scholarly journals A simple method for spray-on gene editing in planta

2019 ◽  
Author(s):  
Cara Doyle ◽  
Katie Higginbottom ◽  
Thomas A. Swift ◽  
Mark Winfield ◽  
Christopher Bellas ◽  
...  
Keyword(s):  
Carbon Dots ◽  
Plant Transformation ◽  
Gene Editing ◽  
Production Systems ◽  
Foliar Application ◽  
Great Promise ◽  
In Planta ◽  
Crop Species ◽  
Simple Method ◽  
Negative Impacts

Potential innovation in Plant research using gene-edited and genetically modified plants is currently being hindered by inefficient and costly plant transformation. We show that carbon dots formed from natural materials (quasi-spherical, <10nm nanoparticles) can act as a fast vehicle for carrying plasmids into mature plant cells, resulting in transient plant transformation in a number of important crop species with no negative impacts on photosynthesis or growth. We further show that GFP, Cas9, and gRNA introduced into wheat via foliar application (spraying on) of plasmid coated carbon dots are expressed and, in the case of Cas9, make genome edits in SPO11 genes. Therefore, we present a protocol for spray-on gene editing that is simple, inexpensive, fast, transforms in planta, and is applicable to multiple crop species. We believe this technique creates many opportunities for the future of plant transformation in research and shows great promise for plant protein production systems.

scholarly journals Plant viral vectors: Expanding the Possibilities of Precise Gene Editing in Plant Genomes

2021 ◽  
Author(s):  
Stuti Kujur ◽  
Muthappa Senthil-Kumar ◽  
Rahul Kumar
Keyword(s):  
Genome Editing ◽  
Plant Transformation ◽  
Viral Vectors ◽  
Gene Editing ◽  
Genome Engineering ◽  
Plant Cells ◽  
In Planta ◽  
Plant Genomes ◽  
Efficient Gene ◽  
Transformation Methods

Abstract The lack of a highly efficient method for delivering reagents for genome engineering to plant cells remains a bottleneck in achieving efficient gene-editing in plant genomes. A suite of recent reports uncovers the newly emerged roles of viral vectors, which can introduce gene-edits in plants with high mutation frequencies through in planta delivery. Here, we focus on the emerging protocols that utilized different approaches for virus-mediated genome editing in model plants. Testing of these protocols and the newly identified hypercompact Casɸ systems is needed to broaden the scope of genome-editing in most plant species, including crops, with minimized reliance on conventional plant transformation methods in the future.

scholarly journals Influence of Foliar Application of Magnesium on Horticultural Crops: A Review

2021 ◽  
Vol 4 (1) ◽  
pp. 13-21
Author(s):  
Muhammad Adnan ◽  
Koko Tampubolon ◽  
Fazal Ur Rehman ◽  
Muhammad Sulaman Saeed ◽  
Muhammad Sikander Hayyat ◽  
...  
Keyword(s):  
Crop Production ◽  
Foliar Application ◽  
Residual Effect ◽  
Nutrient Status ◽  
Fertilizer Application ◽  
Crop Species ◽  
Horticultural Crops ◽  
Physiological Processes ◽  
Negative Impacts ◽  
The Impact

Introduction: Magnesium is very important nutrient and performs a significant part in development and formation of many sink organs like roots and seeds. Furthermore, its fertilization significantly affects yield and numerous physiological mechanisms in different horticulture crop species. Moreover, its deficiency caused germination and reduction in horticulture crop stand. Nevertheless, its adequate concentration by foliar application plays important role in biochemical and physiological processes of plants like proteins synthesis, metabolism of carbohydrates, enzymes activation and energy transferring. Worldwide, many of our horticulture crops are facing low yield and quality problem due to fertilizer application at inadequate rate. The current review focuses on the impact of foliar applied Mg on some important cultivated horticultural crops (sugar beet, tomato, banana, potato, spinach, cauliflower, cassava, garlic, green case, potus, cucumber and grapes). Review results: Our extensive review has demonstrated that magnesium is very important factor limiting horticulture crop production but its negative impacts can be reduced by foliar application of magnesium. Foliar application of Mg can be recommended for correcting deficiencies because foliar sprays have no long term residual effect and every time fresh applications must be given to each crop. Moreover, amount depends on the nutrient status of crop and soil.

scholarly journals Noval Dual-Emission Fluorescence Carbon Dots as a Ratiometric Probe for Cu2+ and ClO− Detection

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1232
Author(s):  
Jiaqing Guo ◽  
Aikun Liu ◽  
Yutian Zeng ◽  
Haojie Cai ◽  
Shuai Ye ◽  
...  
Keyword(s):  
Carbon Dots ◽  
Background Noise ◽  
Good Recovery ◽  
Ratiometric Fluorescence ◽  
Dual Emission ◽  
Simple Method ◽  
Real Samples ◽  
Nitrogen Doped ◽  
Probe Concentration ◽  
Ratiometric Probe

