1
|
Lorenzo CD, Blasco-Escámez D, Beauchet A, Wytynck P, Sanches M, Garcia Del Campo JR, Inzé D, Nelissen H. Maize mutant screens: from classical methods to new CRISPR-based approaches. THE NEW PHYTOLOGIST 2024. [PMID: 39212458 DOI: 10.1111/nph.20084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site-directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR-Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.
Collapse
Affiliation(s)
- Christian Damian Lorenzo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - David Blasco-Escámez
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Arthur Beauchet
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Pieter Wytynck
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Matilde Sanches
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Jose Rodrigo Garcia Del Campo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| |
Collapse
|
2
|
Vandeputte W, Coussens G, Aesaert S, Haeghebaert J, Impens L, Karimi M, Debernardi JM, Pauwels L. Use of GRF-GIF chimeras and a ternary vector system to improve maize (Zea mays L.) transformation frequency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2116-2132. [PMID: 38923048 DOI: 10.1111/tpj.16880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
Maize (Zea mays L.) is an important crop that has been widely studied for its agronomic and industrial applications and is one of the main classical model organisms for genetic research. Agrobacterium-mediated transformation of immature maize embryos is a commonly used method to introduce transgenes, but a low transformation frequency remains a bottleneck for many gene-editing applications. Previous approaches to enhance transformation included the improvement of tissue culture media and the use of morphogenic regulators such as BABY BOOM and WUSCHEL2. Here, we show that the frequency can be increased using a pVS1-VIR2 virulence helper plasmid to improve T-DNA delivery, and/or expressing a fusion protein between a GROWTH-REGULATING FACTOR (GRF) and GRF-INTERACTING FACTOR (GIF) protein to improve regeneration. Using hygromycin as a selection agent to avoid escapes, the transformation frequency in the maize inbred line B104 significantly improved from 2.3 to 8.1% when using the pVS1-VIR2 helper vector with no effect on event quality regarding T-DNA copy number. Combined with a novel fusion protein between ZmGRF1 and ZmGIF1, transformation frequencies further improved another 3.5- to 6.5-fold with no obvious impact on plant growth, while simultaneously allowing efficient CRISPR-/Cas9-mediated gene editing. Our results demonstrate how a GRF-GIF chimera in conjunction with a ternary vector system has the potential to further improve the efficiency of gene-editing applications and molecular biology studies in maize.
Collapse
Affiliation(s)
- Wout Vandeputte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Jari Haeghebaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Lennert Impens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Mansour Karimi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Juan M Debernardi
- Plant Transformation Facility, University of California, Davis, Davis, California, USA
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| |
Collapse
|
3
|
Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [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: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
Collapse
Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
4
|
Shi Y, Wang J, Yu T, Song R, Qi W. Callus-specific CRISPR/Cas9 system to increase heritable gene mutations in maize. PLANTA 2024; 260:16. [PMID: 38833022 DOI: 10.1007/s00425-024-04451-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
MAIN CONCLUSION A callus-specific CRISPR/Cas9 (CSC) system with Cas9 gene driven by the promoters of ZmCTA1 and ZmPLTP reduces somatic mutations and improves the production of heritable mutations in maize. The CRISPR/Cas9 system, due to its editing accuracy, provides an excellent tool for crop genetic breeding. Nevertheless, the traditional design utilizing CRISPR/Cas9 with ubiquitous expression leads to an abundance of somatic mutations, thereby complicating the detection of heritable mutations. We constructed a callus-specific CRISPR/Cas9 (CSC) system using callus-specific promoters of maize Chitinase A1 and Phospholipid transferase protein (pZmCTA1 and pZmPLTP) to drive Cas9 expression, and the target gene chosen for this study was the bZIP transcription factor Opaque2 (O2). The CRISPR/Cas9 system driven by the maize Ubiquitin promoter (pZmUbi) was employed as a comparative control. Editing efficiency analysis based on high-throughput tracking of mutations (Hi-TOM) showed that the CSC systems generated more target gene mutations than the ubiquitously expressed CRISPR/Cas9 (UC) system in calli. Transgenic plants were generated for the CSC and UC systems. We found that the CSC systems generated fewer target gene mutations than the UC system in the T0 seedlings but reduced the influence of somatic mutations. Nearly 100% of mutations in the T1 generation generated by the CSC systems were derived from the T0 plants. Only 6.3-16.7% of T1 mutations generated by the UC system were from the T0 generation. Our results demonstrated that the CSC system consistently produced more stable, heritable mutants in the subsequent generation, suggesting its potential application across various crops to facilitate the genetic breeding of desired mutations.
Collapse
Affiliation(s)
- Yuan Shi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jing Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Tante Yu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-Breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, People's Republic of China.
- Sanya Institute of China Agricultural University, Sanya, People's Republic of China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, People's Republic of China.
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| |
Collapse
|
5
|
Masani MYA, Norfaezah J, Bahariah B, Fizree MDPMAA, Sulaiman WNSW, Shaharuddin NA, Rasid OA, Parveez GKA. Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement. 3 Biotech 2024; 14:166. [PMID: 38817736 PMCID: PMC11133284 DOI: 10.1007/s13205-024-04010-w] [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: 01/04/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.
Collapse
Affiliation(s)
- Mat Yunus Abdul Masani
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Jamaludin Norfaezah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Bohari Bahariah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Malaysia
| | - Omar Abdul Rasid
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| |
Collapse
|
6
|
Zhang S, Wang B, Li Q, Hui W, Yang L, Wang Z, Zhang W, Yue F, Liu N, Li H, Lu F, Zhang K, Zeng Q, Wu AM. CRISPR/Cas9 mutated p-coumaroyl shikimate 3'-hydroxylase 3 gene in Populus tomentosa reveals lignin functioning on supporting tree upright. Int J Biol Macromol 2023; 253:126762. [PMID: 37683750 DOI: 10.1016/j.ijbiomac.2023.126762] [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: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
The lignin plays one of the most important roles in plant secondary metabolism. However, it is still unclear how lignin can contribute to the impressive height of wood growth. In this study, C3'H, a rate-limiting enzyme of the lignin pathway, was used as the target gene. C3'H3 was knocked out by CRISPR/Cas9 in Populus tomentosa. Compared with wild-type popular trees, c3'h3 mutants exhibited dwarf phenotypes, collapsed xylem vessels, weakened phloem thickening, decreased hydraulic conductivity and photosynthetic efficiency, and reduced auxin content, except for reduced total lignin content and significantly increased H-subunit lignin. In the c3'h3 mutant, the flavonoid biosynthesis genes CHS, CHI, F3H, DFR, ANR, and LAR were upregulated, and flavonoid metabolite accumulations were detected, indicating that decreasing the lignin biosynthesis pathway enhanced flavonoid metabolic flux. Furthermore, flavonoid metabolites, such as naringenin and hesperetin, were largely increased, while higher hesperetin content suppressed plant cell division. Thus, studying the c3'h3 mutant allows us to deduce that lignin deficiency suppresses tree growth and leads to the dwarf phenotype due to collapsed xylem and thickened phloem, limiting material exchanges and transport.
