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Inam S, Muhammad A, Irum S, Rehman N, Riaz A, Uzair M, Khan MR. Genome editing for improvement of biotic and abiotic stress tolerance in cereals. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24092. [PMID: 39222468 DOI: 10.1071/fp24092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems.
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Affiliation(s)
- Safeena Inam
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Amna Muhammad
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Samra Irum
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Nazia Rehman
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Aamir Riaz
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Uzair
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Ramzan Khan
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
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Hwarari D, Radani Y, Ke Y, Chen J, Yang L. CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks. Funct Integr Genomics 2024; 24:50. [PMID: 38441816 DOI: 10.1007/s10142-024-01314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
The CRISPR/Cas systems have emerged as transformative tools for precisely manipulating plant genomes and enhancement. It has provided unparalleled applications from modifying the plant genomes to resistant enhancement. This review manuscript summarises the mechanism, application, and current challenges in the CRISPR/Cas genome editing technology. It addresses the molecular mechanisms of different Cas genes, elucidating their applications in various plants through crop improvement, disease resistance, and trait improvement. The advent of the CRISPR/Cas systems has enabled researchers to precisely modify plant genomes through gene knockouts, knock-ins, and gene expression modulation. Despite these successes, the CRISPR/Cas technology faces challenges, including off-target effects, Cas toxicity, and efficiency. In this manuscript, we also discuss these challenges and outline ongoing strategies employed to overcome these challenges, including the development of novel CRISPR/Cas variants with improved specificity and specific delivery methods for different plant species. The manuscript will conclude by addressing the future perspectives of the CRISPR/Cas technology in plants. Although this review manuscript is not conclusive, it aims to provide immense insights into the current state and future potential of CRISPR/Cas in sustainable and secure plant production.
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Affiliation(s)
- Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongchao Ke
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Nadeem S, Riaz Ahmed S, Luqman T, Tan DKY, Maryum Z, Akhtar KP, Muhy Ud Din Khan S, Tariq MS, Muhammad N, Khan MKR, Liu Y. A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus. Front Genet 2024; 15:1306469. [PMID: 38440193 PMCID: PMC10909863 DOI: 10.3389/fgene.2024.1306469] [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: 10/03/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.
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Affiliation(s)
- Sahar Nadeem
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Pakistan Agriculture Research Council (PARC), Horticulture Research Institute Khuzdar Baghbana, Khuzdar, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Zahra Maryum
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Nazar Muhammad
- Agriculture and Cooperative Department, Quetta, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Wang ML, Lin XJ, Mo BX, Kong WW. Plant Artificial Chromosomes: Construction and Transformation. ACS Synth Biol 2024; 13:15-24. [PMID: 38163256 DOI: 10.1021/acssynbio.3c00555] [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] [Indexed: 01/03/2024]
Abstract
With the decline of cultivated land and increase of the population in recent years, an agricultural revolution is urgently needed to produce more food to improve the living standards of humans. As one of the foundations of synthetic biology, artificial chromosomes hold great potential for advancing crop improvement. They offer opportunities to increase crop yield and quality, while enhancing crop resistance to disease. The progress made in plant artificial chromosome technology enables selective modification of existing chromosomes or the synthesis of new ones to improve crops and study gene function. However, current artificial chromosome technologies still face limitations, particularly in the synthesis of repeat sequences and the transformation of large DNA fragments. In this review, we will introduce the structure of plant centromeres, the construction of plant artificial chromosomes, and possible methods for transforming large fragments into plant cells.
