monitor the production of harmful substances, or allelochemicals, is unparalleled in other countries. The potential for allelochemicals to be secreted from the roots of transgenic crops to affect other plants or soil microflora or for substances in the plant body to affect other plants after dying out must be evaluated. We evaluated the allelopathic potential of seven transgenic oilseed rape (Brassica napus L.) lines that express glufosinate tolerance in terms of substantial equivalence to conventional oilseed rape lines, and established evaluation methods. Our results indicate no potential production of allelochemicals for any of the seven transgenic oilseed rape lines compared with conventional oilseed rape lines.     

Improving the monitoring of crop productivity using spaceborne solar‐induced fluorescence

Large‐scale monitoring of crop growth and yield has important value for forecasting food production and prices and ensuring regional food security. A newly emerging satellite retrieval, solar‐induced fluorescence (SIF) of chlorophyll, provides for the first time a direct measurement related to plant photosynthetic activity (i.e. electron transport rate). Here, we provide a framework to link SIF retrievals and crop yield, accounting for stoichiometry, photosynthetic pathways, and respiration losses. We apply this framework to estimate United States crop productivity for 2007–2012, where we use the spaceborne SIF retrievals from the Global Ozone Monitoring Experiment‐2 satellite, benchmarked with county‐level crop yield statistics, and compare it with various traditional crop monitoring approaches. We find that a SIF‐based approach accounting for photosynthetic pathways (i.e. C₃ and C₄ crops) provides the best measure of crop productivity among these approaches, despite the fact that SIF sensors are not yet optimized for terrestrial applications. We further show that SIF provides the ability to infer the impacts of environmental stresses on autotrophic respiration and carbon‐use‐efficiency, with a substantial sensitivity of both to high temperatures. These results indicate new opportunities for improved mechanistic understanding of crop yield responses to climate variability and change.     

Engineering of PHB synthesis causes improved elastic properties of flax fibers

Flax stem is a source of fiber used by the textile industry. Flax fibers are separated from other parts of stems in the process called retting and are probably the first plant fibers used by man for textile purposes (1). Nowadays flax cultivation is often limited because of its lower elastic property compared to cotton fibers. Thus the goal of this study was to increase the flax fiber quality using a transgenic approach. Expression of three bacterial genes coding for beta-ketothiolase (phb A), acetoacetyl-CoA reductase (phb B), and PHB synthase (phb C) resulted in poly-beta-hydroxybutyrate (PHB) accumulation in the plant stem. PHB is known as a biodegradable thermoplastic displaying chemical and physical properties similar to those of conventional plastics (i.e., polypropylene). The fibers isolated from transgenic flax plants cultivated in the field and synthesizing PHB were then studied for biomechanical properties. All measured parameters, strength, Young's modulus, and energy for failure of flax fibers, were significantly increased. Thus the substantial improvement in elastic properties of fibers from the transgenic line has been achieved. Since the acetyl CoA, substrate for PHB synthesis, is involved not only for energy production but also for synthesis of many cellular constituents, the goal of this study was also the analysis of those metabolites, which interfere with plant physiology and thus fiber quality. The analyzed plants showed that reduction in lignin, pectin, and hemicellulose levels resulted in increased retting efficiency. A significant increase in phenolic acids was also detected, and this was the reason for improved plant resistance to pathogen infection. However, a slight decrease in crop production was detected.     

Production of insect-resistant transgenic rice plants for use in practical agriculture

Plant biotechnology provides a powerful solution to boost agricultural productivity and nutritional quality. The development process of a transgenic crop includes multiple steps that consist of gene isolation for a target trait, generation of T₀ transgenic crops, characterization of the transgene, evaluation of agronomic performance of transgenic crops, selection of elite transgenic lines and assessment of target trait efficacy. Here, we developed elite insect-resistant transgenic rice plants that may satisfy the standards of biosafety assessments. We made a construct with the insecticide cry1Ac gene for a target trait. A total of 310 T₀ transgenic lines were generated and underwent extensive analysis. We selected four T₃ lines that contain a single-copy transgene inserted into intergenic regions of the rice genome. During this process, we critically analyzed the transgenic lines with five checkpoints that include single copy of transgene, its integration into intergenic region, clean T-DNA arrangement, stability of transgene through generations and substantial equivalence of transgenic plants in agronomic traits other than insect resistance. Consequently, we obtained insect-resistant transgenic rice plants that can be used in practical agriculture.     

