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Akanmu AO, Asemoloye MD, Marchisio MA, Babalola OO. Adoption of CRISPR-Cas for crop production: present status and future prospects. PeerJ 2024; 12:e17402. [PMID: 38860212 PMCID: PMC11164064 DOI: 10.7717/peerj.17402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time. Methods This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security. Results The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops. Conclusion Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.
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Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | - Michael Dare Asemoloye
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
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Rengasamy B, Manna M, Thajuddin NB, Sathiyabama M, Sinha AK. Breeding rice for yield improvement through CRISPR/Cas9 genome editing method: current technologies and examples. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:185-198. [PMID: 38623165 PMCID: PMC11016042 DOI: 10.1007/s12298-024-01423-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/23/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
The impending climate change is threatening the rice productivity of the Asian subcontinent as instances of crop failures due to adverse abiotic and biotic stress factors are becoming common occurrences. CRISPR-Cas9 mediated genome editing offers a potential solution for improving rice yield as well as its stress adaptation. This technology allows modification of plant's genetic elements and is not dependent on foreign DNA/gene insertion for incorporating a particular trait. In this review, we have discussed various CRISPR-Cas9 mediated genome editing tools for gene knockout, gene knock-in, simultaneously disrupting multiple genes by multiplexing, base editing and prime editing the genes. The review here also presents how these genome editing technologies have been employed to improve rice productivity by directly targeting the yield related genes or by indirectly manipulating various abiotic and biotic stress responsive genes. Lately, many countries treat genome-edited crops as non-GMOs because of the absence of foreign DNA in the final product. Thus, genome edited rice plants with improved yield attributes and stress resilience are expected to be accepted by the public and solve food crisis of a major portion of the globe. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01423-y.
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Affiliation(s)
- Balakrishnan Rengasamy
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Mrinalini Manna
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Nargis Begum Thajuddin
- P. G. and Research Department of Biotechnology, Jamal Mohamed College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
| | | | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
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Švara A, De Storme N, Carpentier S, Keulemans W, De Coninck B. Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab ( Venturia inaequalis) in apple cultivars ( Malus × domestica). HORTICULTURE RESEARCH 2024; 11:uhae002. [PMID: 38371632 PMCID: PMC10873587 DOI: 10.1093/hr/uhae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024]
Abstract
Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
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Affiliation(s)
- Anže Švara
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Genetic resources, Bioversity International, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Barbara De Coninck
- Laboratory of Plant Health and Protection, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
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Ludwig Y, Dueñas C, Arcillas E, Macalalad-Cabral RJ, Kohli A, Reinke R, Slamet-Loedin IH. CRISPR-mediated promoter editing of a cis-regulatory element of OsNAS2 increases Zn uptake/translocation and plant yield in rice. Front Genome Ed 2024; 5:1308228. [PMID: 38322756 PMCID: PMC10844396 DOI: 10.3389/fgeed.2023.1308228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024] Open
Abstract
Developing nutritious rice with a higher yield is one approach to alleviating the problem of micronutrient deficiency in developing countries, especially human malnutrition involving zinc and iron (Fe) deficiency, and achieving better adoption. The transport of micronutrients such as Fe and Zn is mainly regulated via the nicotianamine synthase (OsNAS) gene family, whereas yield is a complex trait that involves multiple loci. Genome editing via CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9, focusing on the OsNAS2 promoter, particularly the deletion of the cis-regulatory element ARR1AT at position -933, was conducted for an enhanced accumulation of Zn in the grain and per plant. The results showed that our promoter editing increased Zn concentration per plant. Evidence also showed that an improved spikelet number per main panicle led to increased grain per plant. The traits were inherited in "transgene-free" and homozygous plant progenies. Further investigation needs to be conducted to validate trait performance under field conditions and elucidate the cause of the spikelet increase.
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Affiliation(s)
- Yvonne Ludwig
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
| | - Conrado Dueñas
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Erwin Arcillas
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
| | - Reena Jesusa Macalalad-Cabral
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
| | - Ajay Kohli
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
| | - Russell Reinke
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
| | - Inez H. Slamet-Loedin
- International Rice Research Institute, Rice Genetic Design and Validation Unit, Rice Breeding Innovations, Los Baños, Philippines
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Hasselbeck S, Cheng X. Molecular Marvels: Small Molecules Paving the Way for Enhanced Gene Therapy. Pharmaceuticals (Basel) 2023; 17:41. [PMID: 38256875 PMCID: PMC10818943 DOI: 10.3390/ph17010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprecedented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas systems, recent advancements have witnessed the integration of small molecules to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applications. This review delves into the synergy between CRISPR-Cas technologies based specifically on Cas9 and small-molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas9-mediated genetic modifications. In this review, we emphasize the significance of small-molecule drugs in fine-tuning the CRISPR-Cas9 machinery, which allows researchers to exert meticulous control over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene editing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas9 technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas9 technologies continue to evolve, the integration of small-molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This review not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas9 systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.
