Preface: Genome editing in plants

Transgenic Research -     

Special issue: Genome editing and gene therapy

Gene therapy is one of the most rapidly developing fields of molecular medicine. Gene therapy allows simple transfer of genetic methods aimed at correcting pathological processes into clinical practice. However, a number of technical problems still exists limiting broad use of gene therapy approaches. This special issue discusses modern methods and approaches used for the development of novel, effective, and safe agents for gene therapy.     

Blurring the germline: Genome editing and transgenerational epigenetic inheritance

Sperm, eggs and embryos are made up of more than genes, and there are indications that changes to non-genetic structures in these elements of the germline can also be inherited. It is, therefore, a mistake to treat phrases like ‘germline inheritance’ and ‘genetic inheritance’ as simple synonyms, and bioethical discussion should expand its focus beyond alterations to the genome when considering the ethics of germline modification. Moreover, additional research on non-genetic inheritance draws attention to a variety of means whereby differences can be inherited in offspring generations that do not rely on differences in germline structures. Research on these diverse forms of inheritance challenges the notion that there is some special form of ethical concern that falls on germline interventions in general, and on interventions to the nuclear genome within the germline in particular.     

An update of the suicide plasmid-mediated genome editing system in Corynebacterium glutamicum

Corynebacterium glutamicum is an important industrial microorganism, but the availability of tools for its genetic modification has lagged compared to other model microorganisms such as Escherichia coli. Despite great progress in CRISPR-based technologies, the most feasible genome editing method in C. glutamicum is suicide plasmid-mediated, the editing efficiency of which is low due to high false-positive rates of sacB counter selection, and the requirement for tedious two-round selection and verification of rare double-cross-over events. In this study, an rpsL mutant conferring streptomycin resistance was harnessed for counter selection, significantly increasing the positive selection rate. More importantly, with the aid of high selection efficiencies through the use of antibiotics, namely kanamycin and streptomycin, the two-step verification strategy can be simplified to just one-step verification of the final edited strain. As proof of concept, a 2.5-kb DNA fragment comprising aroG^fbrpheA^fbr expressing cassettes was integrated into the genome of C. glutamicum, with an efficiency of 20% out of the theoretical 50%. The resulting strain produced 110 mg l⁻¹ l -tyrosine in shake-flask fermentation. This updated suicide plasmid-mediated genome editing system will greatly facilitate genetic manipulations including single nucleotide mutation, gene deletion and gene insertion in C. glutamicum and can be easily applied to other microbes.     

Genome editing in cereal crops: an overview

Transgenic Research - Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of...     

Genome organization in and around the nucleolus

The nucleolus is the largest compartment of the cell nucleus and is where ribosomal RNAs (rRNAs) are synthesized, processed and assembled with ribosomal proteins. In addition to rRNA gene clusters that build the core of this subnuclear structure, nucleoli are associated with condensed chromatin. Although the higher order structures of rRNA genes and nucleolus-associated chromatin have been studied for decades, detailed molecular insights into the constituents and organization of the nucleolar genome are only beginning to emerge. Here, we summarize current views on the structural organization of nucleolar DNA and on the targeting and anchoring of chromatin domains to this subnuclear compartment.     

Genome editing: intellectual property and product development in plant biotechnology

Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market.     

Genome editing of polyploid crops: prospects,achievements and bottlenecks

Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.

     

基因编辑技术研究进展及其在苜蓿等豆科饲草作物中的应用

基因编辑是对生物基因组进行靶向修饰的一项新型生物技术,可以在不同物种中实现对目标基因的定点敲除、基因片段置换以及基因定点插入等基因定向编辑,目前基因编辑技术已在植物基因功能解析和作物遗传改良研究中得到广泛应用。本文简要回顾基因编辑技术的发展历程,重点介绍新近发展的CRISPR/Cas9技术在植物中的研究进展,并对CRISPR/Cas基因编辑技术在苜蓿等饲草作物中的应用进行探讨和展望。     

Genome editing for resistance against plant pests and pathogens

The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.