Collapse
Affiliation(s)
- Sufang Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Bo Wang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qian Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wenkai Hui
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Linjie Yang
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zhihua Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wenjuan Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Fengxia Yue
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Nian Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Huiling Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Fachuang Lu
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; Department of Biochemistry and Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Kewei Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Qingyin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Jalilian A, Bagheri A, Chalvon V, Meusnier I, Kroj T, Kakhki AM. The RLCK subfamily VII-4 controls pattern-triggered immunity and basal resistance to bacterial and fungal pathogens in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1345-1356. [PMID: 37248636 DOI: 10.1111/tpj.16323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Receptor-like cytoplasmic kinases (RLCKs) mediate the intracellular signaling downstream of pattern-recognition receptors (PRRs). Several RLCKs from subfamily VII of rice (Oryza sativa) have important roles in plant immunity, but the role of RLCK VII-4 in pattern-triggered immune (PTI) signaling and resistance to pathogens has not yet been investigated. Here, we generated by multiplex clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing rice sextuple mutant lines where the entire RLCK VII-4 subfamily is inactivated and then analyzed the resulting lines for their response to chitin and flg22 and for their immunity to Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae. Analysis of the rlckvii-4 mutants revealed that they have an impaired reactive oxygen system burst and reduced defense gene expression in response to flg22 and chitin. This indicates that members of the rice RLCK VII-4 subfamily are required for immune signaling downstream of multiple PRRs. Furthermore, we found that the rice RLCK VII-4 subfamily is important for chitin-induced callose deposition and mitogen-activated protein kinase activation and that it is crucial for basal resistance against Xoo and M. oryzae pathogens. This establishes that the RLCK VII-4 subfamily has critical functions in the regulation of multiple PTI pathways in rice and opens the way for deciphering the precise role of its members in the control of rice PTI.
Collapse
Affiliation(s)
- Ahmad Jalilian
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Isabelle Meusnier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Amin Mirshamsi Kakhki
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
9
|
Ye M, Yao M, Li C, Gong M. Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato. PeerJ 2023; 11:e15771. [PMID: 37547711 PMCID: PMC10399558 DOI: 10.7717/peerj.15771] [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: 04/19/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato.
Collapse
Affiliation(s)
- Mingwang Ye
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
| | - Mengfan Yao
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
| | - Canhui Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
- Joint Academy of Potato Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Ming Gong
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, China
| |
Collapse
|
10
|
Zhu X, Xu W, Liu B, Zhan Y, Xia T. Adaptation of high-efficiency CRISPR/Cas9-based multiplex genome editing system in white lupin by using endogenous promoters. PHYSIOLOGIA PLANTARUM 2023; 175:e13976. [PMID: 37616014 DOI: 10.1111/ppl.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023]
Abstract
White lupin (Lupinus albus L.) is an important crop with high phosphorus (P) use efficiency; however, technologies for its functional genomic and molecular analyses are limited. Cluster regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system has been applied to gene editing and function genomics in many crops, but its application in white lupin has not been well documented. Here, we adapted the CRISPR/Cas9-based multiplex genome editing system by using the native U3/U6 and ubiquitin (UBQ) promoters to drive sgRNAs and Cas9. Two target sites (T1 and T2) within the Lalb_Chr05g0223881 gene, encoding a putative trehalase, were selected to validate its efficacy in white lupin based on the Agrobacterium rhizogenes-mediated transformation. We found that the T0 hairy roots were efficiently mutated at T1 and T2 with a frequency of 6.25%-35% and 50%-92.31%, respectively. The mutation types include nucleotide insertion, deletion, substitution, and complicated variant. Simultaneous mutations of the two targets were also observed with a range of 6.25%-35%. The combination of LaU6.6 promoter for sgRNA and LaUBQ12 promoter for Cas9 generated the highest frequency of homozygous/biallelic mutations at 38.46%. In addition, the target-sgRNA sequence also contributes to the editing efficiency of the CRISPR/Cas9 system in white lupin. In conclusion, our results expand the toolbox of the CRISPR/Cas9 system and benefit the basic research in white lupin.
Collapse
Affiliation(s)
- Xiaoqi Zhu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bowen Liu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yujie Zhan
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianyu Xia
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
11
|
Chamness JC, Kumar J, Cruz AJ, Rhuby E, Holum MJ, Cody JP, Tibebu R, Gamo ME, Starker CG, Zhang F, Voytas DF. An extensible vector toolkit and parts library for advanced engineering of plant genomes. THE PLANT GENOME 2023:e20312. [PMID: 36896468 DOI: 10.1002/tpg2.20312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T-DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site-specific recombinases. Finally, we use a series of dual-luciferase assays to measure contributions to expression from promoters, terminators, and from cross-cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
Collapse
Affiliation(s)
- James C Chamness
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jitesh Kumar
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Anna J Cruz
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Elissa Rhuby
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Mason J Holum
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Jon P Cody
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Redeat Tibebu
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Feng Zhang
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
12
|
Sony SK, Kaul T, Motelb KFA, Thangaraj A, Bharti J, Kaul R, Verma R, Nehra M. CRISPR/Cas9-mediated homology donor repair base editing confers glyphosate resistance to rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1122926. [PMID: 36959937 PMCID: PMC10027715 DOI: 10.3389/fpls.2023.1122926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Globally, CRISPR-Cas9-based genome editing has ushered in a novel era of crop advancements. Weeds pose serious a threat to rice crop productivity. Among the numerous herbicides, glyphosate [N-(phosphonomethyl)-glycine] has been employed as a post-emergent, broad-spectrum herbicide that represses the shikimate pathway via inhibition of EPSPS (5'-enolpyruvylshikimate-3-phosphate synthase) enzyme in chloroplasts. Here, we describe the development of glyphosate-resistant rice lines by site-specific amino acid substitutions (G172A, T173I, and P177S: GATIPS-mOsEPSPS) and modification of phosphoenolpyruvate-binding site in the native OsEPSPS gene employing fragment knockout and knock-in of homology donor repair (HDR) template harboring desired mutations through CRISPR-Cas9-based genome editing. The indigenously designed two-sgRNA OsEPSPS-NICTK-1_pCRISPR-Cas9 construct harboring rice codon-optimized SpCas9 along with OsEPSPS-HDR template was transformed into rice. Stable homozygous T2 edited rice lines revealed significantly high degree of glyphosate-resistance both in vitro (4 mM/L) and field conditions (6 ml/L; Roundup Ready) in contrast to wild type (WT). Edited T2 rice lines (ER1-6) with enhanced glyphosate resistance revealed lower levels of endogenous shikimate (14.5-fold) in contrast to treated WT but quite similar to WT. ER1-6 lines exhibited increased aromatic amino acid contents (Phe, two-fold; Trp, 2.5-fold; and Tyr, two-fold) than WT. Interestingly, glyphosate-resistant Cas9-free EL1-6 rice lines displayed a significant increment in grain yield (20%-22%) in comparison to WT. Together, results highlighted that the efficacy of GATIPS mutations in OsEPSPS has tremendously contributed in glyphosate resistance (foliar spray of 6 ml/L), enhanced aromatic amino acids, and improved grain yields in rice. These results ensure a novel strategy for weed management without yield penalties, with a higher probability of commercial release.