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Affiliation(s)
- Sebastian Hasselbeck
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
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Teng Z, Chen J, Wang J, Wu S, Chen R, Lin Y, Shen L, Jackson R, Zhou J, Yang C. Panicle-Cloud: An Open and AI-Powered Cloud Computing Platform for Quantifying Rice Panicles from Drone-Collected Imagery to Enable the Classification of Yield Production in Rice. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0105. [PMID: 37850120 PMCID: PMC10578299 DOI: 10.34133/plantphenomics.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Rice (Oryza sativa) is an essential stable food for many rice consumption nations in the world and, thus, the importance to improve its yield production under global climate changes. To evaluate different rice varieties' yield performance, key yield-related traits such as panicle number per unit area (PNpM2) are key indicators, which have attracted much attention by many plant research groups. Nevertheless, it is still challenging to conduct large-scale screening of rice panicles to quantify the PNpM2 trait due to complex field conditions, a large variation of rice cultivars, and their panicle morphological features. Here, we present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery. To facilitate the development of AI-powered detection models, we first established an open diverse rice panicle detection dataset that was annotated by a group of rice specialists; then, we integrated several state-of-the-art deep learning models (including a preferred model called Panicle-AI) into the Panicle-Cloud platform, so that nonexpert users could select a pretrained model to detect rice panicles from their own aerial images. We trialed the AI models with images collected at different attitudes and growth stages, through which the right timing and preferred image resolutions for phenotyping rice panicles in the field were identified. Then, we applied the platform in a 2-season rice breeding trial to valid its biological relevance and classified yield production using the platform-derived PNpM2 trait from hundreds of rice varieties. Through correlation analysis between computational analysis and manual scoring, we found that the platform could quantify the PNpM2 trait reliably, based on which yield production was classified with high accuracy. Hence, we trust that our work demonstrates a valuable advance in phenotyping the PNpM2 trait in rice, which provides a useful toolkit to enable rice breeders to screen and select desired rice varieties under field conditions.
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Affiliation(s)
- Zixuan Teng
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Smart Agriculture and Forestry (Fujian Agriculture and Forestry University),
Fujian Province University, Fuzhou 350002, China
| | - Jiawei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Wang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Shuixiu Wu
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Mechanical and Electrical Engineering,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Riqing Chen
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaohai Lin
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liyan Shen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
| | - Robert Jackson
- Cambridge Crop Research,
National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
| | - Ji Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
- Cambridge Crop Research,
National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
| | - Changcai Yang
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Center for Agroforestry Mega Data Science, School of Future Technology,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
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7
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Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
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Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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Errum A, Rehman N, Uzair M, Inam S, Ali GM, Khan MR. CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits. Funct Integr Genomics 2023; 23:66. [PMID: 36840774 DOI: 10.1007/s10142-023-00989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]
Abstract
Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T0-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T1 and T2 progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.
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Affiliation(s)
- Aliya Errum
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
- PARC Institute of Advanced Studies in Agriculture (PIASA), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | | | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.
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Ma B, Zhang L, He Z. Understanding the regulation of cereal grain filling: The way forward. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:526-547. [PMID: 36648157 DOI: 10.1111/jipb.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.
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Affiliation(s)
- Bin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Zhang Q, Zhang S, Yu X, Wei X, Huang X, Zhou X. Fine-tuning grain amylose contents by genome editing of Waxy cis-regulatory region in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:72. [PMID: 37313325 PMCID: PMC10248690 DOI: 10.1007/s11032-022-01342-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/12/2022] [Indexed: 06/15/2023]
Abstract
Rice grain amylose contents (ACs) is a key quantitative trait influencing eating and cooking quality. Regulating the expression level of Waxy, a key gene controlling ACs, and in turn fine-tuning the grain ACs, is an ideal approach to improve grain quality of rice varieties. Based on CRISPR/Cas9 genome editing technology, we designed eight targets in the cis-regulatory region of Wxa background, screened phenotypic changes of the transgenic lines and generated eight novel Waxy alleles with altered grain ACs. Among the eight alleles, we found that a 407-bp non-homologous substitution (NHS) in the 5'UTR-intron caused by genome editing regulated Waxy expression and decreased grain ACs by 2.9%. Moreover, embedding the 407-bp NHS into the cis-regulatory region of Wxb allele can also affect gene activity. Our work suggested the effect of 5'UTR-intron on Waxy gene expression regulation, and provided a potentially useful allele in breeding that can finely adjust rice grain ACs.
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Affiliation(s)
- Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Sinan Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xiting Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
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12
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Wani SH, Choudhary M, Barmukh R, Bagaria PK, Samantara K, Razzaq A, Jaba J, Ba MN, Varshney RK. Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3875-3895. [PMID: 35267056 PMCID: PMC9729161 DOI: 10.1007/s00122-022-04060-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/11/2022] [Indexed: 05/03/2023]
Abstract
Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.
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Affiliation(s)
- Shabir H Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, J&K, 192101, India.
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU Campus, Ludhiana, Punjab, 141001, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pravin K Bagaria
- ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU Campus, Ludhiana, Punjab, 141001, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Paralakhemundi, Odisha, 761211, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Jagdish Jaba
- Intergated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Malick Niango Ba
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
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13
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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14
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Kumar D, Yadav A, Ahmad R, Dwivedi UN, Yadav K. CRISPR-Based Genome Editing for Nutrient Enrichment in Crops: A Promising Approach Toward Global Food Security. Front Genet 2022; 13:932859. [PMID: 35910203 PMCID: PMC9329789 DOI: 10.3389/fgene.2022.932859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The global malnutrition burden imparts long-term developmental, economic, social, and medical consequences to individuals, communities, and countries. The current developments in biotechnology have infused biofortification in several food crops to fight malnutrition. However, these methods are not sustainable and suffer from several limitations, which are being solved by the CRISPR-Cas-based system of genome editing. The pin-pointed approach of CRISPR-based genome editing has made it a top-notch method due to targeted gene editing, thus making it free from ethical issues faced by transgenic crops. The CRISPR-Cas genome-editing tool has been extensively used in crop improvement programs due to its more straightforward design, low methodology cost, high efficiency, good reproducibility, and quick cycle. The system is now being utilized in the biofortification of cereal crops such as rice, wheat, barley, and maize, including vegetable crops such as potato and tomato. The CRISPR-Cas-based crop genome editing has been utilized in imparting/producing qualitative enhancement in aroma, shelf life, sweetness, and quantitative improvement in starch, protein, gamma-aminobutyric acid (GABA), oleic acid, anthocyanin, phytic acid, gluten, and steroidal glycoalkaloid contents. Some varieties have even been modified to become disease and stress-resistant. Thus, the present review critically discusses CRISPR-Cas genome editing-based biofortification of crops for imparting nutraceutical properties.
