Transgenic crops for the agricultural improvement in Pakistan: a perspective of environmental stresses and the current status of genetically modified crops

3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape

The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01397-3.

GMOs or non-GMOs? The CRISPR Conundrum

CRISPR-Cas9, the "genetic scissors", is being presaged as a revolutionary technology, having tremendous potential to create designer crops by introducing precise and targeted modifications in the genome to achieve global food security in the face of climate change and increasing population. Traditional genetic engineering relies on random and unpredictable insertion of isolated genes or foreign DNA elements into the plant genome. However, CRISPR-Cas based gene editing does not necessarily involve inserting a foreign DNA element into the plant genome from different species but introducing new traits by precisely altering the existing genes. CRISPR edited crops are touching markets, however, the world community is divided over whether these crops should be considered genetically modified (GM) or non-GM. Classification of CRISPR edited crops, especially transgene free crops as traditional GM crops, will significantly affect their future and public acceptance in some regions. Therefore, the future of the CRISPR edited crops is depending upon their regulation as GM or non-GMs, and their public perception. Here we briefly discuss how CRISPR edited crops are different from traditional genetically modified crops. In addition, we discuss different CRISPR reagents and their delivery tools to produce transgene-free CRISPR edited crops. Moreover, we also summarize the regulatory classification of CRISPR modifications and how different countries are regulating CRISPR edited crops. We summarize that the controversy of CRISPR-edited plants as GM or non-GM will continue until a universal, transparent, and scalable regulatory framework for CRISPR-edited plants will be introduced worldwide, with increased public awareness by involving all stakeholders.

Predicting the insecticide-driven mutations in a crop pest insect: Evidence for multiple polymorphisms of acetylcholinesterase gene with potential relevance for resistance to chemicals

The silverleaf whitefly Bemisia tabaci (Gennadius, 1889) (Homoptera: Aleyrodidae) is a serious invasive herbivorous insect pest worldwide. The excessive use of pesticides has progressively selected B. tabaci specimens, reducing the effectiveness of the treatments, and ultimately ending in the selection of pesticide-resistant strains. The management of this crop pest has thus become challenging owing to the level of resistance to all major classes of recommended insecticides. Here, we used in silico techniques for detecting sequence polymorphisms in ace1 gene from naturally occurring B. tabaci variants, and monitor the presence and frequency of the detected putative mutations from 30 populations of the silverleaf whitefly from Egypt and Pakistan. We found several point mutations in ace1-type acetylcholinesterase (ace1) in the studied B. tabaci variants naturally occurring in the field. By comparing ace1 sequence data from an organophosphate-susceptible and an organophosphate-resistant strains of B. tabaci to ace1 sequence data retrieved from GenBank for that species and to nucleotide polymorphisms from other arthropods, we identified novel mutations that could potentially influence insecticide resistance. Homology modeling and molecular docking analyses were performed to determine if the mutation-induced changes in form 1 acetylcholinesterase (AChE1) structure could confer resistance to carbamate and organophosphate insecticides. Mutations had small effects on binding energy (ΔG_b) interactions between mutant AChE1 and insecticides; they altered the conformation of the peripheral anionic site of AChE1, and modified the enzyme surface, and these changes have potential effects on the target-site sensitivity. Altogether, the results from this study provide information on genic variants of B. tabaci ace1 for future monitoring insecticide resistance development and report a potential case of environmentally driven gene variations.

Confirmation of 'Pollen- and Seed-Specific Gene Deletor' System Efficiency for Transgene Excision from Transgenic Nicotiana tabacum under Field Conditions

The commercial application of genetically modified plants has been seriously impeded by public concern surrounding the potential risks posed by such plants to the ecosystem and human health. Previously, we have developed a 'pollen- and seed-specific Gene Deletor' system that automatically excised all transgenes from the pollen and seeds of greenhouse-grown transgenic Nicotiana tabacum. In this study, we conducted seven field experiments over three consecutive years to evaluate the stability of transgene excision under field conditions. Our results showed that transgenes were stably excised from transgenic Nicotiana tabacum under field conditions with 100% efficiency. The stability of transgene excision was confirmed based on PCR, as well as the GUS staining patterns of various organs (roots, leaves, petiole, stem, flower, fruit, and seeds) from transgenic N. tabacum. In six transgenic lines (D4, D10, D31, D56, and D43), the transgenes were stably deleted in the T0 and T1 generations. Thus, the 'Gene Deletor' system is an efficient and reliable method to reduce pollen- and seed-mediated unintentional gene flow. This system might help to alleviate the food safety concerns associated with transgenic crops.

