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Nguyen TTH, Bez C, Bertani I, Nguyen MH, Nguyen TKN, Venturi V, Dinh HT. Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam. THE PLANT PATHOLOGY JOURNAL 2024; 40:225-332. [PMID: 38606451 PMCID: PMC11016553 DOI: 10.5423/ppj.nt.12.2023.0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/19/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.
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Affiliation(s)
- Thu Thi Hieu Nguyen
- VNU Institute of Microbiology and Biotechnology, Hanoi 1000, Vietnam
- Vietnam-Russia Tropical Science and Technology Research Center, Hanoi 1000, Vietnam
| | - Cristina Bez
- International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste 34149, Italy
| | - Iris Bertani
- International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste 34149, Italy
| | | | - Thao Kim Nu Nguyen
- VNU University of Science, Vietnam National University, Hanoi 1000, Vietnam
| | - Vittorio Venturi
- International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste 34149, Italy
| | - Hang Thuy Dinh
- VNU Institute of Microbiology and Biotechnology, Hanoi 1000, Vietnam
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Fu ZW, Li JH, Gao X, Wang SJ, Yuan TT, Lu YT. Pathogen-induced methylglyoxal negatively regulates rice bacterial blight resistance by inhibiting OsCDR1 protease activity. MOLECULAR PLANT 2024; 17:325-341. [PMID: 38178576 DOI: 10.1016/j.molp.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/10/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB), a globally devastating disease of rice (Oryza sativa) that is responsible for significant crop loss. Sugars and sugar metabolites are important for pathogen infection, providing energy and regulating events associated with defense responses; however, the mechanisms by which they regulate such events in BB are unclear. As an inevitable sugar metabolite, methylglyoxal (MG) is involved in plant growth and responses to various abiotic stresses, but the underlying mechanisms remain enigmatic. Whether and how MG functions in plant biotic stress responses is almost completely unknown. Here, we report that the Xoo strain PXO99 induces OsWRKY62.1 to repress transcription of OsGLY II genes by directly binding to their promoters, resulting in overaccumulation of MG. MG negatively regulates rice resistance against PXO99: osglyII2 mutants with higher MG levels are more susceptible to the pathogen, whereas OsGLYII2-overexpressing plants with lower MG content show greater resistance than the wild type. Overexpression of OsGLYII2 to prevent excessive MG accumulation confers broad-spectrum resistance against the biotrophic bacterial pathogens Xoo and Xanthomonas oryzae pv. oryzicola and the necrotrophic fungal pathogen Rhizoctonia solani, which causes rice sheath blight. Further evidence shows that MG reduces rice resistance against PXO99 through CONSTITUTIVE DISEASE RESISTANCE 1 (OsCDR1). MG modifies the Arg97 residue of OsCDR1 to inhibit its aspartic protease activity, which is essential for OsCDR1-enhanced immunity. Taken together, these findings illustrate how Xoo promotes infection by hijacking a sugar metabolite in the host plant.
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Affiliation(s)
- Zheng-Wei Fu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jian-Hui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Xiang Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Shi-Jia Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Zhu Y, Su H, Liu XX, Sun JF, Xiang L, Liu YJ, Hu ZW, Xiong XY, Yang XM, Bhutto SH, Li GB, Peng YY, Wang H, Shen X, Zhao ZX, Zhang JW, Huang YY, Fan J, Wang WM, Li Y. Identification of NADPH Oxidase Genes Crucial for Rice Multiple Disease Resistance and Yield Traits. RICE (NEW YORK, N.Y.) 2024; 17:1. [PMID: 38170415 PMCID: PMC10764683 DOI: 10.1186/s12284-023-00678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
Reactive oxygen species (ROS) act as a group of signaling molecules in rice functioning in regulation of development and stress responses. Respiratory burst oxidase homologues (Rbohs) are key enzymes in generation of ROS. However, the role of the nine Rboh family members was not fully understood in rice multiple disease resistance and yield traits. In this study, we constructed mutants of each Rboh genes and detected their requirement in rice multiple disease resistance and yield traits. Our results revealed that mutations of five Rboh genes (RbohA, RbohB, RbohE, RbohH, and RbohI) lead to compromised rice blast disease resistance in a disease nursery and lab conditions; mutations of five Rbohs (RbohA, RbohB, RbohC, RbohE, and RbohH) result in suppressed rice sheath blight resistance in a disease nursery and lab conditions; mutations of six Rbohs (RbohA, RbohB, RbohC, RbohE, RbohH and RbohI) lead to decreased rice leaf blight resistance in a paddy yard and ROS production induced by PAMPs and pathogen. Moreover, all Rboh genes participate in the regulation of rice yield traits, for all rboh mutants display one or more compromised yield traits, such as panicle number, grain number per panicle, seed setting rate, and grain weight, resulting in reduced yield per plant except rbohb and rbohf. Our results identified the Rboh family members involved in the regulation of rice resistance against multiple pathogens that caused the most serious diseases worldwide and provide theoretical supporting for breeding application of these Rbohs to coordinate rice disease resistance and yield traits.
