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Liu Y, Cheng Z, Chen W, Wu C, Chen J, Sui Y. Establishment of genome-editing system and assembly of a near-complete genome in broomcorn millet. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1688-1702. [PMID: 38695644 DOI: 10.1111/jipb.13664] [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: 01/18/2024] [Accepted: 03/29/2024] [Indexed: 08/17/2024]
Abstract
The ancient crop broomcorn millet (Panicum miliaceum L.) is an indispensable orphan crop in semi-arid regions due to its short life cycle and excellent abiotic stress tolerance. These advantages make it an important alternative crop to increase food security and achieve the goal of zero hunger, particularly in light of the uncertainty of global climate change. However, functional genomic and biotechnological research in broomcorn millet has been hampered due to a lack of genetic tools such as transformation and genome-editing techniques. Here, we successfully performed genome editing of broomcorn millet. We identified an elite variety, Hongmi, that produces embryogenic callus and has high shoot regeneration ability in in vitro culture. We established an Agrobacterium tumefaciens-mediated genetic transformation protocol and a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated genome-editing system for Hongmi. Using these techniques, we produced herbicide-resistant transgenic plants and edited phytoene desaturase (PmPDS), which is involved in chlorophyll biosynthesis. To facilitate the rapid adoption of Hongmi as a model line for broomcorn millet research, we assembled a near-complete genome sequence of Hongmi and comprehensively annotated its genome. Together, our results open the door to improving broomcorn millet using biotechnology.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Zixiang Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Sui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Kanai M, Hikino K, Mano S. Cloning and Functional Verification of Endogenous U6 Promoters for the Establishment of Efficient CRISPR/Cas9-Based Genome Editing in Castor ( Ricinus communis). Genes (Basel) 2023; 14:1327. [PMID: 37510232 PMCID: PMC10379810 DOI: 10.3390/genes14071327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Castor (Ricinus communis) seeds are rich in a type of hydroxy fatty acid called ricinoleic acid, which is in high demand for the production of plant-based plastics, lubricants, and hydraulic oils. However, the high content of ricin, a toxic protein, in these seeds has restricted further expansion in the area of castor cultivation. Therefore, the development of ricin-free castor is needed. Genome editing technology, although successfully applied in several plant species, is still in the developing stages in castor and awaits the identification of an endogenous U6 promoter with robust function. Here, we searched for U6 small nuclear RNA (snRNA) genes in the castor genome. This led to the identification of six U6 snRNA genes. The promoters of these U6 snRNA genes were cloned, and their function was examined in castor cells using the particle delivery method. The results showed that a U6 promoter length of approximately 300 bp from the transcription start site was sufficient to activate gene expression. This study provides insights into the endogenous castor U6 promoter sequences and outlines a method for verifying the function of U6 promoters in plants using the particle delivery system.
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Affiliation(s)
- Masatake Kanai
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Kazumi Hikino
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shoji Mano
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Basic Biology Program, Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
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Lastochkina O, Aliniaeifard S, SeifiKalhor M, Bosacchi M, Maslennikova D, Lubyanova A. Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects. HORTICULTURAE 2022; 8:910. [DOI: 10.3390/horticulturae8100910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.
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Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernández F, Smýkal P, Brus J. How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? FRONTIERS IN PLANT SCIENCE 2022; 13:886162. [PMID: 35783966 PMCID: PMC9243378 DOI: 10.3389/fpls.2022.886162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/01/2023]
Abstract
Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.
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Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi, Argentina
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | | | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for Environment, University of Vermont, Burlington, VT, United States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Matthew Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Soledad Ureta
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Fernando Hernández
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, Olomouc, Czechia
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