Cisgenics - A Sustainable Approach for Crop Improvement

The implication of molecular biology in crop improvement is now more than three decades old. Not surprisingly, technology has moved on, and there are a number of new techniques that may or may not come under the genetically modified (GM) banner and, therefore, GM regulations. In cisgenic technology, cisgenes from crossable plants are used and it is a single procedure of gene introduction whereby the problem of linkage drag of other genes is overcome. The gene used in cisgenic approach is similar compared with classical breeding and cisgenic plant should be treated equally as classically bred plant and differently from transgenic plants. Therefore, it offers a sturdy reference to treat cisgenic plants similarly as classically bred plants, by exemption of cisgenesis from the current GMO legislations. This review covers the implications of cisgenesis towards the sustainable development in the genetic improvement of crops and considers the prospects for the technology.     

转不可翻译PVYN CP基因烟草的抗病性分析

我们曾报道表达不可翻译PVY~N CP基因的转基因烟草抗病性是由RNA介导的,其抗病性类似于转录后的基因沉默(PTGS)。本研究以这类不同抗性的Tn代转基因烟草植株为材料,对自交后的T1代转基因植株的遗传和抗病性进行了分析,并选取部分T_1代抗病株系自交留种。对T_2代RNA介导抗病性转基因植株进行了分子分析和一系列抗病性研究。结果表明,含1-2个转基因拷贝的T_0代感病植株,在T_1代中的Km抗性分离符合单位点插入的3∶1的遗传规律;含3个或3个以上转基因拷贝的T_0代中抗或高抗植株,在T_1代中的Km抗性分离符合多位点插入的15∶1或63∶1的遗传规律。大多数T_1、T_2代转基因植株的抗病性与转基因拷贝数成正相关,转基因在T_1、T_2代植株中能够转录表达,且转基因植株之间转基因mRNA在细胞质中的积累水平与转基因植株的抗病性成负相关。转基因植株的抗病性能够在T_1、T_2代中遗传,且T_2代转基因植株的抗病性具有以下特征:1)既抗病毒粒体又抗病毒RNA的侵染,且这种抗病性不受接种物剂量的影响;2)抗病谱较窄,只对PVY的某些株系具有高度抗病性;3)与传毒方式无关,既抗摩擦接种又抗带毒蚜虫接种;4)与植株的发育阶段没有关系。     

Palatability of transgenic birch and aspen to roe deer and mountain hare

Genetic engineering of plant resistance characteristics against fungi may unintentionally influence traits that are important for plant–herbivore interactions. We studied the palatability of transgenic birch (Betula pendula), aspen (Populus tremula) and hybrid aspen (P. tremula x tremuloides) genetically modified with the aim to improve fungal disease resistance, to selective mammalian herbivores in cafeteria tests. Roe deer (Capreolus capreolus) were fed with transgenic birch carrying a sugar beet chitinase IV gene. In the experiment with roe deer, none of the six transgenic birch lines differed significantly from the wild-type control in the proportion of consumed plant biomass. Correlation analyses suggested that sugar content did not guide the feeding preferences of roe deer but revealed a positive correlation between starch content and proportion of mass consumed. However, the variation in starch content could not be related to the level of transgene expression. Mountain hares (Lepus timidus) were fed with plant material from chitinase transgenic birch and aspen and hybrid aspen that carried a pinosylvin synthase gene from Scots pine. One transgenic birch line was significantly less palatable to hares than the wild-type control. The results of this study suggest that plant genotype may be related to the palatability of plant material when transgenic and wild-type woody plant material is used as winter food for hares. The results of this case study did not reveal changes in the palatability of the studied transgenic lines that could be readily related to the functioning of the used transgenes.     