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Affiliation(s)
- Dileep Kumar
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Anurag Yadav
- Department of Microbiology, College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agriculture University, Banaskantha, India
| | - Rumana Ahmad
- Department of Biochemistry, Era Medical University and Hospital, Lucknow, India
| | | | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, India
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15
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Nerkar G, Devarumath S, Purankar M, Kumar A, Valarmathi R, Devarumath R, Appunu C. Advances in Crop Breeding Through Precision Genome Editing. Front Genet 2022; 13:880195. [PMID: 35910205 PMCID: PMC9329802 DOI: 10.3389/fgene.2022.880195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.
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Affiliation(s)
- Gauri Nerkar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Suman Devarumath
- Vidya Pratishthan's College of Agricultural Biotechnology, Baramati, India
| | - Madhavi Purankar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Atul Kumar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Rachayya Devarumath
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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16
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Yu H, Yang Q, Fu F, Li W. Three strategies of transgenic manipulation for crop improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:948518. [PMID: 35937379 PMCID: PMC9354092 DOI: 10.3389/fpls.2022.948518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops.
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Affiliation(s)
| | | | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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17
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Zhang RX, Li BB, Yang ZG, Huang JQ, Sun WH, Bhanbhro N, Liu WT, Chen KM. Dissecting Plant Gene Functions Using CRISPR Toolsets for Crop Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7343-7359. [PMID: 35695482 DOI: 10.1021/acs.jafc.2c01754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The CRISPR-based gene editing technology has become more and more powerful in genome manipulation for agricultural breeding, with numerous improved toolsets springing up. In recent years, many CRISPR toolsets for gene editing, such as base editors (BEs), CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and plant epigenetic editors (PEEs), have been developed to clarify gene function and full-level gene regulation. Here, we comprehensively summarize the application and capacity of the different CRISPR toolsets in the study of plant gene expression regulation, highlighting their potential application in gene regulatory networks' analysis. The general problems in CRISPR application and the optimal solutions in the existing schemes for high-throughput gene function analysis are also discussed. The CRISPR toolsets targeting gene manipulation discussed here provide new solutions for further genetic improvement and molecular breeding of crops.
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Affiliation(s)
- Rui-Xiang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin-Bin Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zheng-Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia-Qi Huang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nadeem Bhanbhro
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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18
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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19
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Kouhen M, García-Caparrós P, Twyman RM, Abdelly C, Mahmoudi H, Schillberg S, Debez A. Improving environmental stress resilience in crops by genome editing: insights from extremophile plants. Crit Rev Biotechnol 2022; 43:559-574. [PMID: 35606905 DOI: 10.1080/07388551.2022.2042481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.
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Affiliation(s)
- Mohamed Kouhen
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia.,Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Pedro García-Caparrós
- Agronomy Department of Superior School Engineering, University of Almeria, CIAIMBITAL, Almería, Spain
| | | | - Chedly Abdelly
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Academic City, Near Zayed University, Dubai, United Arab Emirates
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Ahmed Debez
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
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20
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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21
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Abdullah M, Okemo P, Furtado A, Henry R. Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives. Front Genome Ed 2022; 4:875243. [PMID: 35572739 PMCID: PMC9091330 DOI: 10.3389/fgeed.2022.875243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.
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Affiliation(s)
- Muhammad Abdullah
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Pauline Okemo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Robert Henry,
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22
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CRISPR-Based Genome Editing: Advancements and Opportunities for Rice Improvement. Int J Mol Sci 2022; 23:ijms23084454. [PMID: 35457271 PMCID: PMC9027422 DOI: 10.3390/ijms23084454] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
To increase the potentiality of crop production for future food security, new technologies for plant breeding are required, including genome editing technology—being one of the most promising. Genome editing with the CRISPR/Cas system has attracted researchers in the last decade as a safer and easier tool for genome editing in a variety of living organisms including rice. Genome editing has transformed agriculture by reducing biotic and abiotic stresses and increasing yield. Recently, genome editing technologies have been developed quickly in order to avoid the challenges that genetically modified crops face. Developing transgenic-free edited plants without introducing foreign DNA has received regulatory approval in a number of countries. Several ongoing efforts from various countries are rapidly expanding to adopt the innovations. This review covers the mechanisms of CRISPR/Cas9, comparisons of CRISPR/Cas9 with other gene-editing technologies—including newly emerged Cas variants—and focuses on CRISPR/Cas9-targeted genes for rice crop improvement. We have further highlighted CRISPR/Cas9 vector construction model design and different bioinformatics tools for target site selection.
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23
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Huang J, Gao L, Luo S, Liu K, Qing D, Pan Y, Dai G, Deng G, Zhu C. The genetic editing of GS3 via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:22. [PMID: 37309462 PMCID: PMC10248666 DOI: 10.1007/s11032-022-01290-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Grain size is one of the major traits that determine rice grain yield and quality. The GS3 gene is the first major quantitative trait locus (QTL) that was identified in regulating rice grain length and weight. It was reported that the gs3 allele with a mutation in the organ size regulation (OSR) domain of the GS3 protein produced longer grains. In this study, we used the CRISPR/Cas9 gene editing technology to introduce an edited gs3 allele into our indica maintainer line, Mei1B, to enhance its grain yield and quality. Through molecular analysis and sequencing, a homologous edited-gs3 mutant line without any transgene was obtained in the T1 generation and was named Mei2B. A superior male sterile line Mei2A was generated by backcrossing the cytoplasmic male sterile (CMS) line Mei1A with Mei2B. Mei2B had a higher grain quality and yield compared to its wild-type Mei1B. Its grain length increased by 7.9%, its length/width ratio increased from 3.89 to 4.19, TGW increased by 6.7%, and grain yield per plant increased by 14.9%. In addition, genetic improvement of other quality traits including brown rice length (6.83 mm), brown rice grain length/width ratio (3.61), matched the appearance standards set for traditional Simiao (silk seedling) type cultivars. Two restorer lines were outcrossed to both Mei1A and Mei2A to produce hybrid rice. Compared to two hybrids of Mei1A, the hybrids of Mei2A had longer grains, higher length/width ratio, TGW, and yield per plant. In addition, the hybrids of Mei2A showed a better grain appearance including better translucency, a lower chalky rice rate, and degree of chalkiness than the hybrids of Mei1A. These results demonstrated that the introduction of an elite gs3 allele into Mei1A via CRISPR/Cas9 gene editing technology led to significant genetic improvement of the rice grain. The resultant CMS line Mei2A(gs3) displayed much higher grain quality and yield than the original Mei1A. Therefore, our study demonstrated that the targeted genetic improvement via gene editing technology can enhance rice breeding, especially the breeding of three-line hybrid rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01290-z.
