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Liu D, Chen M, Mendoza B, Cheng H, Hu R, Li L, Trinh CT, Tuskan GA, Yang X. CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6621-6629. [PMID: 31562521 PMCID: PMC6883263 DOI: 10.1093/jxb/erz415] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/29/2019] [Indexed: 05/17/2023]
Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mei Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Brian Mendoza
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Cong T Trinh
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Liu D, Chen M, Mendoza B, Cheng H, Hu R, Li L, Trinh CT, Tuskan GA, Yang X. CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6621-6629. [PMID: 31562521 DOI: 10.5061/dryad.3qk1303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/29/2019] [Indexed: 05/28/2023]
Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mei Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Brian Mendoza
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Cong T Trinh
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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