转不可翻译PVY^N CP基因烟草的抗病性分析

我们曾报道表达不可翻译PVY^N CP基因的转基因烟草抗病性是由RNA介导的,其抗病性类似于转录后的基因沉默(PTGS)。本研究以这类不同抗性的T0代转基因烟草植株为材料,对自交后的T1代转基因植株的遗传和抗病性进行了分析,并选取部分T1代抗病株系自交留种。对T2代RNA介导抗病性转基因植株进行了分子分析和一系列抗病性研究。结果表明,含1—2个转基因拷贝的T0代感病植株,在T1代中的Km抗性分离符合单位点插入的3：1的遗传规律;含3个或3个以上转基因拷贝的T0代中抗或高抗植株,在T1代中的Km抗性分离符合多位点插入的15：1或63：1的遗传规律。大多数T1、T2代转基因植株的抗病性与转基因拷贝数成正相关,转基因在T1、T2代植株中能够转录表达,且转基因植株之间转基因mRNA在细胞质中的积累水平与转基因植株的抗病性成负相关。转基因植株的抗病性能够在T1、T2代中遗传,且T2代转基因植株的抗病性具有以下特征：1)既抗病毒粒体又抗病毒RNA的侵染,且这种抗病性不受接种物剂量的影响;2)抗病谱较窄,只对PVY的某些株系具有高度抗病性;3)与传毒方式无关,既抗摩擦接种又抗带毒蚜虫接种;4)与植株的发育阶段没有关系。     

Antioxidative enzymes,calcium, and ABA signaling pathway are required for the stress tolerance of transgenic wheat plant by the ectopic expression of harpin protein fragment Hpa1<Subscript>10–42</Subscript> under heat stress

Genetic engineering for heat stress tolerance can promote crop growth and improve yield. One wheat (Triticum aestivum L.) line Y16 (wild type) and two transgenic plants (Y16-3 and Y16-46) that express Hpa1_10-42, a functional fragment of harpin protein, were used in this study to investigate their possible abiotic stress tolerance under heat stress. Results showed that enhanced thermotolerance was observed in the Y16-3 and Y16-46 lines over the control wheat under stress conditions. However, this increased stress tolerance was significantly abolished by specific inhibitors such as fluridone or sodium tungstate (i.e., arrests abscisic acid (ABA) biosynthesis) and EGTA or La³⁺ (i.e., arrests Ca²⁺ signaling pathway) under heat exposure. By contrast, high activities of antioxidant enzymes such as superoxide dismutase, catalase, and ascorbate peroxidase (but not peroxidase) and low levels of oxidative damage (thiobarbituric acid reactive substance (TBARS) and chlorophyll) were detected in transgenic wheat lines compared with the control plant under stress exposure. However, this significant difference diminished after the addition of these specific inhibitors. Furthermore, a slight increase of H₂O₂ was observed in the transgenic plant, instead of the control, without the addition of chemicals under heat stress. These results suggested that antioxidant enzymes, calcium, and ABA signaling pathways were involved in this Hpa1_10–42-mediated thermotolerance of transgenic wheat plants under stress exposure. Finally, a hypothetical model based on H₂O₂ signaling was proposed to illustrate the possible mechanism of this enhanced heat stress tolerance.     