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Affiliation(s)
- Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Su
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xin-Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Fen Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan-Jing Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhang-Wei Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Yu Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue-Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Sadam Hussain Bhutto
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuan-Ying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xu Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi-Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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Manoj CA, Muralidhara B, Basavaraj PS, Honnappa M, Ajitha V, Aleena D, Ishwaryalakshmi VG, Usha G, Gireesh C, Senguttuvel P, Kemparaju KB, Rao LVS, Basavaraj K, Laha GS, Sundaram RM, Kumar RM, Rathod S, Salimath PM, Lokesha R, Diwan J, Nidagundi JM, Gowrisankar M, Anantha MS. Improvement of bacterial blight resistance of the high yielding, fine-grain, rice variety, Gangavati sona through marker-assisted backcross breeding. 3 Biotech 2023; 13:393. [PMID: 37953830 PMCID: PMC10638137 DOI: 10.1007/s13205-023-03828-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB.
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Affiliation(s)
- C. A. Manoj
- University of Agricultural Sciences, Raichur, India
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Muralidhara
- University of Agricultural Sciences, Raichur, India
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - P. S. Basavaraj
- ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - M. Honnappa
- University of Agricultural Sciences, Raichur, India
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - V. Ajitha
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - D. Aleena
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - G. Usha
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gireesh
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - P. Senguttuvel
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | - K. Basavaraj
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - G. S. Laha
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | | | - R. Lokesha
- University of Agricultural Sciences, Raichur, India
| | | | | | | | - M. S. Anantha
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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6
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Khan S, Srivastava S, Karnwal A, Malik T. Streptomyces as a promising biological control agents for plant pathogens. Front Microbiol 2023; 14:1285543. [PMID: 38033592 PMCID: PMC10682734 DOI: 10.3389/fmicb.2023.1285543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.
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Affiliation(s)
- Shaista Khan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Srivastava
- School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Arun Karnwal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical sciences, Jimma University, Jimma, Ethiopia
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Luo H, Wang Q, Dong C, Shi Z, He C, Guo Z, Shi J, Li C, Gao W, Li J. Establishment of Functional PCR-Based Markers against Bacterial Leaf Blight Disease in Rice Landraces of Yunnan Province of China. Life (Basel) 2023; 13:2101. [PMID: 37895481 PMCID: PMC10608166 DOI: 10.3390/life13102101] [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: 09/06/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Bacterial leaf blight is a devastating disease of rice worldwide. The resistant genes are routinely transferred from landraces to cultivated varieties through backcross breeding along with marker-assisted selection. In the present study, we use the gene-specific markers to screen the rice landraces in Yunnan Province of China. We collected 404 representative samples of 24 different rice landraces from Yunnan Province of China. The initial PCR-based screening suggested that the leaf blight resistance was not evenly distributed in Yunnan Province. Our results indicate that there is a complete loss of resistance for landraces based on xa5 and xa13 genes. On the other hand, landraces harboring Xa7 and Xa21 showed a high level of resistance. Using gene-specific PCR-based data, we were able to identify the resistant, susceptible and heterozygous populations across Yunnan Province. The widely used Xa21 gene alone showed a remarkable level of resistance throughout the province, indicating its potential to develop broad-spectrum resistance in rice germplasm. The key aspects of bacterial blight spread according to local sites in Yunnan Province and the resistance conferred by different landraces due to the presence of different resistance genes are discussed.
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Affiliation(s)
- Hengming Luo
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Qun Wang
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chao Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
- Yunnan Seed Laboratory, Kunming 650205, China
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming 650205, China
- Scientific Observation Station for Rice Germplasm Resources of Yunnan, Ministry of Agriculture and Rural Affairs, Kunming 650205, China
| | - Zhufeng Shi
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chengxing He
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Zhixiang Guo
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Junyi Shi
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chun Li
- Wenshan Plant Protection and Quarantine Station, Wenshan 663099, China; (C.L.); (W.G.)
| | - Wei Gao
- Wenshan Plant Protection and Quarantine Station, Wenshan 663099, China; (C.L.); (W.G.)
