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Comparative analysis of genetically-modified crops: Part 1. Conditional difference testing with a given genetic background.
Jiang, C, Meng, C, Schapaugh, A
PloS one. 2019;(1):e0210747
Abstract
The European Food Safety Authority (EFSA) mandates two sets of statistical tests in the comparative assessment of a genetically-modified (GM) crop: difference testing to demonstrate whether the GM crop is different from its appropriate non-traited control; and equivalence testing to demonstrate whether it is equivalent to conventional references with an history-of-safe-use. The equivalence testing method prescribed by EFSA confounds the so-called GM trait effect with genotypic differences between the reference varieties and non-traited control. Critically, these genotypic differences, which we define as a 'control background effect', are the result of conventional plant breeding. Thus, the result of EFSA equivalence testing often has little or nothing to do with the GM trait effect, which should be the sole focus of the comparative assessment. Here, an integrated method is introduced for both difference and equivalence testing that considers the differences of the three genotype groups (GM, control, and references) as a two-dimensional random variable. A novel statistical model is proposed, called the trait model, that treats the effects of the GM and control materials as fixed for their difference, and as random for their common background. For significance testing, the covariance structure of the three genotype groups is utilized to decompose the differences into the trait effect and the control background effect. The trait difference is then derived as a conditional mean, given the background effect. The comparative assessment can then focus on the conditional mean difference, which is independent of the control background effect. Furthermore, the trait model is flexible enough to include various types of genotype-by-environment (G×E) interactions inherent to the experimental design of the trial. Numerical evaluations and simulations show that this new method is substantially more efficient than the current EFSA method in reducing both Type I and Type II errors (protecting both the consumer and producer risk) after the background effect is removed from the test statistic, and successfully addresses two major criticisms (i.e. statistical model lack of G×E, and study-specific equivalence criterion) that have been raised.
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Comparative assessment of multiple criteria for the in silico prediction of cross-reactivity of proteins to known allergens.
Mirsky, HP, Cressman, RF, Ladics, GS
Regulatory toxicology and pharmacology : RTP. 2013;(2):232-9
Abstract
Genetically modified crops are becoming important components of a sustainable food supply and must be brought to market efficiently while also safeguarding the public from cross-reactivity of novel proteins to known allergens. Bioinformatic assessments can help to identify proteins warranting further experimental checks for cross-reactivity. This study is a large-scale in silico evaluation of assessment criteria, including searches for: alignments between a query and an allergen having ≥ 35% identity over a length ≥ 80; any sequence (of some minimum length) found in both a query and an allergen; any alignment between a query and an allergen with an E-value below some threshold. The criteria and an allergen database (AllergenOnline) are used to assess 27,243 Viridiplantae proteins for potential allergenicity. (A protein is classed as a "real allergen" if it exceeds a test-specific level of identity to an AllergenOnline entry; assessment of real allergens in the query set is against a reduced database from which the identifying allergen has been removed.) Each criterion's ability to minimize false positives without increasing false negative levels of current methods is determined. At best, the data show a reduction in false positives to ∼6% (from ∼10% under current methods) without any increase in false negatives.
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3.
Comparative safety assessment of plant-derived foods.
Kok, EJ, Keijer, J, Kleter, GA, Kuiper, HA
Regulatory toxicology and pharmacology : RTP. 2008;(1):98-113
Abstract
The second generation of genetically modified (GM) plants that are moving towards the market are characterized by modifications that may be more complex and traits that more often are to the benefit of the consumer. These developments will have implications for the safety assessment of the resulting plant products. In part of the cases the same crop plant can, however, also be obtained by 'conventional' breeding strategies. The breeder will decide on a case-by-case basis what will be the best strategy to reach the set target and whether genetic modification will form part of this strategy. This article discusses important aspects of the safety assessment of complex products derived from newly bred plant varieties obtained by different breeding strategies. On the basis of this overview, we conclude that the current process of the safety evaluation of GM versus conventionally bred plants is not well balanced. GM varieties are elaborately assessed, yet at the same time other crop plants resulting from conventional breeding strategies may warrant further food safety assessment for the benefit of the consumer. We propose to develop a general screening frame for all newly developed plant varieties to select varieties that cannot, on the basis of scientific criteria, be considered as safe as plant varieties that are already on the market.
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4.
[Comparison of commercialization of transgenic crops in China and world-wide].
Wang, X, Jia, S
Sheng wu gong cheng xue bao = Chinese journal of biotechnology. 2008;(4):541-6
Abstract
Currently, transgenic crops create huge economic, social and ecological benefits with the development of its commercial production. For China, the speed of development and commercialization of transgenic crops is a strategic issue for the sustainable agriculture development and the international competitiveness of our agricultural products. In this paper, we compared and analyzed the status of commercialization of transgenic crops in China and world-wide.
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5.
Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 2. Assessing natural variability.