Engineered selective plant male sterility through pollen‐specific expression of the EcoRI restriction endonuclease

Unintended gene flow from transgenic plants via pollen, seed and vegetative propagation is a regulatory concern because of potential admixture in food and crop systems, as well as hybridization and introgression to wild and weedy relatives. Bioconfinement of transgenic pollen would help address some of these concerns and enable transgenic plant production for several crops where gene flow is an issue. Here, we demonstrate the expression of the restriction endonuclease EcoRI under the control of the tomato pollen‐specific LAT52 promoter is an effective method for generating selective male sterility in Nicotiana tabacum (tobacco). Of nine transgenic events recovered, four events had very high bioconfinement with tightly controlled EcoRI expression in pollen and negligible‐to‐no expression other plant tissues. Transgenic plants had normal morphology wherein vegetative growth and reproductivity were similar to nontransgenic controls. In glasshouse experiments, transgenic lines were hand‐crossed to both male‐sterile and emasculated nontransgenic tobacco varieties. Progeny analysis of 16 000–40 000 seeds per transgenic line demonstrated five lines approached (>99.7%) or attained 100% bioconfinement for one or more generations. Bioconfinement was again demonstrated at or near 100% under field conditions where four transgenic lines were grown in close proximity to male‐sterile tobacco, and 900–2100 seeds per male‐sterile line were analysed for transgenes. Based upon these results, we conclude EcoRI‐driven selective male sterility holds practical potential as a safe and reliable transgene bioconfinement strategy. Given the mechanism of male sterility, this method could be applicable to any plant species.     

A field-grown transgenic tomato line expressing higher levels of polyamines reveals legume cover crop mulch-specific perturbations in fruit phenotype at the levels of metabolite profiles, gene expression, and agronomic characteristics

Genetic modification of crop plants to introduce desirable traits such as nutritional enhancement, disease and pest resistance, and enhanced crop productivity is increasingly seen as a promising technology for sustainable agriculture and boosting food production in the world. Independently, cultural practices that utilize alternative agriculture strategies including organic cultivation subscribe to sustainable agriculture by limiting chemical usage and reduced tillage. How the two together affect fruit metabolism or plant growth in the field or whether they are compatible has not yet been tested. Fruit-specific yeast S-adenosylmethionine decarboxylase (ySAMdc) line 579HO, and a control line 556AZ were grown in leguminous hairy vetch (Vicia villosa Roth) (HV) mulch and conventional black polyethylene (BP) mulch, and their fruit analysed. Significant genotypexmulch-dependent interactions on fruit phenotype were exemplified by differential profiles of 20 fruit metabolites such as amino acids, sugars, and organic acids. Expression patterns of the ySAMdc transgene, and tomato SAMdc, E8, PEPC, and ICDHc genes were compared between the two lines as a function of growth on either BP or HV mulch. HV mulch significantly stimulated the accumulation of asparagine, glutamate, glutamine, choline, and citrate concomitant with a decrease in glucose in the 556AZ fruits during ripening as compared to BP. It enables a metabolic system in tomato somewhat akin to the one in higher polyamine-accumulating transgenic fruit that have higher phytonutrient content. Finally, synergism was found between HV mulch and transgenic tomato in up-regulating N:C indicator genes PEPC and ICDHc in the fruit.     

Advances in selectable marker genes for plant transformation

Plant transformation systems for creating transgenics require separate process for introducing cloned DNA into living plant cells. Identification or selection of those cells that have integrated DNA into appropriate plant genome is a vital step to regenerate fully developed plants from the transformed cells. Selectable marker genes are pivotal for the development of plant transformation technologies because marker genes allow researchers to identify or isolate the cells that are expressing the cloned DNA, to monitor and select the transformed progeny. As only a very small portion of cells are transformed in most experiments, the chances of recovering transgenic lines without selection are usually low. Since the selectable marker gene is expected to function in a range of cell types it is usually constructed as a chimeric gene using regulatory sequences that ensure constitutive expression throughout the plant. Advent of recombinant DNA technology and progress in plant molecular biology had led to a desire to introduce several genes into single transgenic plant line, necessitating the development of various types of selectable markers. This review article describes the developments made in the recent past on plant transformation systems using different selection methods adding a note on their importance as marker genes in transgenic crop plants.     