Collapse
|
13
|
Sánchez-Gómez C, Posé D, Martín-Pizarro C. Genome Editing by CRISPR/Cas9 in Polyploids. Methods Mol Biol 2023; 2545:459-473. [PMID: 36720828 DOI: 10.1007/978-1-0716-2561-3_24] [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: 02/02/2023]
Abstract
CRISPR/Cas system has been widely used for genome editing in the past few years. Even though it has been performed in many polyploid species to date, its efficient accomplishment in these organisms is still a challenge. The presence of multiple homoeologous genes as targets for their editing requires more rigorous work and specific needs to assess successful genome editing. Here, we describe a general stepwise protocol to select target sites, design sgRNAs, indicate vector requirements, and screen CRISPR/Cas9-mediated genome editing in polyploid species.
Collapse
Affiliation(s)
- Carlos Sánchez-Gómez
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain
| | - David Posé
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain
| | - Carmen Martín-Pizarro
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain.
| |
Collapse
|
14
|
Das J, Kumar S, Mishra DC, Chaturvedi KK, Paul RK, Kairi A. Machine learning in the estimation of CRISPR-Cas9 cleavage sites for plant system. Front Genet 2023; 13:1085332. [PMID: 36699447 PMCID: PMC9868961 DOI: 10.3389/fgene.2022.1085332] [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: 10/31/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
CRISPR-Cas9 system is one of the recent most used genome editing techniques. Despite having a high capacity to alter the precise target genes and genomic regions that the planned guide RNA (or sgRNA) complements, the off-target effect still exists. But there are already machine learning algorithms for people, animals, and a few plant species. In this paper, an effort has been made to create models based on three machine learning-based techniques [namely, artificial neural networks (ANN), support vector machines (SVM), and random forests (RF)] for the prediction of the CRISPR-Cas9 cleavage sites that will be cleaved by a particular sgRNA. The plant dataset was the sole source of inspiration for all of these machine learning-based algorithms. 70% of the on-target and off-target dataset of various plant species that was gathered was used to train the models. The remaining 30% of the data set was used to evaluate the model's performance using a variety of evaluation metrics, including specificity, sensitivity, accuracy, precision, F1 score, F2 score, and AUC. Based on the aforementioned machine learning techniques, eleven models in all were developed. Comparative analysis of these produced models suggests that the model based on the random forest technique performs better. The accuracy of the Random Forest model is 96.27%, while the AUC value was found to be 99.21%. The SVM-Linear, SVM-Polynomial, SVM-Gaussian, and SVM-Sigmoid models were trained, making a total of six ANN-based models (ANN1-Logistic, ANN1-Tanh, ANN1-ReLU, ANN2-Logistic, ANN2-Tanh, and ANN-ReLU) and Support Vector Machine models (SVM-Linear, SVM-Polynomial, SVM-Gaussian However, the overall performance of Random Forest is better among all other ML techniques. ANN1-ReLU and SVM-Linear model performance were shown to be better among Artificial Neural Network and Support Vector Machine-based models, respectively.
Collapse
Affiliation(s)
- Jutan Das
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjeev Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India,*Correspondence: Sanjeev Kumar,
| | | | | | - Ranjit Kumar Paul
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amit Kairi
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
15
|
González MN, Massa GA, Andersson M, Storani L, Olsson N, Décima Oneto CA, Hofvander P, Feingold SE. CRISPR/Cas9 Technology for Potato Functional Genomics and Breeding. Methods Mol Biol 2023; 2653:333-361. [PMID: 36995636 DOI: 10.1007/978-1-0716-3131-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cultivated potato (Solanum tuberosum L.) is one of the most important staple food crops worldwide. Its tetraploid and highly heterozygous nature poses a great challenge to its basic research and trait improvement through traditional mutagenesis and/or crossbreeding. The establishment of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) as a gene editing tool has allowed the alteration of specific gene sequences and their concomitant gene function, providing powerful technology for potato gene functional analysis and improvement of elite cultivars. This technology relies on a short RNA molecule called single guide RNA (sgRNA) that directs the Cas9 nuclease to induce a site-specific double-stranded break (DSB). Further, repair of the DSB by the error-prone non-homologous end joining (NHEJ) mechanism leads to the introduction of targeted mutations, which can be used to produce the loss of function of specific gene(s). In this chapter, we describe experimental procedures to apply the CRISPR/Cas9 technology for potato genome editing. First, we provide strategies for target selection and sgRNA design and describe a Golden Gate-based cloning system to obtain a sgRNA/Cas9-encoding binary vector. We also describe an optimized protocol for ribonucleoprotein (RNP) complex assembly. The binary vector can be used for both Agrobacterium-mediated transformation and transient expression in potato protoplasts, while the RNP complexes are intended to obtain edited potato lines through protoplast transfection and plant regeneration. Finally, we describe procedures to identify the gene-edited potato lines. The methods described here are suitable for potato gene functional analysis and breeding.
Collapse
Affiliation(s)
- Matías Nicolás González
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Gabriela Alejandra Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Leonardo Storani
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica, Buenos Aires, Argentina
| | - Niklas Olsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Andrea Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | |
Collapse
|
16
|
Trieu A, Belaffif MB, Hirannaiah P, Manjunatha S, Wood R, Bathula Y, Billingsley RL, Arpan A, Sacks EJ, Clemente TE, Moose SP, Reichert NA, Swaminathan K. Transformation and gene editing in the bioenergy grass Miscanthus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:148. [PMID: 36578060 PMCID: PMC9798709 DOI: 10.1186/s13068-022-02241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. RESULTS We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. CONCLUSIONS We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.
Collapse
Affiliation(s)
- Anthony Trieu
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Mohammad B. Belaffif
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Pradeepa Hirannaiah
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Shilpa Manjunatha
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebekah Wood
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Yokshitha Bathula
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebecca L. Billingsley
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Anjali Arpan
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Erik J. Sacks
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Thomas E. Clemente
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Stephen P. Moose
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Nancy A. Reichert
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Kankshita Swaminathan
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| |
Collapse
|
17
|
Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y. Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. FRONTIERS IN PLANT SCIENCE 2022; 13:1042828. [PMID: 36578341 PMCID: PMC9791139 DOI: 10.3389/fpls.2022.1042828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.
Collapse
Affiliation(s)
- Faiza Shafique Khan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapeng Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Peng Shi
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Zhiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yin Min Htwe
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yong Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| |
Collapse
|
18
|
Liu C, Su H, Sakuma S, Xu M, Birchler JA, Han F. Editorial: Genomics and disease resistance in wheat and maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1064948. [PMID: 36457534 PMCID: PMC9706233 DOI: 10.3389/fpls.2022.1064948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | | | | | | | - Fangpu Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
19
|
Hassan MM, Yuan G, Liu Y, Alam M, Eckert CA, Tuskan GA, Golz JF, Yang X. Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies. Biotechnol J 2022; 17:e2100673. [PMID: 35766313 DOI: 10.1002/biot.202100673] [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: 12/15/2021] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022]
Abstract
Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.