The use of carbon dots (CDs) with dual emission based on ratiometric fluorescence has been attracting attention in recent times for more accurate ion detection since they help avoid interference from background noise, probe concentration, and complexity. Herein, novel dual-emission nitrogen-doped CDs (NCDs) were prepared by a simple method for Cu2+ and ClO- detection. The NCDs showed excellent anti-interference ability and selectivity for different emissions. In addition, a good linear relationship was observed between the fluorescence intensity (FI) of the NCD solutions in different emissions with Cu2+ (0–90 μM) and ClO- (0–75 μM). The limits of both Cu2+ detection and ClO- were very low, at 17.7 and 11.6 nM, respectively. The NCDs developed herein also showed a good recovery rate in water for Cu2+ and ClO− detection. Hence, they are expected to have a more extensive application prospect in real samples.

scholarly journals VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

2021 ◽  
Author(s):  
Arjun Khakhar ◽  
Cecily Wang ◽  
Ryan Swanson ◽  
Sydney Stokke ◽  
Furva Rizvi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Viral Vectors ◽  
Viral Vector ◽  
Tobacco Rattle Virus ◽  
Plant Size ◽  
Great Promise ◽  
Attractive Alternative ◽  
Gibberellin Biosynthesis ◽  
In Planta

Abstract Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work we developed a technology called VipariNama (ViN) in which vectors based on the Tobacco Rattle Virus (TRV) are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, VipariNama accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

scholarly journals Advances in Cereal Crop Genomics for Resilience under Climate Change

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 502
Author(s):  
Tinashe Zenda ◽  
Songtao Liu ◽  
Anyi Dong ◽  
Huijun Duan
Keyword(s):  
Climate Change ◽  
Genome Sequencing ◽  
Gene Editing ◽  
Agronomic Traits ◽  
Cereal Crops ◽  
Agricultural System ◽  
Plant Genomics ◽  
Crop Species ◽  
Underutilized Species ◽  
Recent Developments

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

scholarly journals VipariNama: RNA vectors to rapidly reprogram plant morphology and metabolism

2020 ◽  
Author(s):  
Arjun Khakhar ◽  
Cecily Wang ◽  
Ryan Swanson ◽  
Sydney Stokke ◽  
Furva Rizvi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Plant Morphology ◽  
Plant Size ◽  
Great Promise ◽  
Attractive Alternative ◽  
Biological Processes ◽  
In Planta ◽  
Transcriptional Reprogramming ◽  
Long Timescales

AbstractSynthetic transcription factors have great promise as tools to explore biological processes. By allowing precise alterations in gene expression, they can help elucidate relationships between gene expression and plant morphology or metabolism. However, the years-long timescales, high cost, and technical skill associated with plant transformation have dramatically slowed their use. In this work, we developed a new platform technology called VipariNama (ViN) in which RNA vectors are used to rapidly deploy synthetic transcription factors and reprogram gene expression in planta. We demonstrate how ViN vectors can direct activation or repression of multiple genes, systemically and persistently over several weeks, and in multiple plant species. We also show how this transcriptional reprogramming can create predictable changes to metabolic and morphological phenotypes in the model plants Nicotiana benthamiana and Arabidopsis thaliana in a matter of weeks. Finally, we show how a model of gibberellin signaling can guide ViN vector-based reprogramming to rapidly engineer plant size in both model species as well as the crop Solanum lycopersicum (tomato). In summary, using VipariNama accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

scholarly journals Human Genetic Diversity Alters Therapeutic Gene Editing Off-Target Outcomes

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3993-3993
Author(s):  
Linda Yingqi Lin ◽  
Samuele Cancellieri ◽  
Jing Zeng ◽  
Francesco Masillo ◽  
My Anh Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clinical Trials ◽  
Genome Editing ◽  
Gene Editing ◽  
Conflicts Of Interest ◽  
African Ancestry ◽  
Great Promise ◽  
Personal Genome ◽  
Hematopoietic Stem ◽  
The Impact

Abstract CRISPR gene editing holds great promise to modify somatic genomes to ameliorate disease. In silico prediction of homologous sites coupled with biochemical evaluation of possible genomic off-targets may predict genotoxicity risk of individual gene editing reagents. However, standard computational and biochemical methods focus on reference genomes and do not consider the impact of genetic diversity on off-target potential. Here we developed a web application called CRISPRme that explicitly and efficiently integrates human genetic variant datasets with orthogonal genomic annotations to predict and prioritize off-target sites at scale. The method considers both single-nucleotide variants (SNVs) and indels, accounts for bona fide haplotypes, accepts spacer:protospacer mismatches and bulges, and is suitable for personal genome analyses. We tested the tool with a guide RNA (gRNA) targeting the BCL11A erythroid enhancer that has shown therapeutic promise in clinical trials for sickle cell disease (SCD) and β-thalassemia (Frangoul et al. NEJM 2021). We find that the top predicted off-target site is produced by a non-reference allele common in African-ancestry populations (rs114518452, minor allele frequency (MAF) = 4.5%) that introduces a protospacer adjacent motif (PAM) for SpCas9. We validate that SpCas9 generates indels (~9.6% frequency) and chr2 pericentric inversions in a strictly allele-specific manner in edited CD34+ hematopoietic stem/progenitor cells (HSPCs), although a high-fidelity Cas9 variant mitigates this off-target. This report illustrates how population and private genetic variants should be considered as modifiers of genome editing outcomes. We expect that variant-aware off-target assessment will be required for therapeutic genome editing efforts going forward, including both ongoing and future clinical trials, and we provide a powerful approach for comprehensive off-target prediction. CRISPRme is available at crisprme.di.univr.it. Disclosures No relevant conflicts of interest to declare.

