scholarly journals Generating novel plant genetic variation via genome editing to escape the breeding lottery

2021 ◽  
Author(s):  
Nathaniel Schleif ◽  
Shawn M. Kaeppler ◽  
Heidi F. Kaeppler
Keyword(s):  
Genetic Variation ◽  
Plant Breeding ◽  
Genome Editing ◽  
Breeding Success ◽  
Crop Improvement ◽  
Random Mutagenesis ◽  
Plant Genome ◽  
Gene Pools ◽  
Plant Genotype ◽  
Wild Accessions

AbstractPlant breeding relies on the presence of genetic variation, which is generated by a random process of mutagenesis that acts on existing gene pools. This variation is then recombined into new forms at frequencies impacted by the local euchromatin and heterochromatin environment. The result is a genetic lottery where plant breeders face increasingly low odds of generating a “winning” plant genotype. Genome editing tools enable targeted manipulation of the genome, providing a means to increase genetic variation and enhancing the chances for plant breeding success. Editing can be applied in a targeted way, where known genetic variation that improves performance can be directly brought into lines of interest through either deletion or insertion. This empowers approaches that are traditionally difficult such as novel domestication and introgression of wild accessions into a germplasm pool. Furthermore, broader editing-mediated approaches such as recombination enhancement and targeted random mutagenesis bring novel ways of variation creation to the plant breeding toolbox. Continued development and application of plant genome editing tools will be needed to aid in meeting critical global crop improvement needs.

scholarly journals Current and Future Prospects of Plant Breeding with CRISPR/Cas

2019 ◽  
pp. 1-17
Author(s):  
Wagh Sopan Ganpatrao ◽  
Pohare Manoj Baliram
Keyword(s):  
Plant Breeding ◽  
Genome Editing ◽  
Precision Agriculture ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Plant Genome ◽  
Trait Improvement ◽  
Challenges And Opportunities ◽  
Potential Applications ◽  
Regulation Strategies

Innovative plant breeding technology is an absolute necessity to enhance agriculture production in order to have an ambition of feeding nutritious food to the ever-increasing population. Current advances in CRISPR/Cas genome editing technology have led to effective targeted changes in most plants that promise to accelerate crop improvement. Here we discussed the discovery of CRISPR/Cas technology, associated manipulations for plant genome editing and its potential applications in the plant breeding. We emphasized mainly on the most essential applications of CRISPR/Cas genome editing in crop improvement, such as crop trait improvement (yield and biotic/abiotic stress tolerance), developments in optimizing gene regulation, strategies for generating virus resistance in plants, and the use of high throughput mutant libraries. Finally, the challenges and opportunities for plant breeding in precision agriculture and its bright future discussed.

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

2019 ◽  
Vol 70 (1) ◽  
pp. 667-697 ◽  
Author(s):  
Kunling Chen ◽  
Yanpeng Wang ◽  
Rui Zhang ◽  
Huawei Zhang ◽  
Caixia Gao
Keyword(s):  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Delivery Systems ◽  
Fine Tuning ◽  
Plant Genome ◽  
Nucleotide Substitutions ◽  
Base Editing ◽  
Homology Directed Repair ◽  
Challenges And Opportunities

Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.

Raising climate resilient crops: Journey from the conventional breeding to new breeding approaches

2021 ◽  
Vol 22 ◽  
Author(s):  
Yashika Gaba ◽  
Ashwani Pareek ◽  
Sneh Lata Singla-Pareek
Keyword(s):  
Genetic Engineering ◽  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Good Alternative ◽  
Crop Plants ◽  
Gene Pools ◽  
Precise Integration ◽  
Practical Applications ◽  
Improvement Programs

Background: In order to meet the demands of ever-increasing human population, it has become necessary to raise climate-resilient crops. Plant breeding which involves crossing and selecting superior gene pools has contributed tremendously towards achieving this goal during the past few decades. The relatively newer methods of crop improvement based on genetic engineering are relatively simple and targets can be achieved in an expeditious manner. More recently emerged genome editing technique using CRISPR has raised strong hopes among plant scientists for precise integration of valuable traits and removal of undesirable ones. Conclusion: Genome editing using Site Specific Nucleases (SSNs) is a good alternative to the plant breeding and genetic engineering approaches as it can modify the genomes specifically and precisely at the target site in the host genome. Another added advantage of the genome editing approach is the simpler biosafety regulations that have been adopted by many countries for commercialization of the products thus generated. This review provides a critical assessment of the available methods for improving the stress tolerance in crop plants. Special emphasis has been given on genome editing approach in light of the diversity of tools which are being discovered on everyday basis and the practical applications of the same. This information will serve a beginner’s guide to initiate the crop improvement programs as well as giving technical insight to the expert to plan the research strategically to tackle even multigenic traits in crop plants.