Collapse
Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Nambour, Queensland, Australia
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - John F Golz
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria, 3010, Australia
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| |
Collapse
|
20
|
Genome-wide specificity of plant genome editing by both CRISPR-Cas9 and TALEN. Sci Rep 2022; 12:9330. [PMID: 35665758 PMCID: PMC9167288 DOI: 10.1038/s41598-022-13034-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
CRISPR and TALENs are efficient systems for gene editing in many organisms including plants. In many cases the CRISPR–Cas or TALEN modules are expressed in the plant cell only transiently. Theoretically, transient expression of the editing modules should limit unexpected effects compared to stable transformation. However, very few studies have measured the off-target and unpredicted effects of editing strategies on the plant genome, and none of them have compared these two major editing systems. We conducted, in Physcomitrium patens, a comprehensive genome-wide investigation of off-target mutations using either a CRISPR–Cas9 or a TALEN strategy. We observed a similar number of differences for the two editing strategies compared to control non-transfected plants, with an average of 8.25 SNVs and 19.5 InDels for the CRISPR-edited plants, and an average of 17.5 SNVs and 32 InDels for the TALEN-edited plants. Interestingly, a comparable number of SNVs and InDels could be detected in the PEG-treated control plants. This shows that except for the on-target modifications, the gene editing tools used in this study did not show a significant off-target activity nor unpredicted effects on the genome, and did not lead to transgene integration. The PEG treatment, a well-established biotechnological method, in itself, was the main source of mutations found in the edited plants.
Collapse
|
21
|
Rahman F, Mishra A, Gupta A, Sharma R. Spatiotemporal Regulation of CRISPR/Cas9 Enables Efficient, Precise, and Heritable Edits in Plant Genomes. Front Genome Ed 2022; 4:870108. [PMID: 35558825 PMCID: PMC9087570 DOI: 10.3389/fgeed.2022.870108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
CRISPR/Cas-mediated editing has revolutionized crop engineering. Due to the broad scope and potential of this technology, many studies have been carried out in the past decade towards optimizing genome editing constructs. Clearly, the choice of the promoter used to drive gRNA and Cas9 expression is critical to achieving high editing efficiency, precision, and heritability. While some important considerations for choosing a promoter include the number and nature of targets, host organism, mode of transformation and goal of the experiment, spatiotemporal regulation of Cas9 expression using tissue-specific or inducible promoters enables higher heritability and efficiency of targeted mutagenesis with reduced off-target effects. In this review, we discuss specific studies that highlight the prospects and trade-offs associated with the choice of promoters on genome editing and emphasize the need for inductive exploration and discovery to further advance this area of research in crop plants.
Collapse
Affiliation(s)
- Farhanur Rahman
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Apurva Mishra
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Archit Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
- *Correspondence: Rita Sharma, ,
| |
Collapse
|
22
|
Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
Collapse
Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
| |
Collapse
|
23
|
Aregawi K, Shen J, Pierroz G, Sharma MK, Dahlberg J, Owiti J, Lemaux PG. Morphogene-assisted transformation of Sorghum bicolor allows more efficient genome editing. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:748-760. [PMID: 34837319 PMCID: PMC8989502 DOI: 10.1111/pbi.13754] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 05/08/2023]
Abstract
Sorghum bicolor (L.) Moench, the fifth most important cereal worldwide, is a multi-use crop for feed, food, forage and fuel. To enhance the sorghum and other important crop plants, establishing gene function is essential for their improvement. For sorghum, identifying genes associated with its notable abiotic stress tolerances requires a detailed molecular understanding of the genes associated with those traits. The limits of this knowledge became evident from our earlier in-depth sorghum transcriptome study showing that over 40% of its transcriptome had not been annotated. Here, we describe a full spectrum of tools to engineer, edit, annotate and characterize sorghum's genes. Efforts to develop those tools began with a morphogene-assisted transformation (MAT) method that led to accelerated transformation times, nearly half the time required with classical callus-based, non-MAT approaches. These efforts also led to expanded numbers of amenable genotypes, including several not previously transformed or historically recalcitrant. Another transformation advance, termed altruistic, involved introducing a gene of interest in a separate Agrobacterium strain from the one with morphogenes, leading to plants with the gene of interest but without morphogenes. The MAT approach was also successfully used to edit a target exemplary gene, phytoene desaturase. To identify single-copy transformed plants, we adapted a high-throughput technique and also developed a novel method to determine transgene independent integration. These efforts led to an efficient method to determine gene function, expediting research in numerous genotypes of this widely grown, multi-use crop.
Collapse
Affiliation(s)
- Kiflom Aregawi
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Jianqiang Shen
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Grady Pierroz
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Manoj K. Sharma
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Jeffery Dahlberg
- University of California Ag & Natural ResourcesKearney Agricultural Research & Extension CenterParlierCAUSA
| | - Judith Owiti
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Peggy G. Lemaux
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| |
Collapse
|
24
|
Xu K, Song J, Wu Y, Zhuo C, Wen J, Yi B, Ma C, Shen J, Fu T, Tu J. Brassica evolution of essential BnaFtsH1 genes involved in the PSII repair cycle and loss of FtsH5. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111128. [PMID: 35067298 DOI: 10.1016/j.plantsci.2021.111128] [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] [Received: 06/22/2021] [Revised: 10/23/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
The PSII repair cycle is an important part of photosynthesis and is essential for high photosynthetic efficiency. The study of essential genes in Brassica napus provides significant potential for the improvement of gene editing technology and molecular breeding design. Previously, we identified a B. napus lethal mutant (7-521Y), which was controlled by two recessive genes (cyd1 and cyd2). BnaC06.FtsH1 was identified as a CYD1 target gene through functional verification. In the present study, we employed fine-mapping, genetic complementation, and CRISPR/Cas9 experiments to identify BnaA07.FtsH1 as the target gene of CYD2, functioning similarly to BnaC06.FtsH1. By analyzing CRISPR/Cas9 T1 generation plants of the Westar variety, we found that the copy number of FtsH1 was positively correlated with its biomass accumulation. Transcriptome analysis of cotyledons revealed differences in the expression of photosynthesis antenna and structural proteins between the mutant and complementary seedlings. Phylogenetic and chromosome linear analyses, based on 15 sequenced cruciferous species, revealed that Brassica alone had lost FtsH5 during evolution. This may be related to the fact that FtsH5 was located at the end of chromosome ABK8 in the ancestor species. Cloning and identification of BnaFtsH1s provide a deeper understanding of PSII repair cycle mechanisms and offer new insights for the improvement of photosynthetic efficiency and molecular breeding design in B. napus.
Collapse
Affiliation(s)
- Kai Xu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yujin Wu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
25
|
Zhang S, Wu S, Hu C, Yang Q, Dong T, Sheng O, Deng G, He W, Dou T, Li C, Sun C, Yi G, Bi F. Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct. PeerJ 2022; 10:e12664. [PMID: 35036088 PMCID: PMC8742547 DOI: 10.7717/peerj.12664] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species' triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
Collapse
Affiliation(s)
- Sen Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaoping Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Chunhua Hu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Qiaosong Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tao Dong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Guiming Deng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Weidi He
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tongxin Dou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chenkang Sun
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong
| | - Ganjun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Fangcheng Bi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| |
Collapse
|
26
|
Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
Collapse
Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| |
Collapse
|
27
|
Bhowmik P, Bilichak A. Advances in Gene Editing of Haploid Tissues in Crops. Genes (Basel) 2021; 12:1410. [PMID: 34573392 PMCID: PMC8468125 DOI: 10.3390/genes12091410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 01/14/2023] Open
Abstract
Emerging threats of climate change require the rapid development of improved varieties with a higher tolerance to abiotic and biotic factors. Despite the success of traditional agricultural practices, novel techniques for precise manipulation of the crop's genome are needed. Doubled haploid (DH) methods have been used for decades in major crops to fix desired alleles in elite backgrounds in a short time. DH plants are also widely used for mapping of the quantitative trait loci (QTLs), marker-assisted selection (MAS), genomic selection (GS), and hybrid production. Recent discoveries of genes responsible for haploid induction (HI) allowed engineering this trait through gene editing (GE) in non-inducer varieties of different crops. Direct editing of gametes or haploid embryos increases GE efficiency by generating null homozygous plants following chromosome doubling. Increased understanding of the underlying genetic mechanisms responsible for spontaneous chromosome doubling in haploid plants may allow transferring this trait to different elite varieties. Overall, further improvement in the efficiency of the DH technology combined with the optimized GE could accelerate breeding efforts of the major crops.
