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1.
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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2.
Report on the SCRA Nuts and Bolts Workshop II: case studies of citrus greening, Ultra-low Gossypol Cotton, and blight tolerant, low-acrylamide potato.
Hood, EE, Eversole, KA, Leach, L, Hogan, M, McHughen, A, Cordts, J, Rathore, K, Rood, T, Collinge, S, Irey, M
GM crops & food. 2019;(3):139-158
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Abstract
To be commercialized and grown in the US, genetically engineered (GE) crops typically go through an extensive food, feed, and environmental safety assessment process which, in certain instances, requires complex consultations with three different US regulatory agencies. Many small market, niche, and specialty crops have been genetically engineered using the modern tools of recombinant DNA but few have been commercialized due to real or perceived regulatory constraints. This workshop discussed the practical aspects of developing dossiers on GE specialty, niche, or small-market crops/products for submission to US regulatory agencies. This workshop focused on actual case studies, and provided an opportunity for public or private sector scientists and crop developers to spend time with regulatory officials to learn the specifics of compiling a dossier for regulatory approval. The objective of the workshop was to explain and demystify data requirements and regulatory dossier compilation by small companies, academics, and other developers.
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3.
Implementing an EU opt-in mechanism for GM crop cultivation.
Eriksson, D, de Andrade, E, Bohanec, B, Chatzopoulou, S, Defez, R, Leiva Eriksson, N, van der Meer, P, van der Meulen, B, Ritala, A, Sági, L, et al
EMBO reports. 2019;(5)
Abstract
A proposal for implementing an opt‐in mechanism that would allow individual member states of the EU to cultivate genetically modified crops on their territory. [Image: see text]
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4.
From bacterial battles to CRISPR crops; progress towards agricultural applications of genome editing.
Bryant, JA
Emerging topics in life sciences. 2019;(6):687-693
Abstract
Genome editing is the precise alteration of DNA in living cells by the cutting or removal of specific sequences, sometimes followed by insertion of new sequences at the cut site. CRISPR-Cas9 has become firmly established as the genome-editing method of choice, replacing the systems that had been developed and in use since the early 1990s. The CRISPR-Cas9 system has been developed from a mechanism used in prokaryotes as a defence against bacteriophage but actually functions in cells of all types of organisms. It is widely used in research as a gene knockout and editing tool; applications in veterinary medicine (such as increased resistance to disease) and human medicine (such as correction of disease-causing mutations) are under development. In agriculture and horticulture, the potential for various aspects of crop improvement is very large. Selected aspects of this potential are presented here, with particular focus on crop quality and disease resistance. The article ends with a brief discussion of the regulatory 'environment' in the USA and the EU.
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5.
Hybrid wheat: past, present and future.
Gupta, PK, Balyan, HS, Gahlaut, V, Saripalli, G, Pal, B, Basnet, BR, Joshi, AK
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2019;(9):2463-2483
Abstract
The review outlines past failures, present status and future prospects of hybrid wheat, and includes information on CMS/CHA/transgenic approaches for male sterility, heterotic groups and cost-effective hybrid seed production. Hybrid varieties give increased yield and improved grain quality in both cross- and self-pollinated crops. However, hybrid varieties in self-pollinated crops (particularly cereals) have not been very successful, except for hybrid rice in China. In case of hybrid wheat, despite the earlier failures, renewed efforts in recent years have been made and hybrid varieties with desirable attributes have been produced and marketed in some European countries. This review builds upon previous reviews, with a new outlook and improved knowledge base, not covered in earlier reviews. New technologies have been described, which include the Hordeum chilense-based CMS-fertility restorer system, chromosomal XYZ-4E-ms system and the following transgenic technologies: (1) conditional male sterility involving use of tapetum-specific expression of a gene that converts a pro-toxin into a phytotoxin causing male sterility; (2) barnase-barstar SeedLink system of Bayer CropScience; (3) split-barnase system that obviates the need of a barstar-based male restorer line; and (4) seed production technology of DuPont-Pioneer that makes use of transgenes in production of male-sterile lines, but gives hybrid seed with no transgenes. This review also includes a brief account of studies for discovery of heterotic QTL, genomic prediction of hybrid vigour and the development of heterotic groups/patterns and their importance in hybrid wheat production. The problem of high cost of hybrid seed due to required high seed rate in wheat relative to hybrid rice has also been addressed. The review concludes with a brief account of the current efforts and future possibilities in making hybrid wheat a commercial success.
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6.
Developing Transgenic Agronomic Traits for Crops: Targets, Methods, and Challenges.
