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Son S, Song G, Nam S, Lee G, Im J, Lee KS, Park YJ, Suh EJ, Park SR. CRISPR/Cas9-mediated mutagenesis of rice NAC transcription factor genes results in altered innate immunity. PLANT PHYSIOLOGY 2024; 195:1138-1142. [PMID: 38385754 DOI: 10.1093/plphys/kiae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Mutating transcription factor genes involved in growth, development, and stress response in rice enhances disease resistance to microbial pathogens without suffering a yield penalty.
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Affiliation(s)
- Seungmin Son
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Giha Song
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Suhyeon Nam
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gunhee Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jeonghui Im
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Kyong Sil Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Yeo Jin Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Eun-Jung Suh
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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Kushwaha AK, Ellur RK, Maurya SK, Krishnan S. G, Bashyal BM, Bhowmick PK, Vinod KK, Bollinedi H, Singh NK, Singh AK. Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1265176. [PMID: 38023939 PMCID: PMC10667430 DOI: 10.3389/fpls.2023.1265176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.
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Affiliation(s)
- Amar Kant Kushwaha
- Division of Crop Improvement and Biotechnology, Indian Council of Agricultural Research (ICAR)-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sarvesh Kumar Maurya
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopala Krishnan S.
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Prolay Kumar Bhowmick
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - K. K. Vinod
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Haritha Bollinedi
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra Kumar Singh
- National Professor B.P. Pal Chair, Indian Council of Agricultural Research (ICAR)-National Institute of Plant Biotechnology, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Hake AA, Ballichatla S, Barbadikar KM, Magar N, Dutta S, Gokulan CG, Awalellu K, Patel HK, Sonti RV, Phule AS, Varma EP, Ayeella PG, Vamshi P, Sundaram RM, Maganti SM. Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:69. [PMID: 37622088 PMCID: PMC10444938 DOI: 10.1007/s11032-023-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01412-1.
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Affiliation(s)
- Anil A. Hake
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Suneel Ballichatla
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | | | - Nakul Magar
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Shubhankar Dutta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- Research and Education in Cancer, Advanced Centre for Treatment, Navi Mumbai, Maharashtra 410210 India
| | - CG Gokulan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
| | - Komal Awalellu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Ramesh V. Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007 India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Amol S. Phule
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | | | | | - Poloju Vamshi
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Sheshu Madhav Maganti
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
- ICAR-Central Tobacco Research Institute, Rajahmundry, Andhra Pradesh 533105 India
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Chen SY, Lai MH, Chu YL, Wu DH, Tung CW, Chen YJ, Chung CL. Identification of qBK2.1, a novel QTL controlling rice resistance against Fusarium fujikuroi. BOTANICAL STUDIES 2023; 64:11. [PMID: 37079162 PMCID: PMC10119339 DOI: 10.1186/s40529-023-00375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bakanae disease caused by Fusarium fujikuroi is an increasing threat to rice production. The infected plants show symptoms such as elongation, slenderness, chlorosis, a large leaf angle, and even death. Bakanae disease is traditionally managed by seed treatment. However, fungicide-resistant F. fujikuroi isolates have emerged in several Asian areas, including Taiwan. This study aimed to identify new bakanae resistance quantitative trait loci (QTLs) and provide molecular markers to assist future breeding. RESULTS A population of F2:9 recombinant inbred lines (RILs) was derived from the cross between an elite japonica Taiwanese cultivar 'Taikeng 16 (TK16)' and an indica variety 'Budda'. 'Budda' was found highly resistant to all 24 representative isolates of the F. fujikuroi population in Taiwan. For the RIL population, 6,492 polymorphic single nucleotide polymorphisms (SNPs) spanning the rice genome were obtained by genotyping-by-sequencing (GBS) technique, and the disease severity index (DSI) was evaluated by inoculation with a highly virulent F. fujikuroi isolate Ff266. Trait-marker association analysis of 166 RILs identified two QTLs in 'Budda'. qBK2.1 (21.97-30.15 Mb) is a novel and first bakanae resistance QTL identified on chromosome 2. qBK1.8 (5.24-8.66 Mb) partially overlaps with the previously reported qBK1.3 (4.65-8.41 Mb) on chromosome 1. The log of odds (LOD) scores of qBK1.8 and qBK2.1 were 4.75 and 6.13, accounting for 4.9% and 8.1% of the total phenotypic variation, respectively. 64 RILs carrying both qBK1.8 and qBK2.1 showed lower DSI (7%) than the lines carrying only qBK1.8 (15%), only qBK2.1 (13%), or none of the two QTLs (21%). For the future application of identified QTLs, 11 KBioscience competitive allele-specific PCR (KASP) markers and 3 insertion-deletion (InDel) markers were developed. CONCLUSIONS Compared to other important rice diseases, knowledge of bakanae resistance has been insufficient, which limited the development and deployment of resistant cultivars. The discovery of qBK2.1 has provided a new source of bakanae resistance. The resistant RILs inheriting good plant type, good taste, and high yield characteristics from 'TK16' can be used as good resistance donors. Our newly developed markers targeting qBK2.1 and qBK1.8 can also serve as an important basis for future fine-mapping and resistance breeding.