Improving salinity tolerance of plants through conventional breeding and genetic engineering: An analytical comparison

The last century has witnessed a substantial improvement in yield potential, quality and disease resistance in crops. This was indeed the outcome of conventional breeding, which was achieved with little or no knowledge of underlying physiological and biochemical phenomena related to a trait. Also the resources utilized on programs involving conventional breeding were not of great magnitude. Plant breeders have also been successful during the last century in producing a few salt-tolerant cultivars/lines of some potential crops through conventional breeding, but this again has utilized modest resources. However, this approach seems now inefficient due to a number of reasons, and alternatively, genetic engineering for improving crop salt tolerance is being actively followed these days by the plant scientists, world-over. A large number of transgenic lines with enhanced salt tolerance of different crops can be deciphered from the literature but up to now only a very few field-tested cultivars/lines are known despite the fact that considerable resources have been expended on the sophisticated protocols employed for generating such transgenics. This review analytically compares the achievements made so far in terms of producing salt-tolerant lines/cultivars through conventional breeding or genetic engineering.     

Breeding for micronutrients in staple food crops from a human nutrition perspective

Over three billion people are currently micronutrient (i.e. micronutrient elements and vitamins) malnourished, resulting in egregious societal costs including learning disabilities among children, increased morbidity and mortality rates, lower worker productivity, and high healthcare costs, all factors diminishing human potential, felicity, and national economic development. Nutritional deficiencies (e.g. iron, zinc, vitamin A) account for almost two-thirds of the childhood death worldwide. Most of those afflicted are dependent on staple crops for their sustenance. Importantly, these crops can be enriched (i.e. 'biofortified') with micronutrients using plant breeding and/or transgenic strategies, because micronutrient enrichment traits exist within their genomes that can to used for substantially increasing micronutrient levels in these foods without negatively impacting crop productivity. Furthermore, 'proof of concept' studies have been published using transgenic approaches to biofortify staple crops (e.g. high beta-carotene 'golden rice' grain, high ferritin-Fe rice grain, etc). In addition, micronutrient element enrichment of seeds can increase crop yields when sowed to micronutrient-poor soils, assuring their adoption by farmers. Bioavailability issues must be addressed when employing plant breeding and/or transgenic approaches to reduce micronutrient malnutrition. Enhancing substances (e.g. ascorbic acid, S-containing amino acids, etc) that promote micronutrient bioavailability or decreasing antinutrient substances (e.g. phytate, polyphenolics, etc) that inhibit micronutrient bioavailability, are both options that could be pursued, but the latter approach should be used with caution. The world's agricultural community should adopt plant breeding and other genetic technologies to improve human health, and the world's nutrition and health communities should support these efforts. Sustainable solutions to this enormous global problem of 'hidden hunger' will not come without employing agricultural approaches.     

Transgenic potatoes with enhanced levels of nematode resistance do not have altered susceptibility to nontarget aphids

Cysteine proteinase inhibitors (cystatins) confer resistance to plant-parasitic nematodes when expressed in transgenic plants. The survival and growth of nymphs of the peach-potato aphid, Myzus persicae, were adversely affected when cystatins were added to artificial diets. When aphids were clip-caged onto transgenic plants expressing chicken egg white cystatin (CEWc) there was no adverse effect on aphid fitness. Field populations of aphids on transgenic Desiree potatoes, expressing CEWc or a modified version of oryzacystatin I, were not significantly different from populations on control Desiree plants. The effect of other nematode management options on aphid numbers was also studied. A conventionally bred cultivar, with partial nematode resistance, supported higher populations of aphids than the transgenic lines at the beginning of the sampling period. Peak aphid densities on the untreated control and untreated transgenic lines were 7 and 5.2 aphids per plant. Aldicarb, commonly used to control nematodes on potatoes, reduced the value to less than 0.2 aphids per plant. The results demonstrate that levels of expression in the plant tissue actually consumed are important in determining the risk of cystatins to nontarget invertebrates. The study also highlights the importance of including currently used management options in any assessment of the impact of transgenic plants on nontarget organisms.