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Affiliation(s)
- Juan Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Lijun Gao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory/Guangxi Key Laboratory of Genetic Improvement of Crops, Nanning, 530007 China
| | - Shuming Luo
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Kaiqiang Liu
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Gaoxing Dai
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Guofu Deng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
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24
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Rana S, Aggarwal PR, Shukla V, Giri U, Verma S, Muthamilarasan M. Genome Editing and Designer Crops for the Future. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2408:37-69. [PMID: 35325415 DOI: 10.1007/978-1-0716-1875-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Domestication spanning over thousands of years led to the evolution of crops that are being cultivated in recent times. Later, selective breeding methods were practiced by human to produce improved cultivars/germplasm. Classical breeding was further transformed into molecular- and genomics-assisted breeding strategies, however, these approaches are labor-intensive and time-consuming. The advent of omics technologies has facilitated the identification of genes and genetic determinants that regulate particular traits allowing the direct manipulation of target genes and genomic regions to achieve desirable phenotype. Recently, genome editing technologies such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-Associated protein 9 (Cas9) have gained popularity for precise editing of genes to develop crop varieties with superior agronomic, physiological, climate-resilient, and nutritional traits. Owing to the efficiency and precision, genome editing approaches have been widely used to design the crops that can survive the challenges posed by changing climate, and also cater the food and nutritional requirements for ever-growing population. Here, we briefly review different genome editing technologies deployed for crop improvement, and the fundamental differences between GE technology and transgene-based approach. We also summarize the recent advances in genome editing and how this radical expansion can complement the previously established technologies along with breeding for creating designer crops.
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Affiliation(s)
- Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Varsa Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Urmi Giri
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Shubham Verma
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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25
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Tu B, Tao Z, Wang S, Zhou L, Zheng L, Zhang C, Li X, Zhang X, Yin J, Zhu X, Yuan H, Li T, Chen W, Qin P, Ma B, Wang Y, Li S. Loss of Gn1a/OsCKX2 confers heavy-panicle rice with excellent lodging resistance. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:23-38. [PMID: 34783157 DOI: 10.1111/jipb.13185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Significant achievements have been made in breeding programs for the heavy-panicle-type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1aR498 ) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss-of-function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1aR498 allele with two gain-of-function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor-made crop improvement of both yield and lodging resistance in rice.
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Affiliation(s)
- Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhang Tao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shiguang Wang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Zheng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agriculture and Horticulture, Chengdu Agricultural College, Chengdu, 611130, China
| | - Chun Zhang
- Agriculture and Rural Affairs Bureau of Cuiping District, Yibin Sichuan, 644000, China
| | - Xinzi Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoyu Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Weilan Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bingtian Ma
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuping Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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26
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Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z. A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises. Curr Issues Mol Biol 2021; 43:1950-1976. [PMID: 34889892 PMCID: PMC8929161 DOI: 10.3390/cimb43030135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Genome editing (GE) has revolutionized the biological sciences by creating a novel approach for manipulating the genomes of living organisms. Many tools have been developed in recent years to enable the editing of complex genomes. Therefore, a reliable and rapid approach for increasing yield and tolerance to various environmental stresses is necessary to sustain agricultural crop production for global food security. This critical review elaborates the GE tools used for crop improvement. These tools include mega-nucleases (MNs), such as zinc-finger nucleases (ZFNs), and transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Specifically, this review addresses the latest advancements in the role of CRISPR/Cas9 for genome manipulation for major crop improvement, including yield and quality development of biotic stress- and abiotic stress-tolerant crops. Implementation of this technique will lead to the production of non-transgene crops with preferred characteristics that can result in enhanced yield capacity under various environmental stresses. The CRISPR/Cas9 technique can be combined with current and potential breeding methods (e.g., speed breeding and omics-assisted breeding) to enhance agricultural productivity to ensure food security. We have also discussed the challenges and limitations of CRISPR/Cas9. This information will be useful to plant breeders and researchers in the thorough investigation of the use of CRISPR/Cas9 to boost crops by targeting the gene of interest.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Sameer Qari
- Biology Department, (Genetics and Molecular Biology Central Laboratory), Aljumum University College, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Qamar U. Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Ilyas
- University College of Dera Murad Jamali, Nasirabad 80700, Balochistan, Pakistan;
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Huijie Li
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziming Wu
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- Correspondence:
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27
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Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
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 editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
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Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
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28
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Maximiano MR, Távora FTPK, Prado GS, Dias SC, Mehta A, Franco OL. CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6379-6395. [PMID: 34097395 DOI: 10.1021/acs.jafc.1c01062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.
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Affiliation(s)
- Mariana Rocha Maximiano
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
| | - Fabiano T P K Távora
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal 70770-917, Brazil
- Programa de Pós Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-900, Brazil
| | - Guilherme Souza Prado
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Goiânia, Goiás 75375-000, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal 70770-917, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
- Programa de Pós Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-900, Brazil
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29
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Huang X, Hilscher J, Stoger E, Christou P, Zhu C. Modification of cereal plant architecture by genome editing to improve yields. PLANT CELL REPORTS 2021; 40:953-978. [PMID: 33559722 DOI: 10.1007/s00299-021-02668-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.
