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Sedeek K, Mohammed N, Zhou Y, Zuccolo A, Sanikommu K, Kantharajappa S, Al-Bader N, Tashkandi M, Wing RA, Mahfouz MM. Multitrait engineering of Hassawi red rice for sustainable cultivation. Plant Sci 2024; 341:112018. [PMID: 38325660 DOI: 10.1016/j.plantsci.2024.112018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals. However, Hassawi has a long growth cycle, high cultivation costs, low productivity, and susceptibility to lodging. Here, to improve these undesirable traits via genome editing, we established efficient regeneration and Agrobacterium-mediated transformation protocols for Hassawi. In addition, we generated the first high-quality reference genome and targeted the key flowering repressor gene, Hd4, thus shortening the plant's lifecycle and height. Using CRISPR/Cas9 multiplexing, we simultaneously disrupted negative regulators of flowering time (Hd2, Hd4, and Hd5), grain size (GS3), grain number (GN1a), and plant height (Sd1). The resulting homozygous mutant lines flowered extremely early (∼56 days) and had shorter stems (approximately 107 cm), longer grains (by 5.1%), and more grains per plant (by 50.2%), thereby enhancing overall productivity. Furthermore, the awns of grains were 86.4% shorter compared to unedited plants. Moreover, the modified rice grain displayed improved nutritional attributes. As a result, the modified Hassawi rice combines several desirable traits that can incentivize large-scale cultivation and reduce malnutrition.
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Affiliation(s)
- Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nahed Mohammed
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Krishnaveni Sanikommu
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sunitha Kantharajappa
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manal Tashkandi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Sedeek K, Zuccolo A, Fornasiero A, Weber AM, Sanikommu K, Sampathkumar S, Rivera LF, Butt H, Mussurova S, Alhabsi A, Nurmansyah N, Ryan EP, Wing RA, Mahfouz MM. Multi-omics resources for targeted agronomic improvement of pigmented rice. Nat Food 2023; 4:366-371. [PMID: 37169820 DOI: 10.1038/s43016-023-00742-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/24/2023] [Indexed: 05/13/2023]
Abstract
Pigmented rice (Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.
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Affiliation(s)
- Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Alice Fornasiero
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Annika M Weber
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Krishnaveni Sanikommu
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sangeetha Sampathkumar
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luis F Rivera
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdulrahman Alhabsi
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nurmansyah Nurmansyah
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
- International Rice Research Institute, Strategic Innovation, Los Baños, Philippines
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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