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Affiliation(s)
- Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 413008, Taiwan
| | - Yi-Ling Chu
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 413008, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Yue-Jie Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan.
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Song G, Son S, Nam S, Suh EJ, Lee SI, Park SR. OsWRKY114 Is a Player in Rice Immunity against Fusarium fujikuroi. Int J Mol Sci 2023; 24:ijms24076604. [PMID: 37047576 PMCID: PMC10094899 DOI: 10.3390/ijms24076604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Every year, invasive pathogens cause significant damage to crops. Thus, identifying genes conferring broad-spectrum resistance to invading pathogens is critical for plant breeding. We previously demonstrated that OsWRKY114 contributes to rice (Oryza sativa L.) immunity against the bacterial pathovar Xanthomonas oryzae pv. oryzae (Xoo). However, it is not known whether OsWRKY114 is involved in defense responses to other pathogens. In this study, we revealed that OsWRKY114 enhances innate immunity in rice against the fungal pathogen Fusarium fujikuroi, which is the causal agent of bakanae disease. Transcript levels of various gibberellin-related genes that are required for plant susceptibility to F. fujikuroi were reduced in rice plants overexpressing OsWRKY114. Analysis of disease symptoms revealed increased innate immunity against F. fujikuroi in OsWRKY114-overexpressing rice plants. Moreover, the expression levels of OsJAZ genes, which encode negative regulators of jasmonic acid signaling that confer immunity against F. fujikuroi, were reduced in OsWRKY114-overexpressing rice plants. These results indicate that OsWRKY114 confers broad-spectrum resistance not only to Xoo but also to F. fujikuroi. Our findings provide a basis for developing strategies to mitigate pathogen attack and improve crop resilience to biotic stress.
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Affiliation(s)
- Giha Song
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Seungmin Son
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Suhyeon Nam
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
- Department of Crop Science & Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Eun-Jung Suh
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Soo In Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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Hasan S, Furtado A, Henry R. Gene Expression in the Developing Seed of Wild and Domesticated Rice. Int J Mol Sci 2022; 23:13351. [PMID: 36362135 PMCID: PMC9658725 DOI: 10.3390/ijms232113351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 01/06/2024] Open
Abstract
The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.
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Affiliation(s)
- Sharmin Hasan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia 4072, Australia
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Jacobs JM, Wang GL. Next Generation Rice Disease Research. RICE (NEW YORK, N.Y.) 2021; 14:84. [PMID: 34570288 PMCID: PMC8476694 DOI: 10.1186/s12284-021-00523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210 USA
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 USA
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Leaf Transcriptome Analysis of Broomcorn Millet Uncovers Key Genes and Pathways in Response to Sporisorium destruens. Int J Mol Sci 2021; 22:ijms22179542. [PMID: 34502461 PMCID: PMC8430493 DOI: 10.3390/ijms22179542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 08/27/2021] [Indexed: 01/26/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) affected by smut (caused by the pathogen Sporisorium destruens) has reduced production yields and quality. Determining the tolerance of broomcorn millet varieties is essential for smut control. This study focuses on the differences in the phenotypes, physiological characteristics, and transcriptomes of resistant and susceptible broomcorn millet varieties under Sporisorium destruens stress. In diseased broomcorn millet, the plant height and stem diameter were reduced, while the number of nodes increased. After infection, the activities of superoxide dismutase and peroxidase decreased, and malondialdehyde and relative chlorophyll content (SPAD) decreased. Transcriptome analysis showed 514 and 5452 differentially expressed genes (DEGs) in the resistant and susceptible varieties, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that pathways related to plant disease resistance, such as phenylpropanoid biosynthesis, plant–pathogen interaction, and plant hormone signal transduction, were significantly enriched. In addition, the transcriptome changes of cluster leaves and normal leaves in diseased broomcorn millet were analysed. Gene ontology and KEGG enrichment analyses indicated that photosynthesis played an important role in both varieties. These findings lay a foundation for future research on the molecular mechanism of the interaction between broomcorn millet and Sporisorium destruens.
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