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Affiliation(s)
- Xin Huang
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
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30
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Massel K, Lam Y, Wong ACS, Hickey LT, Borrell AK, Godwin ID. Hotter, drier, CRISPR: the latest edit on climate change. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1691-1709. [PMID: 33420514 DOI: 10.1007/s00122-020-03764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 05/23/2023]
Abstract
Integrating CRISPR/Cas9 genome editing into modern breeding programs for crop improvement in cereals. Global climate trends in many agricultural regions have been rapidly changing over the past decades, and major advances in global food systems are required to ensure food security in the face of these emerging challenges. With increasing climate instability due to warmer temperatures and rising CO2 levels, the productivity of global agriculture will continue to be negatively impacted. To combat these growing concerns, creative approaches will be required, utilising all the tools available to produce more robust and tolerant crops with increased quality and yields under more extreme conditions. The integration of genome editing and transgenics into current breeding strategies is one promising solution to accelerate genetic gains through targeted genetic modifications, producing crops that can overcome the shifting climate realities. This review focuses on how revolutionary genome editing tools can be directly implemented into breeding programs for cereal crop improvement to rapidly counteract many of the issues affecting agriculture production in the years to come.
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Affiliation(s)
- Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Yasmine Lam
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Albert C S Wong
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew K Borrell
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian D Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
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31
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Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S, Ma W, She M. Application of CRISPR/Cas9 in Crop Quality Improvement. Int J Mol Sci 2021; 22:4206. [PMID: 33921600 PMCID: PMC8073294 DOI: 10.3390/ijms22084206] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.
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Affiliation(s)
- Qier Liu
- Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Fan Yang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Hang Liu
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shanjida Rahman
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Maoyun She
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
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32
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Genome engineering for crop improvement and future agriculture. Cell 2021; 184:1621-1635. [PMID: 33581057 DOI: 10.1016/j.cell.2021.01.005] [Citation(s) in RCA: 307] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
Feeding the ever-growing population is a major challenge, especially in light of rapidly changing climate conditions. Genome editing is set to revolutionize plant breeding and could help secure the global food supply. Here, I review the development and application of genome editing tools in plants while highlighting newly developed techniques. I describe new plant breeding strategies based on genome editing and discuss their impact on crop production, with an emphasis on recent advancements in genome editing-based plant improvements that could not be achieved by conventional breeding. I also discuss challenges facing genome editing that must be overcome before realizing the full potential of this technology toward future crops and food production.
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33
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Li G, Yang Q, Li D, Zhang T, Yang L, Qin J, Tang B, Guo X, Cao Y, You S, Li Z, Luo J, Wan X, Liu Y, Huang F, Guo L, Jiang K, Zheng J. Genome‐wide SNP discovery and QTL mapping for economic traits in a recombinant inbred line of
Oryza sativa. Food Energy Secur 2021. [DOI: 10.1002/fes3.274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gengmi Li
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Qianhua Yang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Deqiang Li
- Rice Research Institute/College of Agronomy Sichuan Agricultural University Chengdu China
| | - Tao Zhang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Li Yang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Jian Qin
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Bin Tang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Xiaojiao Guo
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Yingjiang Cao
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Shumei You
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Zhaoxiang Li
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Jing Luo
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Xianqi Wan
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Ying Liu
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Fu Huang
- Rice Research Institute/College of Agronomy Sichuan Agricultural University Chengdu China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology China National Rice Research Institute, Chinese Academy of Agricultural Sciences Hangzhou China
| | - Kaifeng Jiang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
| | - Jiakui Zheng
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences Deyang China
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Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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Kaul T, Sony SK, Verma R, Motelb KFA, Prakash AT, Eswaran M, Bharti J, Nehra M, Kaul R. Revisiting CRISPR/Cas-mediated crop improvement: Special focus on nutrition. J Biosci 2020. [DOI: 10.1007/s12038-020-00094-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Zeng Z, Han N, Liu C, Buerte B, Zhou C, Chen J, Wang M, Zhang Y, Tang Y, Zhu M, Wang J, Yang Y, Bian H. Functional dissection of HGGT and HPT in barley vitamin E biosynthesis via CRISPR/Cas9-enabled genome editing. ANNALS OF BOTANY 2020; 126:929-942. [PMID: 32575125 PMCID: PMC7539355 DOI: 10.1093/aob/mcaa115] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Vitamin E (tocochromanol) is a lipid-soluble antioxidant and an essential nutrient for human health. Among cereal crops, barley (Hordeum vulgare) contains a high level of vitamin E, which includes both tocopherols and tocotrienols. Although the vitamin E biosynthetic pathway has been characterized in dicots, such as Arabidopsis, which only accumulate tocopherols, knowledge regarding vitamin E biosynthesis in monocots is limited because of the lack of functional mutants. This study aimed to obtain gene knockout mutants to elucidate the genetic control of vitamin E composition in barley. METHODS Targeted knockout mutations of HvHPT and HvHGGT in barley were created with CRISPR/Cas9-enabled genome editing. High-performance liquid chromatography (HPLC) was performed to analyse the content of tocochromanol isomers in transgene-free homozygous Hvhpt and Hvhggt mutants. KEY RESULTS Mutagenesis efficiency among T0 regenerated plantlets was 50-65 % as a result of two simultaneously expressed guide RNAs targeting each gene; most of the mutations were stably inherited by the next generation. The transgene-free homozygous mutants of Hvhpt and Hvhggt exhibited decreased grain size and weight, and the HvHGGT mutation led to a shrunken phenotype and significantly lower total starch content in grains. HPLC analysis revealed that targeted mutation of HvHPT significantly reduced the content of both tocopherols and tocotrienols, whereas mutations in HvHGGT completely blocked tocotrienol biosynthesis in barley grains. Transient overexpression of an HvHPT homologue in tobacco leaves significantly increased the production of γ- and δ-tocopherols, which may partly explain why targeted mutation of HvHPT in barley grains did not eliminate tocopherol production. CONCLUSIONS Our results functionally validated that HvHGGT is the only committed gene for the production of tocotrienols, whereas HvHPT is partly responsible for tocopherol biosynthesis in barley.
