scholarly journals Attaining the promise of plant gene editing at scale

2021 ◽  
Vol 118 (22) ◽  
pp. e2004846117
Author(s):  
Ryan A. Nasti ◽  
Daniel F. Voytas
Keyword(s):  
Genetic Variation ◽  
Gene Editing ◽  
Germ Line ◽  
Rna Virus ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Plant Performance ◽  
Plant Gene ◽  
Technological Developments ◽  
Modern Breeding

Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.

scholarly journals Mutation breeding, genetic diversity and crop adaptation to climate change

2021 ◽  
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Mutation Induction ◽  
Adaptation To Climate Change ◽  
Crop Adaptation ◽  
Nutrition Security ◽  
Molecular Variants ◽  
Seed Crops

Abstract This book presents reviews on the application of the technology for crop improvement towards food and nutrition security, and research status on mutation breeding and associated biotechnologies in both seed crops and vegetatively propagated crops. It also presents perspectives on the significance of next-generation sequencing and bioinformatics in determining the molecular variants underlying mutations and on emerging biotechnologies such as gene editing. Reviews and articles are organized into five sections in the publication: (1) Contribution of Crop Mutant Varieties to Food Security; (2) Mutation Breeding in Crop Improvement and Climate-Change Adaptation; (3) Mutation Induction Techniques for Enhanced Genetic Variation; (4) Mutation Breeding in Vegetatively Propagated and Ornamental Crops; and (5) Induced Genetic Variation for Crop Improvement in the Genomic Era. The contents of this volume present excellent reference material for researchers, students and policy makers involved in the application of induced genetic variation in plants for the maintenance of biodiversity and the acceleration of crop adaptation to climate change to feed a growing global population in the coming years and decades.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals Improved Transformation and Regeneration of Indica Rice: Disruption of SUB1A as a Test Case via CRISPR-Cas9

2021 ◽  
Vol 22 (13) ◽  
pp. 6989
Author(s):  
Yuya Liang ◽  
Sudip Biswas ◽  
Backki Kim ◽  
Julia Bailey-Serres ◽  
Endang M. Septiningsih
Keyword(s):  
Gene Editing ◽  
Indica Rice ◽  
Crop Improvement ◽  
Immature Embryo ◽  
Test Case ◽  
Submergence Tolerance ◽  
Embryogenic Calli ◽  
Submergence Stress ◽  
Efficient Vector ◽  
Vector Delivery

Gene editing by use of clustered regularly interspaced short palindromic repeats (CRISPR) has become a powerful tool for crop improvement. However, a common bottleneck in the application of this approach to grain crops, including rice (Oryza sativa), is efficient vector delivery and calli regeneration, which can be hampered by genotype-dependent requirements for plant regeneration. Here, methods for Agrobacterium-mediated and biolistic transformation and regeneration of indica rice were optimized using CRISPR-Cas9 gene-editing of the submergence tolerance regulator SUBMERGENCE 1A-1 gene of the cultivar Ciherang-Sub1. Callus induction and plantlet regeneration methods were optimized for embryogenic calli derived from immature embryos and mature seed-derived calli. Optimized regeneration (95%) and maximal editing efficiency (100%) were obtained from the immature embryo-derived calli. Phenotyping of T1 seeds derived from the edited T0 plants under submergence stress demonstrated inferior phenotype compared to their controls, which phenotypically validates the disruption of SUB1A-1 function. The methods pave the way for rapid CRISPR-Cas9 gene editing of recalcitrant indica rice cultivars.

scholarly journals Unsuccessful attempt at gene-editing by homologous recombination in the zebrafish germ line using the approach of “Rong and Golic”

2012 ◽  
Vol 21 (5) ◽  
pp. 1125-1136 ◽  
Author(s):  
Rosalind Brookfield ◽  
Felix Dafhnis-Calas ◽  
Zhengyao Xu ◽  
William Brown
Keyword(s):  
Homologous Recombination ◽  
Gene Editing ◽  
Germ Line ◽  
Unsuccessful Attempt

Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing

2021 ◽  
Author(s):  
◽  
Mariah Taylor ◽  
Keyword(s):  
Genetic Variation ◽  
Amino Acid ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Animal Health ◽  
Functional Domains ◽  
Whole Genome ◽  
Coding Region

