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Park HJ, Kim M, Lee D, Kim HJ, Jung HW. CRISPR-Cas9 and beyond: identifying target genes for developing disease-resistant plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:369-377. [PMID: 38363032 DOI: 10.1111/plb.13625] [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: 05/15/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Throughout the history of crop domestication, desirable traits have been selected in agricultural products. However, such selection often leads to crops and vegetables with weaker vitality and viability than their wild ancestors when exposed to adverse environmental conditions. Considering the increasing human population and climate change challenges, it is crucial to enhance crop quality and quantity. Accordingly, the identification and utilization of diverse genetic resources are imperative for developing disease-resistant plants that can withstand unexpected epidemics of plant diseases. In this review, we provide a brief overview of recent progress in genome-editing technologies, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) technologies. In particular, we classify disease-resistant mutants of Arabidopsis thaliana and several crop plants based on the roles or functions of the mutated genes in plant immunity and suggest potential target genes for molecular breeding of genome-edited disease-resistant plants. Genome-editing technologies are resilient tools for sustainable development and promising solutions for coping with climate change and population increases.
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Affiliation(s)
- H J Park
- Institute of Agricultural Life Science, Dong-A University, Busan, Korea
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
| | - M Kim
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - D Lee
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - H J Kim
- Department of Molecular Genetics, Dong-A University, Busan, Korea
| | - H W Jung
- Institute of Agricultural Life Science, Dong-A University, Busan, Korea
- Department of Applied Bioscience, Dong-A University, Busan, Korea
- Department of Molecular Genetics, Dong-A University, Busan, Korea
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Gandikota M, Krishnakanth Yadav T, Maram RR, Kalluru S, Sena MB, Siddiq EA, Kalinati Narasimhan Y, Vemireddy LR, Ghanta A. Development of activation-tagged gain-of-functional mutants in indica rice line (BPT 5204) for sheath blight resistance. Mol Biol Rep 2024; 51:381. [PMID: 38430361 DOI: 10.1007/s11033-023-09194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024]
Abstract
BACKGROUND The development of sheath blight (ShB) resistance varieties has been a challenge for scientists for long time in rice. Activation tagging is an efficient gain-of-function mutation approach to create novel phenotypes and to identify their underlying genes. In this study, a mutant population was developed employing activation tagging in the recalcitrant indica rice (Oryza sativa L.) cv. BPT 5204 (Samba Mahsuri) through activation tagging. METHODS AND RESULTS In this study, we have generated more than 1000 activation tagged lines in indica rice, from these mutant population 38 (GFP- RFP+) stable Ds plants were generated through germinal transposition at T2 generation based on molecular analysis and seeds selected on hygromycin (50 mg/L) containing medium segregation analyses confirmed that the transgene inherited as mendelian segregation ratio of 3:1 (3 resistant: 1 susceptible). Of them, five stable activation tagged Ds lines (M-Ds-1, M-Ds-2, M-Ds-3, M-Ds-4 and M-Ds-5) were selected based on phenotypic observation through screening for sheath blight (ShB) resistance caused by fungal pathogen Rhizoctonia solani (R. solani),. Among them, M-Ds-3 and M-Ds-5 lines showed significant resistance for ShB over other tagged lines and wild type (WT) plants. Furthermore, analysed for launch pad insertion through TAIL-PCR results and mapped on corresponding rice chromosomes. Flanking sequence and gene expression analysis revealed that the upregulation of glycoside hydrolase-OsGH or similar to Class III chitinase homologue (LOC_Os08g40680) in M-Ds-3 and a hypothetical protein gene (LOC_Os01g55000) in M-Ds-5 are potential candidate genes for sheath blight resistance in rice. CONCLUSION In the present study, we developed Ac-Ds based ShB resistance gain-of-functional mutants through activation tagging in rice. These activation tagged mutant lines can be excellent sources for the development of ShB resistant cultivars in rice.
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Affiliation(s)
- Mahendranath Gandikota
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - T Krishnakanth Yadav
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | | | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - M Balachandran Sena
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - E A Siddiq
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Yamini Kalinati Narasimhan
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India.
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Cloutier S, Edwards T, Zheng C, Booker HM, Islam T, Nabetani K, Kutcher HR, Molina O, You FM. Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:27. [PMID: 38245903 PMCID: PMC10800302 DOI: 10.1007/s00122-023-04528-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.
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Affiliation(s)
- S Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - T Edwards
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - C Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - H M Booker
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
| | - T Islam
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - K Nabetani
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - H R Kutcher
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - O Molina
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - F M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
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