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Affiliation(s)
- Zhanghui Zeng
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ning Han
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cuicui Liu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - B Buerte
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chenlu Zhou
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianshu Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Mengyao Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuhong Zhang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Muyuan Zhu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junhui Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yinong Yang
- Department of Plant Pathology and Environment Microbiology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
- For correspondence. E-mail
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Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong WJ, Jung KH. A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement. Int J Mol Sci 2020; 21:E5665. [PMID: 32784649 PMCID: PMC7461041 DOI: 10.3390/ijms21165665] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.
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Affiliation(s)
- Sunny Ahmar
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Sumbul Saeed
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Muhammad Hafeez Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Shahid Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Muhammad Kamran
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aroosha Faheem
- Sate Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University Wuhan, Wuhan 430070, China;
| | - Ambreen Maqsood
- Department of Plant Pathology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Muhammad Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan;
| | - Saba Saleem
- Department of Bioscience, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan;
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
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Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. J Adv Res 2020; 24:337-352. [PMID: 32461810 PMCID: PMC7240055 DOI: 10.1016/j.jare.2020.04.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/29/2022] Open
Abstract
Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.
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Affiliation(s)
- Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
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Zafar K, Sedeek KEM, Rao GS, Khan MZ, Amin I, Kamel R, Mukhtar Z, Zafar M, Mansoor S, Mahfouz MM. Genome Editing Technologies for Rice Improvement: Progress, Prospects, and Safety Concerns. Front Genome Ed 2020; 2:5. [PMID: 34713214 PMCID: PMC8525367 DOI: 10.3389/fgeed.2020.00005] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Rice (Oryza sativa) is an important staple food crop worldwide; to meet the growing nutritional requirements of the increasing population in the face of climate change, qualitative and quantitative traits of rice need to be improved. Stress-tolerant crop varieties must be developed with stable or higher yields under stress conditions. Genome editing and speed breeding have improved the accuracy and pace of rice breeding. New breeding technologies including genome editing have been established in rice, expanding the potential for crop improvement. Recently, other genome editing techniques such as CRISPR-directed evolution, CRISPR-Cas12a, and base editors have also been used for efficient genome editing in rice. Since rice is an excellent model system for functional studies due to its small genome and close syntenic relationships with other cereal crops, new genome-editing technologies continue to be developed for use in rice. In this review, we focus on genome-editing tools for rice improvement to address current challenges and provide examples of genome editing in rice. We also shed light on expanding the scope of genome editing and systems for delivering homology-directed repair templates. Finally, we discuss safety concerns and methods for obtaining transgene-free crops.
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Affiliation(s)
- Kashaf Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Khalid E. M. Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Radwa Kamel
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Mehak Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Zhang P, Du H, Wang J, Pu Y, Yang C, Yan R, Yang H, Cheng H, Yu D. Multiplex CRISPR/Cas9-mediated metabolic engineering increases soya bean isoflavone content and resistance to soya bean mosaic virus. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1384-1395. [PMID: 31769589 PMCID: PMC7206993 DOI: 10.1111/pbi.13302] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 11/18/2019] [Indexed: 05/18/2023]
Abstract
Isoflavonoids, which include a variety of secondary metabolites, are derived from the phenylpropanoid pathway and are distributed predominantly in leguminous plants. These compounds play a critical role in plant-environment interactions and are beneficial to human health. Isoflavone synthase (IFS) is a key enzyme in isoflavonoid synthesis and shares a common substrate with flavanone-3-hydroxylase (F3H) and flavone synthase II (FNS II). In this study, CRISPR/Cas9-mediated multiplex gene-editing technology was employed to simultaneously target GmF3H1, GmF3H2 and GmFNSII-1 in soya bean hairy roots and plants. Various mutation types and frequencies were observed in hairy roots. Higher mutation efficiencies were found in the T0 transgenic plants, with a triple gene mutation efficiency of 44.44%, and these results of targeted mutagenesis were stably inherited in the progeny. Metabolomic analysis of T0 triple-mutants leaves revealed significant improvement in isoflavone content. Compared with the wild type, the T3 generation homozygous triple mutants had approximately twice the leaf isoflavone content, and the soya bean mosaic virus (SMV) coat protein content was significantly reduced by one-third after infection with strain SC7, suggesting that increased isoflavone content enhanced the leaf resistance to SMV. The isoflavone content in the seeds of T2 triple mutants was also significantly increased. This study provides not only materials for the improvement of soya bean isoflavone content and resistance to SMV but also a simple system to generate multiplex mutations in soya bean, which may be beneficial for further breeding and metabolic engineering.
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Affiliation(s)
- Peipei Zhang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hongyang Du
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural ScienceHefeiChina
| | - Jiao Wang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yixiang Pu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Changyun Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Rujuan Yan
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hui Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Hao Cheng
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Deyue Yu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
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Anwar A, Kim JK. Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives. Int J Mol Sci 2020; 21:E2695. [PMID: 32295026 PMCID: PMC7216248 DOI: 10.3390/ijms21082695] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.