Collapse
Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
| | - Andriy Bilichak
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
| |
Collapse
|
28
|
Jiang Y, An X, Li Z, Yan T, Zhu T, Xie K, Liu S, Hou Q, Zhao L, Wu S, Liu X, Zhang S, He W, Li F, Li J, Wan X. CRISPR/Cas9-based discovery of maize transcription factors regulating male sterility and their functional conservation in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1769-1784. [PMID: 33772993 PMCID: PMC8428822 DOI: 10.1111/pbi.13590] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 05/12/2023]
Abstract
Identifying genic male-sterility (GMS) genes and elucidating their roles are important to unveil plant male reproduction and promote their application in crop breeding. However, compared with Arabidopsis and rice, relatively fewer maize GMS genes have been discovered and little is known about their regulatory pathways underlying anther and pollen development. Here, by sequencing and analysing anther transcriptomes at 11 developmental stages in maize B73, Zheng58 and M6007 inbred lines, 1100 transcription factor (TF) genes were identified to be stably differentially expressed among different developmental stages. Among them, 14 maize TF genes (9 types belonging to five TF families) were selected and performed CRISPR/Cas9-mediated gene mutagenesis, and then, 12 genes in eight types, including ZmbHLH51, ZmbHLH122, ZmTGA9-1/-2/-3, ZmTGA10, ZmMYB84, ZmMYB33-1/-2, ZmPHD11 and ZmLBD10/27, were identified as maize new GMS genes by using DNA sequencing, phenotypic and cytological analyses. Notably, ZmTGA9-1/-2/-3 triple-gene mutants and ZmMYB33-1/-2 double-gene mutants displayed complete male sterility, but their double- or single-gene mutants showed male fertility. Similarly, ZmLBD10/27 double-gene mutant displayed partial male sterility with 32.18% of aborted pollen grains. In addition, ZmbHLH51 was transcriptionally activated by ZmbHLH122 and their proteins were physically interacted. Molecular markers co-segregating with these GMS mutations were developed to facilitate their application in maize breeding. Finally, all 14-type maize GMS TF genes identified here and reported previously were compared on functional conservation and diversification among maize, rice and Arabidopsis. These findings enrich GMS gene and mutant resources for deeply understanding the regulatory network underlying male fertility and for creating male-sterility lines in maize.
Collapse
Affiliation(s)
- Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Ziwen Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Tingwei Yan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Taotao Zhu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Ke Xie
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Shuangshuang Liu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Lina Zhao
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Xinze Liu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Shaowei Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Wei He
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Fan Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Jinping Li
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| |
Collapse
|
29
|
Xia X, Cheng X, Li R, Yao J, Li Z, Cheng Y. Advances in application of genome editing in tomato and recent development of genome editing technology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2727-2747. [PMID: 34076729 PMCID: PMC8170064 DOI: 10.1007/s00122-021-03874-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 05/07/2023]
Abstract
Genome editing, a revolutionary technology in molecular biology and represented by the CRISPR/Cas9 system, has become widely used in plants for characterizing gene function and crop improvement. Tomato, serving as an excellent model plant for fruit biology research and making a substantial nutritional contribution to the human diet, is one of the most important applied plants for genome editing. Using CRISPR/Cas9-mediated targeted mutagenesis, the re-evaluation of tomato genes essential for fruit ripening highlights that several aspects of fruit ripening should be reconsidered. Genome editing has also been applied in tomato breeding for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and recently customizing tomato cultivars for urban agriculture. In addition, genome editing is continuously innovating, and several new genome editing systems such as the recent prime editing, a breakthrough in precise genome editing, have recently been applied in plants. In this review, these advances in application of genome editing in tomato and recent development of genome editing technology are summarized, and their leaving important enlightenment to plant research and precision plant breeding is also discussed.
Collapse
Affiliation(s)
- Xuehan Xia
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xinhua Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
30
|
Paul NC, Park SW, Liu H, Choi S, Ma J, MacCready JS, Chilvers MI, Sang H. Plant and Fungal Genome Editing to Enhance Plant Disease Resistance Using the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2021; 12:700925. [PMID: 34447401 PMCID: PMC8382960 DOI: 10.3389/fpls.2021.700925] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/30/2021] [Indexed: 05/10/2023]
Abstract
Crop production has been substantially reduced by devastating fungal and oomycete pathogens, and these pathogens continue to threaten global food security. Although chemical and cultural controls have been used for crop protection, these involve continuous costs and time and fungicide resistance among plant pathogens has been increasingly reported. The most efficient way to protect crops from plant pathogens is cultivation of disease-resistant cultivars. However, traditional breeding approaches are laborious and time intensive. Recently, the CRISPR/Cas9 system has been utilized to enhance disease resistance among different crops such as rice, cacao, wheat, tomato, and grape. This system allows for precise genome editing of various organisms via RNA-guided DNA endonuclease activity. Beyond genome editing in crops, editing the genomes of fungal and oomycete pathogens can also provide new strategies for plant disease management. This review focuses on the recent studies of plant disease resistance against fungal and oomycete pathogens using the CRISPR/Cas9 system. For long-term plant disease management, the targeting of multiple plant disease resistance mechanisms with CRISPR/Cas9 and insights gained by probing fungal and oomycete genomes with this system will be powerful approaches.
Collapse
Affiliation(s)
- Narayan Chandra Paul
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Sung-Won Park
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Haifeng Liu
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Sungyu Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jihyeon Ma
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Joshua S. MacCready
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| |
Collapse
|
31
|
Miculan M, Nelissen H, Ben Hassen M, Marroni F, Inzé D, Pè ME, Dell’Acqua M. A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1056-1071. [PMID: 34087008 PMCID: PMC8519057 DOI: 10.1111/tpj.15364] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/31/2021] [Indexed: 05/13/2023]
Abstract
The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.
Collapse
Affiliation(s)
- Mara Miculan
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Manel Ben Hassen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Fabio Marroni
- IGA Technology ServicesUdine33100Italy
- Department of Agricultural, FoodAT, Environmental and Animal Sciences (DI4A)University of UdineUdine33100Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Mario Enrico Pè
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | | |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Bahariah B, Masani MYA, Rasid OA, Parveez GKA. Multiplex CRISPR/Cas9-mediated genome editing of the FAD2 gene in rice: a model genome editing system for oil palm. J Genet Eng Biotechnol 2021; 19:86. [PMID: 34115267 PMCID: PMC8196110 DOI: 10.1186/s43141-021-00185-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/21/2021] [Indexed: 12/30/2022]
Abstract
Background Genome editing employing the CRISPR/Cas9 system has been widely used and has become a promising tool for plant gene functional studies and crop improvement. However, most of the applied CRISPR/Cas9 systems targeting one locus using a sgRNA resulted in low genome editing efficiency. Results Here, we demonstrate the modification of the FAD2 gene in rice using a multiplex sgRNA-CRISPR/Cas9 genome editing system. To test the system’s efficiency for targeting multiple loci in rice, we designed two sgRNAs based on FAD2 gene sequence of the Oryza sativa Japonica rice. We then inserted the validated sgRNAs into a CRISPR/Cas9 basic vector to construct pYLCRISPRCas9PUbi-H:OsFAD2. The vector was then transformed into protoplast cells isolated from rice leaf tissue via PEG-mediated transfection, and rice calli using biolistic transformation. Direct DNA sequencing of PCR products revealed mutations consisting of deletions of the DNA region between the two target sgRNAs. Conclusion The results suggested that the application of the multiplex sgRNA-CRISPR/Cas9 genome editing system may be useful for crop improvement in monocot species that are recalcitrant to genetic modification, such as oil palm. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00185-4.