Two RNA virus families that pose a threat to human and animal health are Hantaviridae and Coronaviridae. These RNA viruses which originate in wildlife continue and will continue to cause disease, and hence, it is critical that scientific research define the mechanisms as to how these viruses spillover and adapt to new hosts to become endemic. One gap in our ability to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within reservoir and spillover hosts. In my research studies, I used the amplicon-based WGS approach to define the genetic plasticity of viral RNA within pathogenic and nonpathogenic hantavirus species. The standing genetic variation of Andes orthohantavirus and Prospect Hill orthohantavirus was mapped out and amino acid changes occurring outside of functional domains were identified within the nucleocapsid and glycoprotein. I observed several amino acid changes in functional domains of the RNA-dependent RNA polymerase, as well as single nucleotide polymorphisms (SNPs) within the 3’ non-coding region (NCR) of the S-segment. To identify whether virus adaptation would occur within the S- and L-segments we attempted to adapt hantaviruses in vitro in a spillover host model through passaging experiments. In early passages we identified few mutations in the M-segment with the majority being identified in the S-segment 3’ NCR and the L-segment. This work suggests that hantavirus adaptation occurs in the S- and L-segments although the effect of these mutants on pathology is yet to be determined. While sequencing laboratory isolates is easily accomplished, sequencing low concentrations of virus within the reservoir is a formidable task. I further translated our amplicon-based WGS approach into a pan-oligonucleotide amplicon-based WGS approach to sequence hantavirus vRNA and mRNA from reservoir and spillover hosts in Ukraine. This approach successfully identified a novel Puumala orthohantavirus (PUUV) strain in Ukraine and using Bayesian phylogenetics we found this strain to be associated with the PUUV Latvian lineage. Early during the SARS-CoV-2 pandemic, I applied the knowledge gained in the hantavirus WGS efforts to sequencing of SARS-CoV-2 from nasopharyngeal swabs collected in April 2020. The genetic diversity of 45 SARS-CoV-2 isolates was evaluated with the methods I developed. We identified D614G, a notable mutation known for increasing transmission, in over 90% of our isolates. Two major lineages distinguish SARS-CoV-2 variants worldwide, lineages A and B. While most of our isolates were found within B lineage, we also identified one isolate within lineage A. We performed in vitro work which confirmed A lineage isolates as having poor replication in the trachea as compared to the nasal cavity. Five of these isolates presented a unique array of mutations which were assessed in the keratin 18 human angiotensin-converting enzyme 2 (K18-hACE2) mouse model for its response immunologically and pathogenically. We identified a distinction of pathogenesis between the A and B lineages with emphysema being common amongst A lineage isolates. Additionally, we discovered a small cohort of likely SNPs that defined the late induction of eosinophils during infection. In summary, this work will further define the dynamics of genetic variation and plasticity within virus populations that cause disease outbreaks and will allow a deeper understanding of the virus-host relationship.

scholarly journals Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

2014 ◽  
Vol 104 (1) ◽  
pp. 108-114 ◽  
Author(s):  
Jeewan Jyot Walia ◽  
Anouk Willemsen ◽  
Eminur Elci ◽  
Kadriye Caglayan ◽  
Bryce W. Falk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mosaic Virus ◽  
Rna Virus ◽  
Plant Viruses ◽  
Long Distance ◽  
Evolutionary Mechanisms ◽  
Plant Materials ◽  
Genomic Rnas ◽  
Fig Trees ◽  
Fig Mosaic Virus

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.

scholarly journals Genetic Variation among and within United States Collard Cultivars and Landraces as Determined by Randomly Amplified Polymorphic DNA Markers

1996 ◽  
Vol 121 (3) ◽  
pp. 374-379 ◽  
Author(s):  
Mark W. Farnham
Keyword(s):  
Genetic Variation ◽  
Dna Markers ◽  
Crop Improvement ◽  
Similarity Index ◽  
Randomly Amplified Polymorphic Dna ◽  
Brussels Sprouts ◽  
Breeding Lines ◽  
Intrapopulation Variation ◽  
Similarity Indices ◽  
Systematic Collection

A collection of collard (Brassica oleracea L., Acephala group) germplasm, including 13 cultivars or breeding lines and 5 landraces, was evaluated using randomly amplified polymorphic DNA (RAPD) markers and compared to representatives of kale (Acephala group), cabbage (Capitata group), broccoli (Italica group), Brussels sprouts (Gemmifera group), and cauliflower (Botrytis group). Objectives were to assess genetic variation and relationships among collard and other crop entries, evaluate intrapopulation variation of open-pollinated (OP) collard lines, and determine the potential of collard landraces to provide new B. oleracea genes. Two hundred nine RAPD bands were scored from 18 oligonucleotide decamer primers when collard and other B. oleracea entries were compared. Of these, 147 (70%) were polymorphic and 29 were specific to collard. Similarity indices between collard entries were computed from RAPD data and these ranged from 0.75 to 0.99 with an average of 0.83. Collard entries were most closely related to cabbage (similarity index = 0.83) and Brussels sprouts entries (index = 0.80). Analysis of individuals of an OP cultivar and landrace indicated that intrapopulation genetic variance accounts for as much variation as that observed between populations. RAPD analysis identified collard landraces as unique genotypes and showed them to be sources of unique DNA markers. The systematic collection of collard landraces should enhance diversity of the B. oleracea germplasm pool and provide genes for future crop improvement.