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Affiliation(s)
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea;
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Paul MJ, Watson A, Griffiths CA. Linking fundamental science to crop improvement through understanding source and sink traits and their integration for yield enhancement. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2270-2280. [PMID: 31665486 PMCID: PMC7134924 DOI: 10.1093/jxb/erz480] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/11/2019] [Indexed: 05/19/2023]
Abstract
Understanding processes in sources and sinks that contribute to crop yields has taken years of painstaking research. For crop yield improvement, processes need to be understood as standalone mechanisms in addition to how these mechanisms perform at the crop level; currently there is often a chasm between the two. Fundamental mechanisms need to be considered in the context of crop ideotypes and the agricultural environment which is often more water limited than carbon limited. Different approaches for improvement should be considered, namely is there genetic variation? Or if not, could genetic modification, genome editing, or alternative approaches be utilized? Currently, there are few examples where genetic modification has improved intrinsic yield in the field for commercial application in a major crop. Genome editing, particularly of negative yield regulators as a first step, is providing new opportunities. Here we highlight key mechanisms in source and sink, arguing that for large yield increases integration of key processes is likely to produce the biggest successes within the framework of crop ideotypes with optimized phenology. We highlight a plethora of recent papers that show breakthroughs in fundamental science and the promise of the trehalose 6-phosphate signalling pathway, which regulates carbohydrate allocation which is key for many crop traits.
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Affiliation(s)
- Matthew J Paul
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
- Correspondence:
| | - Amy Watson
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Cara A Griffiths
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
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Berny Mier y Teran JC, Konzen ER, Palkovic A, Tsai SM, Gepts P. Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations. FRONTIERS IN PLANT SCIENCE 2020; 11:346. [PMID: 32308660 PMCID: PMC7145959 DOI: 10.3389/fpls.2020.00346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/29/2023]
Abstract
Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC1S4) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from -164 to 277 kg ha-1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from drought-stressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression.
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Affiliation(s)
| | - Enéas R. Konzen
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Antonia Palkovic
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Kumar K, Gambhir G, Dass A, Tripathi AK, Singh A, Jha AK, Yadava P, Choudhary M, Rakshit S. Genetically modified crops: current status and future prospects. PLANTA 2020; 251:91. [PMID: 32236850 DOI: 10.1007/s00425-020-03372-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
While transgenic technology has heralded a new era in crop improvement, several concerns have precluded their widespread acceptance. Alternative technologies, such as cisgenesis and genome-editing may address many of such issues and facilitate the development of genetically engineered crop varieties with multiple favourable traits. Genetic engineering and plant transformation have played a pivotal role in crop improvement via introducing beneficial foreign gene(s) or silencing the expression of endogenous gene(s) in crop plants. Genetically modified crops possess one or more useful traits, such as, herbicide tolerance, insect resistance, abiotic stress tolerance, disease resistance, and nutritional improvement. To date, nearly 525 different transgenic events in 32 crops have been approved for cultivation in different parts of the world. The adoption of transgenic technology has been shown to increase crop yields, reduce pesticide and insecticide use, reduce CO2 emissions, and decrease the cost of crop production. However, widespread adoption of transgenic crops carrying foreign genes faces roadblocks due to concerns of potential toxicity and allergenicity to human beings, potential environmental risks, such as chances of gene flow, adverse effects on non-target organisms, evolution of resistance in weeds and insects etc. These concerns have prompted the adoption of alternative technologies like cisgenesis, intragenesis, and most recently, genome editing. Some of these alternative technologies can be utilized to develop crop plants that are free from any foreign gene hence, it is expected that such crops might achieve higher consumer acceptance as compared to the transgenic crops and would get faster regulatory approvals. In this review, we present a comprehensive update on the current status of the genetically modified (GM) crops under cultivation. We also discuss the issues affecting widespread adoption of transgenic GM crops and comment upon the recent tools and techniques developed to address some of these concerns.
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Affiliation(s)
- Krishan Kumar
- ICAR-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
| | - Geetika Gambhir
- ICAR-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Dass
- ICAR-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Amit Kumar Tripathi
- National Institute for Research in Environmental Health, Bhopal, 462001, India
| | - Alla Singh
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India
| | - Abhishek Kumar Jha
- ICAR-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- ICAR-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India
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Zhang Y, Showalter AM. CRISPR/Cas9 Genome Editing Technology: A Valuable Tool for Understanding Plant Cell Wall Biosynthesis and Function. FRONTIERS IN PLANT SCIENCE 2020; 11:589517. [PMID: 33329650 PMCID: PMC7714752 DOI: 10.3389/fpls.2020.589517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
For the past 5 years, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) technology has appeared in the molecular biology research spotlight. As a game-changing player in genome editing, CRISPR/Cas9 technology has revolutionized animal research, including medical research and human gene therapy as well as plant science research, particularly for crop improvement. One of the most common applications of CRISPR/Cas9 is to generate genetic knock-out mutants. Recently, several multiplex genome editing approaches utilizing CRISPR/Cas9 were developed and applied in various aspects of plant research. Here we summarize these approaches as they relate to plants, particularly with respect to understanding the biosynthesis and function of the plant cell wall. The plant cell wall is a polysaccharide-rich cell structure that is vital to plant cell formation, growth, and development. Humans are heavily dependent on the byproducts of the plant cell wall such as shelter, food, clothes, and fuel. Genes involved in the assembly of the plant cell wall are often highly redundant. To identify these redundant genes, higher-order knock-out mutants need to be generated, which is conventionally done by genetic crossing. Compared with genetic crossing, CRISPR/Cas9 multi-gene targeting can greatly shorten the process of higher-order mutant generation and screening, which is especially useful to characterize cell wall related genes in plant species that require longer growth time. Moreover, CRISPR/Cas9 makes it possible to knock out genes when null T-DNA mutants are not available or are genetically linked. Because of these advantages, CRISPR/Cas9 is becoming an ideal and indispensable tool to perform functional studies in plant cell wall research. In this review, we provide perspectives on how to design CRISPR/Cas9 to achieve efficient gene editing and multi-gene targeting in plants. We also discuss the recent development of the virus-based CRISPR/Cas9 system and the application of CRISPR/Cas9 to knock in genes. Lastly, we summarized current progress on using CRISPR/Cas9 for the characterization of plant cell wall-related genes.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
- *Correspondence: Allan M. Showalter,
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Li S, Shen L, Hu P, Liu Q, Zhu X, Qian Q, Wang K, Wang Y. Developing disease-resistant thermosensitive male sterile rice by multiplex gene editing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1201-1205. [PMID: 30623600 DOI: 10.1111/jipb.12774] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/07/2019] [Indexed: 05/25/2023]
Abstract
High-quality and disease-resistant male sterile lines have great potential for applications in hybrid rice breeding. We introduced specific mutations into the TMS5, Pi21, and Xa13 genes in Pinzhan intermediate breeding material using the CRISPR/Cas9 multiplex genome editing system. We found that the transgene-free homozygous triple tms5/pi21/xa13 mutants obtained in the T1 generation displayed characteristics of thermosensitive genic male sterility (TGMS) with enhanced resistance to rice blast and bacterial blight. Our study provides a convenient and effective way of converting breeding intermediate material into TGMS lines through multiplex gene editing, which could significantly accelerate the breeding of sterile lines.