Collapse
Affiliation(s)
- Bohari Bahariah
- Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mat Yunus Abdul Masani
- Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Omar Abd Rasid
- Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| |
Collapse
|
34
|
Abstract
In keeping with the directive in Executive Order 13874 (Modernizing the Regulatory Framework for Agricultural Biotechnology Products) to adopt regulatory approaches that are proportionate to risk and avoid arbitrary distinctions across like products, the US Department of Agriculture (USDA) revised its biotechnology regulations by promulgating the Sustainable, Ecological, Consistent, Uniform, Responsible, and Efficient (SECURE) rule. Specifically, the SECURE rule 1) establishes exemptions for plants modified by genetic engineering where the modification could otherwise have been made through conventional breeding, 2) uses risk posed by the introduced trait to determine whether an organism is regulated, rather than relying on whether the organism was developed using a plant pest, and 3) provides a mechanism for a rapid initial review to efficiently distinguish plants developed using genetic engineering that do not pose plausible pathways to increased plant pest risk from those that do. As a result of the focused oversight on potentially riskier crops developed using genetic engineering, USDA is expected to improve the efficiency and effectiveness of its oversight program. The reduced regulatory burden is expected to promote innovation by expanding the number and diversity of developers to include smaller businesses and academics and to increase the number and variety of traits being developed through biotechnology.
Collapse
Affiliation(s)
- Neil E Hoffman
- Biotechnology Regulatory Services, Animal Plant Health Inspection Services, US Department of Agriculture, Riverdale, MD 20737
| |
Collapse
|
35
|
Abstract
The Knl1-Mis12-Ndc80 (KMN) network is an essential component of the kinetochore-microtubule attachment interface, which is required for genomic stability in eukaryotes. However, little is known about plant Knl1 proteins because of their complex evolutionary history. Here, we cloned the Knl1 homolog from maize (Zea mays) and confirmed it as a constitutive central kinetochore component. Functional assays demonstrated their conserved role in chromosomal congression and segregation during nuclear division, thus causing defective cell division during kernel development when Knl1 transcript was depleted. A 145 aa region in the middle of maize Knl1, that did not involve the MELT repeats, was associated with the interaction of spindle assembly checkpoint (SAC) components Bub1/Mad3 family proteins 1 and 2 (Bmf1/2) but not with the Bmf3 protein. They may form a helical conformation with a hydrophobic interface with the TPR domain of Bmf1/2, which is similar to that of vertebrates. However, this region detected in monocots shows extensive divergence in eudicots, suggesting that distinct modes of the SAC to kinetochore connection are present within plant lineages. These findings elucidate the conserved role of the KMN network in cell division and a striking dynamic of evolutionary patterns in the SAC signaling and kinetochore network.
Collapse
|
36
|
Liu Y, Wang C, Su H, Birchler JA, Han F. Phosphorylation of histone H3 by Haspin regulates chromosome alignment and segregation during mitosis in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1046-1058. [PMID: 33130883 DOI: 10.1093/jxb/eraa506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
In human cells, Haspin-mediated histone H3 threonine 3 (H3T3) phosphorylation promotes centromeric localization of the chromosomal passenger complex, thereby ensuring proper kinetochore-microtubule attachment. Haspin also binds to PDS5 cohesin-associated factor B (Pds5B), antagonizing the Wings apart-like protein homolog (Wapl)-Pds5B interaction and thus preventing Wapl from releasing centromeric cohesion during mitosis. However, the role of Haspin in plant chromosome segregation is not well understood. Here, we show that in maize (Zea mays) mitotic cells, ZmHaspin localized to the centromere during metaphase and anaphase, whereas it localized to the telomeres during meiosis. These results suggest that ZmHaspin plays different roles during mitosis and meiosis. Knockout of ZmHaspin led to decreased H3T3 phosphorylation and histone H3 serine 10 phosphorylation, and defects in chromosome alignment and segregation in mitosis. These lines of evidence suggest that Haspin regulates chromosome segregation in plants via the mechanism described for humans, namely, H3T3 phosphorylation. Plant Haspin proteins lack the RTYGA and PxVxL motifs needed to bind Pds5B and heterochromatin protein 1, and no obvious cohesion defects were detected in ZmHaspin knockout plants. Taken together, these results highlight the conserved but slightly different roles of Haspin proteins in cell division in plants and in animals.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunhui Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
37
|
Xu K, Wu Y, Song J, Hu K, Wu Z, Wen J, Yi B, Ma C, Shen J, Fu T, Tu J. Fine Mapping and Identification of BnaC06.FtsH1, a Lethal Gene That Regulates the PSII Repair Cycle in Brassica napus. Int J Mol Sci 2021; 22:ijms22042087. [PMID: 33669866 PMCID: PMC7923215 DOI: 10.3390/ijms22042087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
Photosystem II (PSII) is an important component of the chloroplast. The PSII repair cycle is crucial for the relief of photoinhibition and may be advantageous when improving stress resistance and photosynthetic efficiency. Lethal genes are widely used in the efficiency detection and method improvement of gene editing. In the present study, we identified the naturally occurring lethal mutant 7-521Y with etiolated cotyledons in Brassica napus, controlled by double-recessive genes (named cyd1 and cyd2). By combining whole-genome resequencing and map-based cloning, CYD1 was fine-mapped to a 29 kb genomic region using 15,167 etiolated individuals. Through cosegregation analysis and functional verification of the transgene, BnaC06.FtsH1 was determined to be the target gene; it encodes an filamentation temperature sensitive protein H 1 (FtsH1) hydrolase that degrades damaged PSII D1 in Arabidopsis thaliana. The expression of BnaC06.FtsH1 was high in the cotyledons, leaves, and flowers of B. napus, and localized in the chloroplasts. In addition, the expression of EngA (upstream regulation gene of FtsH) increased and D1 decreased in 7-521Y. Double mutants of FtsH1 and FtsH5 were lethal in A. thaliana. Through phylogenetic analysis, the loss of FtsH5 was identified in Brassica, and the remaining FtsH1 was required for PSII repair cycle. CYD2 may be a homologous gene of FtsH1 on chromosome A07 of B. napus. Our study provides new insights into lethal mutants, the findings may help improve the efficiency of the PSII repair cycle and biomass accumulation in oilseed rape.