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 Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

2021 ◽  
Vol 22 (11) ◽  
pp. 5585
Author(s):  
Sajid Fiaz ◽  
Sunny Ahmar ◽  
Sajjad Saeed ◽  
Aamir Riaz ◽  
Freddy Mora-Poblete ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Food Security ◽  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Hybrid Seed Production ◽  
Biotic And Abiotic Stress ◽  
Transcription Activator ◽  
Protein System ◽  
Breeding Techniques

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

Concepts of Molecular Plant Breeding and Genome Editing

2021 ◽  
pp. 1-15
Keyword(s):  
Plant Breeding ◽  
Genome Editing ◽  
Genetic Linkage ◽  
Selection Process ◽  
Crop Improvement ◽  
Zinc Finger Nucleases ◽  
Induced Mutations ◽  
Transcription Activator ◽  
Targeted Gene Editing ◽  
Breeding Techniques

Traditional plant breeding depends on spontaneous and induced mutations available in the crop plants. Such mutations are rare and occur randomly. By contrast, molecular breeding and genome editing are advanced breeding techniques that can enhance the selection process and produce precisely targeted modifications in any crop. Identification of molecular markers, based on SSRs and SNPs, and the availability of high-throughput (HTP) genotyping platforms have accelerated the process of generating dense genetic linkage maps and thereby enhanced application of marker-assisted breeding for crop improvement. Advanced molecular biology techniques that facilitate precise, efficient, and targeted modifications at genomic loci are termed as “genome editing.” The genome editing tools include “zinc-finger nucleases (ZNFs),” “transcription activator-like effector nucleases (TALENs),” oligonucleotide-directed mutagenesis (ODM), and “clustered regularly interspersed short palindromic repeats (CRISPER/Cas) system,” which can be used for targeted gene editing. Concepts of molecular plant breeding and genome editing systems are presented in this chapter.

scholarly journals 230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 56-56
Author(s):  
Michael Thomson
Keyword(s):  
Genome Editing ◽  
High Throughput ◽  
Positional Cloning ◽  
Gene Editing ◽  
Crop Improvement ◽  
Cost Effective ◽  
Gene Families ◽  
Ease Of Use ◽  
Plant Genome ◽  
Wide Range

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.

scholarly journals Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243238
Author(s):  
Wilson Nkhata ◽  
Hussein Shimelis ◽  
Rob Melis ◽  
Rowland Chirwa ◽  
Tenyson Mzengeza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Common Bean ◽  
Southern Africa ◽  
Crop Improvement ◽  
Phenotypic Expression ◽  
Snp Markers ◽  
High Yield ◽  
Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Engineering Resistance Against Viruses in Field Crops Using CRISPR-Cas9

2021 ◽  
Vol 22 ◽  
Author(s):  
Vidya R. Hinge ◽  
Rahul L. Chavhan ◽  
Sandeep P. Kale ◽  
Penna Suprasanna ◽  
Ulhas S. Kadam
Keyword(s):  
Genome Editing ◽  
Host Resistance ◽  
Virus Resistance ◽  
Plant Virus ◽  
Crop Improvement ◽  
Plant Viruses ◽  
Plant Genome ◽  
Change Scenario ◽  
Field Crops ◽  
Plant Virus Resistance

: Various types biotic stresses affect growth and production of agricultural crops, among them viruses are of most concern which cause yield losses in all field crops; challenging global food security. Enhancement of host resistance against plant viruses is a priority for effective management of plant viral diseases. In the present context of climate change scenario, plant viruses are rapidly evolving and defeating the host resistance. Advances in genome editing techniques such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9] have been recognized as a promising tool for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simple, efficient, and reproducible genetic manipulation. CRISPR-Cas9 based virus resistance in plants has been successfully achieved through gene targeting and cleaving viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have outlined the CRISPR-Cas9 system, plant immunity against viruses and use of CRISPR-Cas9 system to engineer virus resistance in plants. We also discuss prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.

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