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Affiliation(s)
- Sanfeng Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Ping Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Qing Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Xudong Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, the Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
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OsCAF1, a CRM Domain Containing Protein, Influences Chloroplast Development. Int J Mol Sci 2019; 20:ijms20184386. [PMID: 31500108 PMCID: PMC6770308 DOI: 10.3390/ijms20184386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 01/15/2023] Open
Abstract
The chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are involved in the splicing of chloroplast gene introns. Numerous CRM domain proteins have been reported to play key roles in chloroplast development in several plant species. However, the functions of CRM domain proteins in chloroplast development in rice remain poorly understood. In the study, we generated oscaf1 albino mutants, which eventually died at the seedling stage, through the editing of OsCAF1 with two CRM domains using CRISPR/Cas9 technology. The mesophyll cells in oscaf1 mutant had decreased chloroplast numbers and damaged chloroplast structures. OsCAF1 was located in the chloroplast, and transcripts revealed high levels in green tissues. In addition, the OsCAF1 promoted the splicing of group IIA and group IIB introns, unlike orthologous proteins of AtCAF1 and ZmCAF1, which only affected the splicing of subgroup IIB introns. We also observed that the C-terminal of OsCAF1 interacts with OsCRS2, and OsCAF1–OsCRS2 complex may participate in the splicing of group IIA and group IIB introns in rice chloroplasts. OsCAF1 regulates chloroplast development by influencing the splicing of group II introns.
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Razzaq A, Saleem F, Kanwal M, Mustafa G, Yousaf S, Imran Arshad HM, Hameed MK, Khan MS, Joyia FA. Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox. Int J Mol Sci 2019; 20:E4045. [PMID: 31430902 PMCID: PMC6720679 DOI: 10.3390/ijms20164045] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Mehak Kanwal
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | - Ghulam Mustafa
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | | | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Sarwar Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz Ahmad Joyia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
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Hua K, Zhang J, Botella JR, Ma C, Kong F, Liu B, Zhu JK. Perspectives on the Application of Genome-Editing Technologies in Crop Breeding. MOLECULAR PLANT 2019; 12:1047-1059. [PMID: 31260812 DOI: 10.1016/j.molp.2019.06.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/23/2019] [Accepted: 06/24/2019] [Indexed: 05/20/2023]
Abstract
Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses. Genome-editing systems, in contrast, provide the means to rapidly modify genomes in a precise and predictable way, making it possible to introduce improvements directly into elite varieties. Here, we describe the range of applications available to agricultural researchers using existing genome-editing tools. In addition to providing examples of genome-editing applications in crop breeding, we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.
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Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jinshan Zhang
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Changle Ma
- Shandong Provincial Key Lab of Plant Stress, School of Life Sciences, Shandong Normal University, Jinan, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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50
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Kaul T, Raman NM, Eswaran M, Thangaraj A, Verma R, Sony SK, Sathelly KM, Kaul R, Yadava P, Agrawal PK. Data Mining by Pluralistic Approach on CRISPR Gene Editing in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:801. [PMID: 31354748 PMCID: PMC6632506 DOI: 10.3389/fpls.2019.00801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Genome engineering by site-specific nucleases enables reverse genetics and targeted editing of genomes in an efficacious manner. Contemporary revolutionized progress in targeted-genome engineering technologies based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-related RNA-guided endonucleases facilitate coherent interrogation of crop genome function. Evolved as an innate component of the adaptive immune response in bacterial and archaeal systems, CRISPR/Cas system is now identified as a versatile molecular tool that ensures specific and targeted genome modification in plants. Applications of this genome redaction tool-kit include somatic genome editing, rectification of genetic disorders or gene therapy, treatment of infectious diseases, generation of animal models, and crop improvement. We review the utilization of these synthetic nucleases as precision, targeted-genome editing platforms with the inherent potential to accentuate basic science "strengths and shortcomings" of gene function, complement plant breeding techniques for crop improvement, and charter a knowledge base for effective use of editing technology for ever-increasing agricultural demands. Furthermore, the emerging importance of Cpf1, Cas9 nickase, C2c2, as well as other innovative candidates that may prove more effective in driving novel applications in crops are also discussed. The mined data has been prepared as a library and opened for public use at www.lipre.org.
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Affiliation(s)
- Tanushri Kaul
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nitya Meenakshi Raman
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Murugesh Eswaran
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Arulprakash Thangaraj
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Krishnamurthy M. Sathelly
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pranjal Yadava
- Department of Biotechnology, Indian Institute of Maize Research, Indian Institute of Agricultural Biotechnology (ICAR), New Delhi, India
| | - Pawan Kumar Agrawal
- National Agricultural Science Fund, Indian Council of Agricultural Research, New Delhi, India
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