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Affiliation(s)
- Ming L Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiao J Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Bei X Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wen W Kong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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Goyal L, Kaur M, Mandal M, Panda D, Karmakar S, Molla KA, Bhatia D. Potential gene editing targets for developing haploid inducer stocks in rice and wheat with high haploid induction frequency. 3 Biotech 2024; 14:14. [PMID: 38111612 PMCID: PMC10725411 DOI: 10.1007/s13205-023-03857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023] Open
Abstract
Doubled haploid (DH) breeding is a powerful technique to ensure global food security via accelerated crop improvement. DH can be produced in planta by employing haploid inducer stock (HIS). Widely used HIS in maize is known to be governed by ZmPLA, ZmDMP, ZmPLD3, and ZmPOD65 genes. To develop such HIS in rice and wheat, we have identified putative orthologs of these genes using in silico approaches. The OsPLD1; TaPLD1, and OsPOD6; TaPOD8 were identified as putative orthologs of ZmPLD3 and ZmPOD65 in rice and wheat, respectively. Despite being closely related to ZmPLD3, OsPLD1 and TaPLD1 have shown higher anther-specific expression. Similarly, OsPOD6 and TaPOD8 were found closely related to the ZmPOD65 based on both phylogenetic and expression analysis. However, unlike ZmPLD3 and ZmPOD65, two ZmDMP orthologs have been found for each crop. OsDMP1 and OsDMP2 in rice and TaDMP3 and TaDMP13 in wheat have shown similarity to ZmDMP in terms of both sequence and expression pattern. Furthermore, analogs to maize DMP proteins, these genes possess four transmembrane helices making them best suited to be regarded as ZmDMP orthologs. Modifying these predicted orthologous genes by CRISPR/Cas9-based genome editing can produce a highly efficient HIS in both rice and wheat. Besides revealing the genetic mechanism of haploid induction, the development of HIS would advance the genetic improvement of these crops. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03857-9.
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Affiliation(s)
- Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Mehardeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Meghna Mandal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Subhasis Karmakar
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | | | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Mainkar P, Manape TK, Satheesh V, Anandhan S. CRISPR/Cas9-mediated editing of PHYTOENE DESATURASE gene in onion ( Allium cepa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226911. [PMID: 37701798 PMCID: PMC10494252 DOI: 10.3389/fpls.2023.1226911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/28/2023] [Indexed: 09/14/2023]
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) is a precise genome editing tool used to introduce genetic modifications in a wide range of crop species. Thus far, there is no report of CRISPR/Cas9-mediated genome editing in onions (Allium cepa L.). Methods In the present study, we targeted two exons of the gene coding for Phytoene desaturase (AcPDS) in onion cv. Bhima Super. The sgRNA-carrying constructs were co-cultivated with 8-week-old embryogenic calli using an Agrobacterium-mediated transformation protocol and incubated on the media without hygromycin B selection. Results and discussion Out of the total 617 co-cultivated calli, 21 (3.4%) regenerated shoots exhibited three distinct phenotypes: albino, chimeric, and pale green; in comparison to the wild-type non-transformed regenerated shoots. Total chlorophyll content was drastically reduced in albino shoots and significantly decreased in chimeric shoots. Out of the six Cas9 gene PCR-confirmed regenerated shoots, two exhibited the albino phenotype due to insertions/deletions (InDels) and substitution-based mutations in and around the AcPDS target sites. Deep amplicon sequencing revealed a significantly variable InDel frequency between two sgRNAs, ranging from 1.2% to 63.4%, along with a 53.4% substitution frequency. The mutation of the AcPDS gene generated a visually detectable albino phenotype, thus confirming the successful editing of the AcPDS gene. This is the first time a CRISPR/Cas9-mediated genome editing protocol has been successfully established in onion, with the AcPDS gene serving as an example. This study will provide the necessary momentum for researchers to further basic and applied research on onions.
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Affiliation(s)
- Pawan Mainkar
- ICAR-Directorate of Onion and Garlic Research, Pune, Maharashtra, India
| | | | - Viswanathan Satheesh
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, United States
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Ali S, Mir RA, Tyagi A, Manzar N, Kashyap AS, Mushtaq M, Raina A, Park S, Sharma S, Mir ZA, Lone SA, Bhat AA, Baba U, Mahmoudi H, Bae H. Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12071502. [PMID: 37050128 PMCID: PMC10097182 DOI: 10.3390/plants12071502] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 05/31/2023]
Abstract
Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Rakeeb A. Mir
- Department of Biotechnology, Central University of Kashmir, Ganderbal 191201, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Abhijeet Shankar Kashyap
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bajhol 173229, India
| | - Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Suvin Park
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Zahoor A. Mir
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Showkat A. Lone
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India
| | - Ajaz A. Bhat
- Govt. Degree College for Women, University of Kashmir, Baramulla 193101, India
| | - Uqab Baba
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India
| | - Henda Mahmoudi
- Directorate of Programs, International Center for Biosaline Agriculture, Dubai P.O. Box 14660, United Arab Emirates
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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