     

Genome editing technologies and their applications in crop improvement

Crop improvement is very essential to meet the increasing global food demands and enhance food nutrition. Conventional crop-breeding methods have certain limitations such as taking lot of time and resources, and causing biosafety concerns. These limitations could be overcome by the recently emerged-genome editing technologies that can precisely modify DNA sequences at the genomic level using sequence-specific nucleases (SSNs). Among the artificially engineered SSNs, the CRISPR/Cas9 is the most recently developed targeted genome modification system and seems to be more efficient, inexpensive, easy, user-friendly and rapidly adopted genome-editing tool. Large-scale genome editing has not only improved the yield and quality but also has enhanced the disease resistance ability in several model and other major crops. Increasing case studies suggest that genome editing is an efficient, precise and powerful technology that can accelerate basic and applied research towards crop improvement. In this review, we briefly overviewed the structure and mechanism of genome editing tools and then emphatically reviewed the advances in the application of genome editing tools for crop improvement, including the most recent case studies with CRISPR/Cpf1 and base-editing technologies. We have also discussed the future prospects towards the improvement of agronomic traits in crops.     

Current approaches to cyanotoxin risk assessment and risk management around the globe

Toxic cyanobacteria became more widely recognized as a potential health hazard in the 1990s, and in 1998 the World Health Organization (WHO) first published a provisional Guideline Value of 1 μg L⁻¹ for microcystin-LR in drinking-water. In this publication we compare risk assessment and risk management of toxic cyanobacteria in 17 countries across all five continents. We focus on the three main (oral) exposure vehicles to cyanotoxins: drinking-water, water related recreational and freshwater seafood. Most countries have implemented the provisional WHO Guideline Value, some as legally binding standard, to ensure the distribution of safe drinking-water with respect to microcystins. Regulation, however, also needs to address the possible presence of a wide range of other cyanotoxins and bioactive compounds, for which no guideline values can be derived due to insufficient toxicological data. The presence of microcystins (commonly expressed as microcystin-LR equivalents) may be used as proxy for overall guidance on risk management, but this simplification may miss certain risks, for instance from dissolved fractions of cylindrospermopsin and cyanobacterial neurotoxins. An alternative approach, often taken for risk assessment and management in recreational waters, is to regulate cyanobacterial presence – as cell numbers or biomass – rather than individual toxins. Here, many countries have implemented a two or three tier alert level system with incremental severity. These systems define the levels where responses are switched from Surveillance to Alert and finally to Action Mode and they specify the short-term actions that follow. Surface bloom formation is commonly judged to be a significant risk because of the elevated concentration of microcystins in a scum. Countries have based their derivations of legally binding standards, guideline values, maximally allowed concentrations (or limits named otherwise) on very similar scientific methodology, but underlying assumptions such as bloom duration, average body size and the amount of water consumed while swimming vary according to local circumstances. Furthermore, for toxins with incomplete toxicological data elements of expert judgment become more relevant and this also leads to a larger degree of variation between countries’ thresholds triggering certain actions. Cyanobacterial blooms and their cyanotoxin content are a highly variable phenomenon, largely depending on local conditions, and likely concentrations can be assessed and managed best if the specific conditions of the locality are known and their impact on bloom occurrence are understood. Risk Management Frameworks, such as for example the Water Safety Plan concept of the WHO and the ‘bathing water profile’ of the European Union are suggested to be effective approaches for preventing human exposure by managing toxic cyanobacteria from catchment to consumer for drinking water and at recreational sites.     

基因组编辑技术在猪遗传改良中的应用

核酸酶介导的基因组编辑技术大幅度提高了编辑真核细胞基因组的能力,给生命科学领域带来了革命性地发展,也给猪的遗传改良带来了全新的契机。本文介绍了基因组编辑技术尤其是CRISPR/Cas9系统的发展以及各种天然存在的和人为改造的Cas9变体的作用特点;汇总了利用基因组编辑技术提高猪生产性能,尤其是改善猪肉品质和抵抗病毒感染的研究进展;分析了目前利用基因组编辑技术推进猪遗传改良所面临的挑战;最后,展望了基于基因组编辑技术的猪遗传改良和品种培育的发展趋势。     

Genome editing of potato using CRISPR technologies: current development and future prospective

Potato (Solanum tuberosum L.) has tremendous significance due to its nutritional quality. The mounting pressure of increasing population further reinforces its importance as potato is believed to be a vital crop to meet food needs for population growth. Although conventional approaches of breeding, irradiation/mutagens and introgression of quality and yield related traits have improved potato yield, biotic and abiotic stresses continue to impose crop damages. Modern tools such as CRISPR/Cas have assisted plant scientists in accelerating breeding processes by providing new, simple, versatile and robust technologies. These tools make it possible to eliminate traits that are involved in negative regulation of quality and yield parameters. Besides that, genes of interest can also be introduced in close proximity to specific loci that may remain linked throughout the generations. This review focuses on the endeavors, applications and prospects of CRISPR/Cas-based approaches in potato with the potential to increase sustainable crop productivity.