The main component of the aphid alarm pheromone (E)-β-farnesene affects the growth and development of Spodoptera exigua by mediating juvenile hormone-related genes

The (E)-β-farnesene (EβF) is one of the most important secondary metabolites in some plants and provides indirect defense against aphids. However, the direct effect of EβF against pests is still unclear. In this study, various concentrations of EβF (0.16, 0.8, and 4 g/kg) were provided in an artificial diet to determine the direct effects of EβF on Spodoptera exigua. The results showed that an artificial diet containing 4 g/kg of EβF reduced the final survival of the S. exigua larvae and per female fecundity of adults significantly when compared with CK and SC controls (p < 0.05), then ultimately it also significantly affected the intrinsic rate of increase (p < 0.05). Furthermore, the results of the EβF bioassay in an artificial diet also indicated that the proliferation of the S. exigua population was inhibited by the ingestion of EβF in a dose-dependent manner. Combined differential RNA-seq data and RT-qPCR analysis, it was found that four key genes involved in juvenile hormone degradation significantly upregulated in S. exigua larvae treated by EβF at a dose of 0.8 and 4 g/kg when compared with two controls (p < 0.05). This indicated that EβF could disturb the normal function of juvenile hormones and reduce the survival rate of S. exigua larvae. Additionally, two key genes that regulate per fecundity of S. exigua females, including SeVg and SeVgR, were significantly downregulated in adult females (p < 0.05) when they were treated with 0.8 and 4 g/kg of EβF at the larval stage, relative to the expression of these genes after treatment with controls. These findings suggested that EβF first disturbed the normal function of juvenile hormone by upregulating key degradation genes, and then inhibited the expression of SeVg/SeVgR genes and proteins, thus reducing the population size of S. exigua by increasing larval mortality and inhibiting per female fecundity.

Mechanism of cotton resistance to abiotic stress, and recent research advances in the osmoregulation related genes

Abiotic stress is an important factor affecting the normal growth and development of plants and crop yield. To reduce the impact of abiotic adversity on cotton growth and development, the material basis of cotton resistance and its physiological functions are analyzed at the molecular level. At the same time, the use of genetic engineering methods to recombine resistance genes has become a hot spot in cotton resistance research. This paper provides an overviews of the resistance mechanism of cotton against the threat of non-biological adversity, as well as the research progress of osmoregulation-related genes, protein-acting genes, and transcription regulatory factor genes in recent years, and outlines the explored gene resources in cotton resistance genetic engineering, with the aim to provide ideas and reference bases for future research on cotton resistance.

Investigating the status of transgenic crops in Iran in terms of cultivation, consumption, laws and rights in comparison with the world

Recently, there has been a development in transgenic technologies in many countries to meet nutritional needs of increasing worlds҆ population. However, there are some concerns about possible risks in the field of growing genetically modified (GM) food, such as threats of biodiversity and food allergies making their use a challenge. Therefore, the present study was conducted to investigate the economic effects and political scopes of GM foods in production sector and policies made by different countries in the world and Iran. Moreover, essential (practical and legal) solutions and guidelines were provided for production and consumption of GM foods, which are useful for governmental entities, Iranian politicians, and consumers' rights. The latest situation of transgenic crops in the countries with which Iran has the highest exchange of agricultural products (including Turkey, Pakistan, and the European Union (EU)) was also studied. Although, Iran has been one of leading Asian countries not only in the field of transfer of technical knowledge of genetic engineering, but also in development of the specialized knowledge of biosafety, and despite production of several transgenic plant lines by Iranian researchers, unfortunately no GM crop has obtained release and cultivation license except for GM rice that its growing process was banned after change of government. According to findings of this study, in Iran, growing and production process of GM crops does not follow the global trend owing to scientific and legal infrastructures.

Global Regulation of Genetically Modified Crops Amid the Gene Edited Crop Boom - A Review

Products derived from agricultural biotechnology is fast becoming one of the biggest agricultural trade commodities globally, clothing us, feeding our livestock, and fueling our eco-friendly cars. This exponential growth occurs despite asynchronous regulatory schemes around the world, ranging from moratoriums and prohibitions on genetically modified (GM) organisms, to regulations that treat both conventional and biotech novel plant products under the same regulatory framework. Given the enormous surface area being cultivated, there is no longer a question of acceptance or outright need for biotech crop varieties. Recent recognition of the researchers for the development of a genome editing technique using CRISPR/Cas9 by the Nobel Prize committee is another step closer to developing and cultivating new varieties of agricultural crops. By employing precise, efficient, yet affordable genome editing techniques, new genome edited crops are entering country regulatory schemes for commercialization. Countries which currently dominate in cultivating and exporting GM crops are quickly recognizing different types of gene-edited products by comparing the products to conventionally bred varieties. This nuanced legislative development, first implemented in Argentina, and soon followed by many, shows considerable shifts in the landscape of agricultural biotechnology products. The evolution of the law on gene edited crops demonstrates that the law is not static and must adjust to the mores of society, informed by the experiences of 25 years of cultivation and regulation of GM crops. The crux of this review is a consolidation of the global legislative landscape on GM crops, as it stands, building on earlier works by specifically addressing how gene edited crops will fit into the existing frameworks. This work is the first of its kind to synthesize the applicable regulatory documents across the globe, with a focus on GM crop cultivation, and provides links to original legislation on GM and gene edited crops.