Optimizing ruminant production systems for sustainable intensification, human health, food security and environmental stewardship

2019 ◽  
Vol 48 (2) ◽  
pp. 85-93 ◽  
Author(s):  
Victor Mlambo ◽  
Caven M Mnisi
Keyword(s):  
Crop Production ◽  
Production Systems ◽  
Negative Consequences ◽  
Health Food ◽  
Animal Products ◽  
Root Cause ◽  
Nutrition Security ◽  
Food And Nutrition ◽  
Negative Impacts ◽  
High Standards

Whereas the contribution of ruminants to human civilization remains unequivocal, there are concerns regarding the unintended negative consequences of rearing these animals for food. These concerns range from the ruminant’s contribution to greenhouse gas emissions to negative impacts of its products on the health of consumers. Rearing ruminants for food is thus seen as the root cause of ills such as climate change, species extinction, deforestation, food insecurity, cardiovascular disease, obesity, cancer and diabetes. Indeed, critics of ruminant production envision a future where humanity does not have to rely on animal products for food. They are convinced that this would be the panacea to food and nutrition insecurity, environmental pollution and meat-induced nutritional disorders and diseases in humans. The critics seem to be unaware of the wide diversity of ruminant production systems in use as well as the array of benefits that can be derived from these enterprises. For instance, there are large human communities that inhabit climatically hostile areas, which have no food crop production potential. Food and nutrition needs of these communities are largely dependent on nourishment provided by products and income derived from ruminants and other herbivores. The aim of this review article is to interrogate the validity of the concerns around the use of ruminants for food and highlight appropriate strategies and technologies that may be applied to mitigate some of these challenges. We conclude that solutions already exist that have the potential to deliver efficient, environmentally friendly and consumer-conscious ruminant production systems based on high standards of animal welfare. Such sustainable production systems will ensure that ruminants continue to play a crucial role in food and nutrition security of humans as they have done for millennia.

scholarly journals Revisiting Sustainability of Fungicide Seed Treatments for Field Crops

Plant Disease ◽  
2020 ◽  
Vol 104 (3) ◽  
pp. 610-623 ◽  
Author(s):  
Jay Ram Lamichhane ◽  
Ming Pei You ◽  
Véronique Laudinot ◽  
Martin J. Barbetti ◽  
Jean-Noël Aubertot
Keyword(s):  
Seed Treatment ◽  
Foliar Spray ◽  
Economic Benefits ◽  
Soil Organisms ◽  
Seed Treatments ◽  
User Friendliness ◽  
Crop Species ◽  
Nontarget Effects ◽  
Development Of Resistance ◽  
Negative Impacts

The use of fungicide seed treatment (FST) is a very common practice worldwide. The purported effectiveness of many fungicides in providing broad-spectrum and systemic control of important diseases and the perception that FST reduces overall pesticide use, hence lowering environmental impacts, have greatly promoted the use of FST in the last five decades. Since there have been rapid advancements in the types, formulations, and application methods for seed treatments, there is a need to re-evaluate the benefits versus the risks of FST as a practice. While the use of seeds treated with neonicotinoid insecticides has come under scrutiny due to concern over potential nontarget effects, there are knowledge gaps on potential negative impacts of FST on operators’ (those who apply, handle, and use treated seeds) health and nontarget soil organisms (both macro- and microorganisms). Here we review existing knowledge on key fungicides used for seed treatments, benefits and risks related to FST, and propose recommendations to increase benefits and limit risks related to the use of FST. We found FST is applied to almost 100% of sown seeds for the most important arable crops worldwide. Fungicides belonging to 10 chemical families and with one or several types of mobility (contact, locally systemic, and xylem mobile) are used for seed treatment, although the majority are xylem mobile. Seed treatments are applied by the seed distributor, the seed company, and the farmer, although the proportion of seed lots treated by these three groups vary from one crop to another. The average quantity of fungicide active ingredient (a.i.) applied via seed treatment depends on the crop species, environment(s) into which seed is planted, and regional or local regulations. Cost-effectiveness, protection of the seed and seedlings from pathogens up to 4–5 weeks from sowing, user friendliness, and lower impact on human health and nontarget soil organisms compared with foliar spray and broadcast application techniques, are among the most claimed benefits attributed to FST. In contrast, inconsistent economic benefits, development of resistance by soilborne pathogens to many fungicides, exposure risks to operators, and negative impacts on nontarget soil organisms are the key identified risks related to FST. We propose eight recommendations to reduce risks related to FST and to increase their benefits.

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