Collapse
|
38
|
Nuccio ML, Claeys H, Heyndrickx KS. CRISPR-Cas technology in corn: a new key to unlock genetic knowledge and create novel products. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:11. [PMID: 37309473 PMCID: PMC10236071 DOI: 10.1007/s11032-021-01200-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/04/2021] [Indexed: 06/14/2023]
Abstract
Since its inception in 2012, CRISPR-Cas technologies have taken the life science community by storm. Maize genetics research is no exception. Investigators around the world have adapted CRISPR tools to advance maize genetics research in many ways. The principle application has been targeted mutagenesis to confirm candidate genes identified using map-based methods. Researchers are also developing tools to more effectively apply CRISPR-Cas technologies to maize because successful application of CRISPR-Cas relies on target gene identification, guide RNA development, vector design and construction, CRISPR-Cas reagent delivery to maize tissues, and plant characterization, each contributing unique challenges to CRISPR-Cas efficacy. Recent advances continue to chip away at major barriers that prevent more widespread use of CRISPR-Cas technologies in maize, including germplasm-independent delivery of CRISPR-Cas reagents and production of high-resolution genomic data in relevant germplasm to facilitate CRISPR-Cas experimental design. This has led to the development of novel breeding tools to advance maize genetics and demonstrations of how CRISPR-Cas technologies might be used to enhance maize germplasm. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01200-9.
Collapse
|
39
|
An unbiased method for evaluating the genome-wide specificity of base editors in rice. Nat Protoc 2020; 16:431-457. [PMID: 33349703 DOI: 10.1038/s41596-020-00423-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Base editors can achieve targeted genomic base conversion. However, the off-target issue is one of the major concerns in their application. Whole-genome sequencing (WGS) at the individual level can provide direct information on genome-wide specificity, but it is difficult to distinguish true off-target single-nucleotide variants (SNVs) induced by base editors from background variation. Here we describe an unbiased WGS method for evaluating the specificity of base editors in rice. In this protocol, we describe the experimental design and provide details of vector construction, rice transformation and tissue culture, as well as a comprehensive WGS data analysis pipeline for overcoming two related core problems in various plant species: high background mutation rates and the heterogeneity of examined populations. Using this protocol, researchers can straightforwardly and accurately assess the genome-wide specificity of base editors and other genome editing tools in 12-15 weeks.
Collapse
|
40
|
Tiwari M, Trivedi P, Pandey A. Emerging tools and paradigm shift of gene editing in cereals, fruits, and horticultural crops for enhancing nutritional value and food security. Food Energy Secur 2020. [DOI: 10.1002/fes3.258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome Research New Delhi India
| | - Prabodh Trivedi
- CSIR‐Central Institute of Medicinal and Aromatic Plants Lucknow India
| | | |
Collapse
|
41
|
Xu X, Yuan Y, Feng B, Deng W. CRISPR/Cas9-mediated gene-editing technology in fruit quality improvement. FOOD QUALITY AND SAFETY 2020. [DOI: 10.1093/fqsafe/fyaa028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Fruits are an essential part of a healthy, balanced diet and it is particularly important for fibre, essential vitamins, and trace elements. Improvement in the quality of fruit and elongation of shelf life are crucial goals for researchers. However, traditional techniques have some drawbacks, such as long period, low efficiency, and difficulty in the modification of target genes, which limit the progress of the study. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technique was developed and has become the most popular gene-editing technology with high efficiency, simplicity, and low cost. CRISPR/Cas9 technique is widely accepted to analyse gene function and complete genetic modification. This review introduces the latest progress of CRISPR/Cas9 technology in fruit quality improvement. For example, CRISPR/Cas9-mediated targeted mutagenesis of RIPENING INHIBITOR gene (RIN), Lycopene desaturase (PDS), Pectate lyases (PL), SlMYB12, and CLAVATA3 (CLV3) can affect fruit ripening, fruit bioactive compounds, fruit texture, fruit colouration, and fruit size. CRISPR/Cas9-mediated mutagenesis has become an efficient method to modify target genes and improve fruit quality.
Collapse
Affiliation(s)
- Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Yujin Yuan
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Bihong Feng
- College of Agriculture, Guangxi University, Nanning, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| |
Collapse
|
42
|
Bhatta BP, Malla S. Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1360. [PMID: 33066510 PMCID: PMC7602190 DOI: 10.3390/plants9101360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.
Collapse
Affiliation(s)
- Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA;
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
| | - Subas Malla
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
| |
Collapse
|
43
|
Shinoyama H, Ichikawa H, Nishizawa-Yokoi A, Skaptsov M, Toki S. Simultaneous TALEN-mediated knockout of chrysanthemum DMC1 genes confers male and female sterility. Sci Rep 2020; 10:16165. [PMID: 32999297 PMCID: PMC7527520 DOI: 10.1038/s41598-020-72356-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 08/30/2020] [Indexed: 02/06/2023] Open
Abstract
Genome editing has become one of the key technologies for plant breeding. However, in polyploid species such as chrysanthemum, knockout of all loci of multiple genes is needed to eliminate functional redundancies. We identified six cDNAs for the CmDMC1 genes involved in meiotic homologous recombination in chrysanthemum. Since all six cDNAs harbored a homologous core region, simultaneous knockout via TALEN-mediated genome editing should be possible. We isolated the CmDMC1 loci corresponding to the six cDNAs and constructed a TALEN-expression vector bearing a CmDMC1 target site containing the homologous core region. After transforming two chrysanthemum cultivars with the TALEN-expression vector, seven lines exhibited disruption of all six CmDMC1 loci at the target site as well as stable male and female sterility at 10–30 °C. This strategy to produce completely sterile plants could be widely applicable to prevent the risk of transgene flow from transgenic plants to their wild relatives.
Collapse
Affiliation(s)
- Harue Shinoyama
- Fukui Agricultural Experiment Station, Fukui, 918-8215, Japan. .,Department of Bioscience, Fukui Prefectural University, Awara, 910-4103, Japan.
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
| | - Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Mikhail Skaptsov
- South Siberian Botanical Garden, Altai State University, Barnaul, Russia, 656049
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan.,Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
| |
Collapse
|
44
|
|
45
|
Sant’Ana RRA, Caprestano CA, Nodari RO, Agapito-Tenfen SZ. PEG-Delivered CRISPR-Cas9 Ribonucleoproteins System for Gene-Editing Screening of Maize Protoplasts. Genes (Basel) 2020; 11:E1029. [PMID: 32887261 PMCID: PMC7564243 DOI: 10.3390/genes11091029] [Citation(s) in RCA: 28] [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: 08/18/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology allows the modification of DNA sequences in vivo at the location of interest. Although CRISPR-Cas9 can produce genomic changes that do not require DNA vector carriers, the use of transgenesis for the stable integration of DNA coding for gene-editing tools into plant genomes is still the most used approach. However, it can generate unintended transgenic integrations, while Cas9 prolonged-expression can increase cleavage at off-target sites. In addition, the selection of genetically modified cells from millions of treated ones, especially plant cells, is still challenging. In a protoplast system, previous studies claimed that such pitfalls would be averted by delivering pre-assembled ribonucleoprotein complexes (RNPs) composed of purified recombinant Cas9 enzyme and in vitro transcribed guide RNA (gRNA) molecules. We, therefore, aimed to develop the first DNA-free protocol for gene-editing in maize and introduced RNPs into their protoplasts with polyethylene glycol (PEG) 4000. We performed an effective transformation of maize protoplasts using different gRNAs sequences targeting the inositol phosphate kinase gene, and by applying two different exposure times to RNPs. Using a low-cost Sanger sequencing protocol, we observed an efficiency rate of 0.85 up to 5.85%, which is equivalent to DNA-free protocols used in other plant species. A positive correlation was displayed between the exposure time and mutation frequency. The mutation frequency was gRNA sequence- and exposure time-dependent. In the present study, we demonstrated that the suitability of RNP transfection was proven as an effective screening platform for gene-editing in maize. This efficient and relatively easy assay method for the selection of gRNA suitable for the editing of the gene of interest will be highly useful for genome editing in maize, since the genome size and GC-content are large and high in the maize genome, respectively. Nevertheless, the large amplitude of mutations at the target site require scrutiny when checking mutations at off-target sites and potential safety concerns.