scholarly journals Mutagenic effect of EMS and DES on Tenai (Setaria italica) in M1 generation

1970 ◽  
pp. 06-08
Author(s):  
I. Anittha, L. Mullainathan
Keyword(s):  
Seed Weight ◽  
Quantitative Traits ◽  
Crop Improvement ◽  
Mutagenic Effect ◽  
Mutation Breeding ◽  
Setaria Italica ◽  
Mutagenic Treatment ◽  
Genetic Manipulations ◽  
Number Of Leaves ◽  
Breeding Techniques

Mutation breeding gives better results for crop improvement through genetic manipulations when compared  to  other conventional breeding techniques. The present work focused in order to find out the effect of chemical mutagens; EMS and DES on Setaria italica in M1 generation. The seeds of Tenai, variety CO(Te)7 treated with different concentration of EMS and DES. The LD50 was observed at 30mM in EMS and 40mM in DES. Selection studies were conducted to improve the yield and to generate genetic variability in different quantitative traits such as days to first bloom, plant height, number of leaves, number of nodes, length and breadth of ear head, 1000 seed weight and yield per plant. The results revealed that, all the parameters were decreased with increasing concentration in both EMS and DES, while days to first bloom was increasing with increasing concentration. According to the result all the parameters  studied  shows a negative direction towards crop improvement in M1 generation because of the stress caused by mutagenic treatment.

scholarly journals CRISPR Gene-Editing Models Geared Toward Therapy for Hereditary and Developmental Neurological Disorders

2021 ◽  
Vol 9 ◽  
Author(s):  
Poh Kuan Wong ◽  
Fook Choe Cheah ◽  
Saiful Effendi Syafruddin ◽  
M. Aiman Mohtar ◽  
Norazrina Azmi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Neurological Disorders ◽  
Gene Editing ◽  
Fragile X ◽  
Genetic Diseases ◽  
Basic Principles ◽  
Short Palindromic Repeat

Hereditary or developmental neurological disorders (HNDs or DNDs) affect the quality of life and contribute to the high mortality rates among neonates. Most HNDs are incurable, and the search for new and effective treatments is hampered by challenges peculiar to the human brain, which is guarded by the near-impervious blood-brain barrier. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), a gene-editing tool repurposed from bacterial defense systems against viruses, has been touted by some as a panacea for genetic diseases. CRISPR has expedited the research into HNDs, enabling the generation of in vitro and in vivo models to simulate the changes in human physiology caused by genetic variation. In this review, we describe the basic principles and workings of CRISPR and the modifications that have been made to broaden its applications. Then, we review important CRISPR-based studies that have opened new doors to the treatment of HNDs such as fragile X syndrome and Down syndrome. We also discuss how CRISPR can be used to generate research models to examine the effects of genetic variation and caffeine therapy on the developing brain. Several drawbacks of CRISPR may preclude its use at the clinics, particularly the vulnerability of neuronal cells to the adverse effect of gene editing, and the inefficiency of CRISPR delivery into the brain. In concluding the review, we offer some suggestions for enhancing the gene-editing efficacy of CRISPR and how it may be morphed into safe and effective therapy for HNDs and other brain disorders.

Gene silencing or gene editing: the pros and cons.

2021 ◽  
pp. 47-53
Author(s):  
Huw D. Jones
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Gene Function ◽  
Gene Editing ◽  
Mutation Breeding ◽  
Gene Transcript ◽  
Commercial Activities ◽  
Targeted Mutation ◽  
Pros And Cons ◽  
Or Gene

Abstract Research into plant genetics often requires the suppression or complete knockout of gene expression to scientifically validate gene function. In addition, the phenotypes obtained from gene suppression can occasionally have commercial value for plant breeders. Until recently, the methodological choices to achieve these goals fell into two broad types: either some form of RNA-based gene silencing; or the screening of large numbers of natural or induced random genomic mutations. The more recent invention of gene editing as a tool for targeted mutation potentially gives researchers and plant breeders another route to block gene function. RNAi is widely used in animal and plant research and functions to silence gene expression by degrading the target gene transcript. Although RNAi offers unique advantages over genomic mutations, it often leads to the formation of a genetically modified organism (GMO), which for commercial activities has major regulatory and acceptance issues in some regions of the world. Traditional methods of generating genomic mutations are more laborious and uncertain to achieve the desired goals but possess a distinct advantage of not being governed by GMO regulations. Gene editing (GE) technologies have some of the advantages of both RNAi and classical mutation breeding in that they can be designed to give simple knockouts or to modulate gene expression more subtly. GE also has a more complex regulatory position, with some countries treating it as another conventional breeding method whilst the EU defines GE as a technique of genetic modification and applies the normal GMO authorization procedures. This chapter explores the pros and cons of RNAi alongside other methods of modulating gene function.

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