Ruebelt, MC, Lipp, M, Reynolds, TL, Astwood, JD, Engel, KH, Jany, KD
Journal of agricultural and food chemistry. 2006;(6):2162-8
Abstract
Proteomics is currently tested as a complementary tool for the safety assessment of genetically modified (GM) crops. Understanding the natural variability of the proteome is crucial for the interpretation of biological differences between transgenic and nontransgenic parental lines. The natural variation of seed protein profiles among a set of 12 Arabidopsis thaliana ecotypes was determined by utilizing two-dimensional electrophoresis (2DE). The total number of different resolved protein spots found among the 12 ecotypes was 931 with a range of 573 (Mt-0) to 653 (Condara) in any one ecotype. Although the ecotypes were grown side-by-side in an environmentally controlled growth chamber, almost half of the resolved spots varied with respect to their presence/absence, and 95% of the spots present in all ecotypes varied in spot quantity (2-53-fold). In the evaluation of unintended effects of genetic modification, it is concluded that the experimental design must account for existing natural variability, which, in the case of the expressed proteome, can be substantial.
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6.
Transgene escape: what potential for crop-wild hybridization?
Armstrong, TT, Fitzjohn, RG, Newstrom, LE, Wilton, AD, Lee, WG
Molecular ecology. 2005;(7):2111-32
Abstract
To date, regional surveys assessing the risk of transgene escape from GM crops have focused on records of spontaneous hybridization to infer the likelihood of crop transgene escape. However, reliable observations of spontaneous hybridization are lacking for most floras, particularly outside Europe. Here, we argue that evidence of interspecific reproductive compatibility derived from experimental crosses is an important component of risk assessment, and a useful first step especially where data from field observations are unavailable. We used this approach to assess the potential for transgene escape via hybridization for 123 widely grown temperate crops and their indigenous and naturalized relatives present in the New Zealand flora. We found that 66 crops (54%) are reproductively compatible with at least one other indigenous or naturalized species in the flora. Limited reproductive compatibility with wild relatives was evident for a further 12 crops (10%). Twenty-five crops (20%) were found to be reproductively isolated from all their wild relatives in New Zealand. For the remaining 20 crops (16%), insufficient information was available to determine levels of reproductive compatibility with wild relatives. Our approach may be useful in other regions where spontaneous crop-wild hybridization has yet to be well documented.
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Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content.
Cahoon, EB, Hall, SE, Ripp, KG, Ganzke, TS, Hitz, WD, Coughlan, SJ
Nature biotechnology. 2003;(9):1082-7
Abstract
Tocotrienols are the primary form of vitamin E in seeds of most monocot plants, including cereals such as rice and wheat. As potent antioxidants, tocotrienols contribute to the nutritive value of cereal grains in human and livestock diets. cDNAs encoding homogentisic acid geranylgeranyl transferase (HGGT), which catalyzes the committed step of tocotrienol biosynthesis, were isolated from barley, wheat and rice seeds. Transgenic expression of the barley HGGT in Arabidopsis thaliana leaves resulted in accumulation of tocotrienols, which were absent from leaves of nontransformed plants, and a 10- to 15-fold increase in total vitamin E antioxidants (tocotrienols plus tocopherols). Overexpression of the barley HGGT in corn seeds resulted in an increase in tocotrienol and tocopherol content of as much as six-fold. These results provide insight into the genetic basis for tocotrienol biosynthesis in plants and demonstrate the ability to enhance the antioxidant content of crops by introduction of an enzyme that redirects metabolic flux.
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8.
A lignin-specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification.
Blee, KA, Choi, JW, O'Connell, AP, Schuch, W, Lewis, NG, Bolwell, GP
Phytochemistry. 2003;(1):163-76
Abstract
A tobacco peroxidase isoenzyme (TP60) was down-regulated in tobacco using an antisense strategy, this affording transformants with lignin reductions of up to 40-50% of wild type (control) plants. Significantly, both guaiacyl and syringyl levels decreased in essentially a linear manner with the reductions in lignin amounts, as determined by both thioacidolysis and nitrobenzene oxidative analyses. These data provisionally suggest that a feedback mechanism is operative in lignifying cells, which prevents build-up of monolignols should oxidative capacity for their subsequent metabolism be reduced. Prior to this study, the only known rate-limiting processes in the monolignol/lignin pathways involved that of Phe supply and the relative activities of cinnamate-4-hydroxylase/p-coumarate-3-hydroxylase, respectively. These transformants thus provide an additional experimental means in which to further dissect and delineate the factors involved in monolignol targeting to precise regions in the cell wall, and of subsequent lignin assembly. Interestingly, the lignin down-regulated tobacco phenotypes displayed no readily observable differences in overall growth and development profiles, although the vascular apparatus was modified.
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9.
Five years of Bt cotton in China - the benefits continue.
Pray, CE, Huang, J, Hu, R, Rozelle, S
The Plant journal : for cell and molecular biology. 2002;(4):423-30
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Abstract
Bt cotton is spreading very rapidly in China, in response to demand from farmers for technology that will reduce both the cost of pesticide applications and exposure to pesticides, and will free up time for other tasks. Based on surveys of hundreds of farmers in the Yellow River cotton-growing region in northern China in 1999, 2000 and 2001, over 4 million smallholders have been able to increase yield per hectare, and reduce pesticide costs, time spent spraying dangerous pesticides, and illnesses due to pesticide poisoning. The expansion of this cost-saving technology is increasing the supply of cotton and pushing down the price, but prices are still sufficiently high for adopters of Bt cotton to make substantial gains in net income.