Davies, JP, Christensen, CA
Methods in molecular biology (Clifton, N.J.). 2019;:343-365
Abstract
The last two decades have witnessed a surge of investment by the agricultural biotechnology industry in the development of transgenic agronomic traits. These are traits that improve yield performance by modifying endogenous physiological processes such as energy capture, nutrient utilization, and stress tolerance. In this chapter we provide a foundation for understanding these fundamental processes and then outline approaches that have been taken to use this knowledge for yield improvement. We characterize the current status of product development pipelines in the industry and illustrate the trait discovery process with three important examples-bacterial cold-shock proteins, alanine aminotransferase, and auxin-regulated genes. The challenges with developing and commercializing an agronomic trait product are discussed.
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7.
The application of the CRISPR-Cas9 genome editing machinery in food and agricultural science: Current status, future perspectives, and associated challenges.
Eş, I, Gavahian, M, Marti-Quijal, FJ, Lorenzo, JM, Mousavi Khaneghah, A, Tsatsanis, C, Kampranis, SC, Barba, FJ
Biotechnology advances. 2019;(3):410-421
Abstract
The recent progress in genetic engineering has brought multiple benefits to the food and agricultural industry by enhancing the essential characteristics of agronomic traits. Powerful tools in the field of genome editing, such as siRNA-mediated RNA interference for targeted suppression of gene expression and transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs) for DNA repair have been widely used for commercial purposes. However, in the last few years, the discovery of the CRISPR-Cas9 system has revolutionized genome editing and has attracted attention as a powerful tool for several industrial applications. Herein, we review current progresses in the utilization of the CRISPR-Cas9 system in the food and agricultural industry, particularly in the development of resistant crops with improved quality and productivity. We compare the CRISPR system with the TALEN and ZFN nucleases-based methods and highlight potential advantages and shortcomings. In addition, we explore the state of the global market and discuss the safety and ethical concerns associated with the application of this technology in the food and agricultural industry.
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8.
An Update on Genetic Modification of Chickpea for Increased Yield and Stress Tolerance.
Kumar, M, Yusuf, MA, Nigam, M, Kumar, M
Molecular biotechnology. 2018;(8):651-663
Abstract
Chickpea is a highly nutritious grain legume crop, widely appreciated as a health food, especially in the Indian subcontinent. The major constraints on chickpea production are biotic (Helicoverpa, bruchid, aphid, ascochyta) and abiotic (drought, heat, salt, cold) stresses, which reduce the yield by up to 90%. Various strategies like conventional breeding, molecular breeding, and modern plant breeding have been used to overcome these problems. Conventionally, breeding programs aim at development of varieties that combine maximum number of traits through inter-specific hybridization, wide hybridization, and hybridization involving more than two parents. Breeding is difficult in this crop because of its self-pollinating nature and limited genetic variation. Recent advances in in vitro culture and gene technologies offer unique opportunities to realize the full potential of chickpea production. However, as of date, no transgenic chickpea variety has been approved for cultivation in the world. In this review, we provide an update on the development of genetically modified chickpea plants, including those resistant to Helicoverpa armigera, Callosobruchus maculatus, Aphis craccivora, as well as to drought and salt stress. The genes utilized for development of resistance against pod borer, bruchid, aphid, drought, and salt tolerance, namely, Bt, alpha amylase inhibitor, ASAL, P5CSF129A, and P5CS, respectively, are discussed.
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9.
Co-existence of GM, conventional and organic crops in developing countries: Main debates and concerns.
Azadi, H, Taube, F, Taheri, F
Critical reviews in food science and nutrition. 2018;(16):2677-2688
Abstract
The co-existence approach of GM crops with conventional agriculture and organic farming as a feasible agricultural farming system has recently been placed in the center of hot debates at the EU-level and become a source of anxiety in developing countries. The main promises of this approach is to ensure "food security" and "food safety" on the one hand, and to avoid the adventitious presence of GM crops in conventional and organic farming on the other, as well as to present concerns in many debates on implementing the approach in developing countries. Here, we discuss the main debates on ("what," "why," "who," "where," "which," and "how") applying this approach in developing countries and review the main considerations and tradeoffs in this regard. The paper concludes that a peaceful co-existence between GM, conventional, and organic farming is not easy but is still possible. The goal should be to implement rules that are well-established proportionately, efficiently and cost-effectively, using crop-case, farming system-based and should be biodiversity-focused ending up with "codes of good agricultural practice" for co-existence.
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10.
Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops.
Christ, B, Pluskal, T, Aubry, S, Weng, JK
Trends in plant science. 2018;(12):1047-1056
Abstract
The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.