Collapse
Affiliation(s)
- Rodrigo Ribeiro Arnt Sant’Ana
- CropScience Department, Federal University of Santa Catarina, Florianópolis 88034000, Brazil; (R.R.A.S.); (C.A.C.); (R.O.N.)
| | - Clarissa Alves Caprestano
- CropScience Department, Federal University of Santa Catarina, Florianópolis 88034000, Brazil; (R.R.A.S.); (C.A.C.); (R.O.N.)
| | - Rubens Onofre Nodari
- CropScience Department, Federal University of Santa Catarina, Florianópolis 88034000, Brazil; (R.R.A.S.); (C.A.C.); (R.O.N.)
| | | |
Collapse
|
46
|
Subedi U, Jayawardhane KN, Pan X, Ozga J, Chen G, Foroud NA, Singer SD. The Potential of Genome Editing for Improving Seed Oil Content and Fatty Acid Composition in Oilseed Crops. Lipids 2020; 55:495-512. [PMID: 32856292 DOI: 10.1002/lipd.12249] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/16/2022]
Abstract
A continuous rise in demand for vegetable oils, which comprise mainly the storage lipid triacylglycerol, is fueling a surge in research efforts to increase seed oil content and improve fatty acid composition in oilseed crops. Progress in this area has been achieved using both conventional breeding and transgenic approaches to date. However, further advancements using traditional breeding methods will be complicated by the polyploid nature of many oilseed crops and associated time constraints, while public perception and the prohibitive cost of regulatory processes hinders the commercialization of transgenic oilseed crops. As such, genome editing using CRISPR/Cas is emerging as a breakthrough breeding tool that could provide a platform to keep pace with escalating demand while potentially minimizing regulatory burden. In this review, we discuss the technology itself and progress that has been made thus far with respect to its use in oilseed crops to improve seed oil content and quality. Furthermore, we examine a number of genes that may provide ideal targets for genome editing in this context, as well as new CRISPR-related tools that have the potential to be applied to oilseed plants and may allow additional gains to be made in the future.
Collapse
Affiliation(s)
- Udaya Subedi
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Kethmi N Jayawardhane
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Xue Pan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Jocelyn Ozga
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Nora A Foroud
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada
| |
Collapse
|
47
|
Zhang D, Hussain A, Manghwar H, Xie K, Xie S, Zhao S, Larkin RM, Qing P, Jin S, Ding F. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1651-1669. [PMID: 32271968 PMCID: PMC7336378 DOI: 10.1111/pbi.13383] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/22/2020] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR-Cas system, has led to significant progress in the field of plant and animal breeding. The CRISPR-Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter diverse genomes (e.g. genomes from both plants and animals) including human genomes with unprecedented ease, accuracy and high efficiency. The recent development and scope of CRISPR-Cas system have raised new regulatory challenges around the world due to moral, ethical, safety and technical concerns associated with its applications in pre-clinical and clinical research, biomedicine and agriculture. Here, we review the art, applications and potential risks of CRISPR-Cas system in genome editing. We also highlight the patent and ethical issues of this technology along with regulatory frameworks established by various nations to regulate CRISPR-Cas-modified organisms/products.
Collapse
Affiliation(s)
- Debin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kabin Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ping Qing
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fang Ding
- Hubei Key Laboratory of Plant PathologyCollege of Plant Sciences and TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
48
|
CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10071033] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.
Collapse
|
49
|
Ishida Y, Hiei Y, Komari T. Tissue culture protocols for gene transfer and editing in maize ( Zea mays L.). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:121-128. [PMID: 32821218 PMCID: PMC7434677 DOI: 10.5511/plantbiotechnology.20.0113a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/13/2020] [Indexed: 05/28/2023]
Abstract
Efficient methods for gene transfer to maize were developed in the 1990s, first mediated by particle bombardment and then by Agrobacterium tumefaciens. Both methods can efficiently create high-quality events. Genetically modified varieties were commercialized in 1996 and are now planted in more than 90% of the US corn field. Tissue culture protocols for both methods have been well developed and widely employed. Thus, various factors, including handling before gene delivery, techniques to protect cells during gene delivery, and culture media, have been well optimized for various genotypes. Typical protocols for both methods are herein presented to show major outputs from the studies conducted since the early 1990s. As the bombardment protocols tended to be optimized specifically for limited genotypes, the one for B104, a new public inbred with favorable agronomic characteristics, is shown. The Agrobacterium protocol is suitable for various inbred lines, including B104. These protocols are also useful starting points in the optimization of tissue culture for gene editing. The rate-limiting step in both transformation and gene editing is in tissue culture and plant regeneration from modified cells in elite germplasm. Despite the prolonged efforts, large varietal differences in tissue culture responses remain a serious issue in maize. Recently, protocols using morphogenic regulator genes, such as Bbm and Wus2, have been developed that show a strong potential of efficiently transforming recalcitrant varieties.
Collapse
Affiliation(s)
- Yuji Ishida
- Plant Innovation Center, Japan Tobacco, Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Yukoh Hiei
- Plant Innovation Center, Japan Tobacco, Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Toshihiko Komari
- Plant Innovation Center, Japan Tobacco, Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| |
Collapse
|
50
|
Wang H, Liu Y, Yuan J, Zhang J, Han F. The condensin subunits SMC2 and SMC4 interact for correct condensation and segregation of mitotic maize chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:467-479. [PMID: 31816133 DOI: 10.1111/tpj.14639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 05/22/2023]
Abstract
Structural Maintenance of Chromosomes 2 (SMC2) and Structural Maintenance of Chromosomes 4 (SMC4) are the core components of the condensin complexes, which are required for chromosome assembly and faithful segregation during cell division. Because of the crucial functions of both proteins in cell division, much work has been done in various vertebrates, but little information is known about their roles in plants. Here, we identified ZmSMC2 and ZmSMC4 in maize (Zea mays) and confirmed that ZmSMC2 associates with ZmSMC4 via their hinge domains. Immunostaining revealed that both proteins showed dynamic localization during mitosis. ZmSMC2 and ZmSMC4 are essential for proper chromosome segregation and for H3 phosphorylation at Serine 10 (H3S10ph) at pericentromeres during mitotic division. The loss of function of ZmSMC2 and ZmSMC4 enlarges mitotic chromosome volume and impairs sister chromatid separation to the opposite poles. Taken together, these findings confirm and extend the coordinated role of ZmSMC2 and ZmSMC4 in maintenance of normal chromosome architecture and accurate segregation during mitosis.
Collapse
Affiliation(s)
- Hefei Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|