| | - Jinbin Li
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
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8
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Gautam RK, Singh PK, Sakthivel K, Venkatesan K, Rao SS, Srikumar M, Vijayan J, Rakesh B, Ray S, Akhtar J, Meena BR, Langyan S, Ali S, Krishnamurthy SL. Marker-assisted enhancement of bacterial blight ( Xanthomonas oryzae pv . oryzae) resistance in a salt-tolerant rice variety for sustaining rice production of tropical islands. FRONTIERS IN PLANT SCIENCE 2023; 14:1221537. [PMID: 37818314 PMCID: PMC10561094 DOI: 10.3389/fpls.2023.1221537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023]
Abstract
Introduction Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice, specially in the tropical regions of the world. Developing rice varieties with host resistance against the disease is the most effective and economical solution for managing the disease. Methods Pyramiding resistance genes (Xa4, xa5, xa13,and Xa21) in popular rice varieties using marker-assisted backcross breeding (MABB) has been demonstrated as a cost-effective and sustainable approach for establishing durable BB resistance. Here, we report our successful efforts in introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) from IRBB60 to CARI Dhan 5, a popular salt-tolerant variety developed from a somaclonal variant of Pokkali rice, through functional MABB. Results and discussion Both BB and coastal salinity are among the major challenges for rice production in tropical island and coastal ecosystems. Plants with four, three, and two gene pyramids were generated, which displayed high levels of resistance to the BB pathogen at the BC3F2 stage. Under controlled salinity microplot environments, the line 131-2-175-1223 identified with the presence of three gene pyramid (Xa21+xa13+xa5) displayed notable resistance across locations and years as well as exhibited a salinity tolerance comparable to the recurrent parent, CARI Dhan 5. Among two BB gene combinations (Xa21+xa13), two lines, 17-1-69-334 and 46-3-95-659, demonstrated resistance across locations and years, as well as salt tolerance and grain production comparable to CARI Dhan 5. Besides salinity tolerance, five lines, 17-1-69-179, 46-3-95-655, 131-2-190-1197, 131-2-175-1209, and 131-2-175-1239, exhibited complete resistance to BB disease. Following multilocation testing, potential lines have been identified that can serve as a prospective candidate for producing varieties for the tropical Andaman and Nicobar Islands and other coastal locations, which are prone to BB and coastal salinity stresses.
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Affiliation(s)
- Raj Kumar Gautam
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pankaj Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Krishnan Sakthivel
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Oilseeds Research, Hyderabad, India
| | - K. Venkatesan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources (NBPGR), Regional Research Station, Thrissur, Kerala, India
| | - Shyam S. Rao
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - M. Srikumar
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Joshitha Vijayan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - B. Rakesh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Soham Ray
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Jameel Akhtar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Bharat Raj Meena
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sharik Ali
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. L. Krishnamurthy
- Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, India
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9
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Halim AABA, Rafii MY, Osman MB, Chukwu SC, Oladosu Y. Physicochemical Properties and Tissue Structure of High Kernel Elongation Rice ( Oryza sativa L.) Varieties as Affected by Heat Treatment. Foods 2023; 12:foods12112207. [PMID: 37297452 DOI: 10.3390/foods12112207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Heat treatment could affect the structure and properties of rice varieties. The present study was conducted in order to determine the effects of heat treatment on the physicochemical properties and tissue structure of Mahsuri Mutan, Basmati 370 and MR219 rice varieties. The three rice varieties were subjected to heat treatment (ageing) at 90 °C, using an oven, for 3 h. After the heat treatment, the samples were cooled at room temperature (25 °C) for 1 h. Physicochemical properties, such as alkali digestion value, water uptake ratio, solids in cooking water, high kernel elongation ratio and amylose contents, were determined. The procedure used in determining both apparent and absolute amylose involved measuring the iodine affinity of defatted whole starch. Ahigh-performance anion-exchange chromatograph was used to analyse branch chain length distribution of amylopectin quantitatively. The starch structure of the rice samples was observed under a scanning electron microscope. Data collected on physicochemical traits, heat treatment and control (ageing and non-ageing) were subjected to an analysis of variance using SAS software version 9.4. In this study, Mahsuri Mutan and Basmati 370 showed superior high kernel elongation as compared to their respective rice progenies. This study also found that heat treatment directly affected the increasingly high kernel elongation for both populations. The phenotypic correlation co-efficient indicated that there was a high positive correlation between high kernel elongation and water uptake ratio, implying that selection for water uptake ratio would increase the high kernel elongation characteristic. The heat treatment showed significant difference in all the physicochemical traits of the varieties studied. Heat treatment also affected the very long branch chains of starch, such as amylose. Observation under an electron microscope showed that the samples subjected to heat treatment had more cracks on the tissue structure compared to normal rice samples. The hexagon structure in Mahsuri Mutan produced a greater elongation effect on its kernel. The findings from this study could be useful to breeders in the selection and development of a new high kernel elongation rice variety.
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Affiliation(s)
- Anna Arina Bt Ab Halim
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohd Y Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohamad B Osman
- Malaysia Agriculture Research and Development Institute (MARDI), Serdang 43400, Selangor, Malaysia
| | - Samuel C Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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10
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Li J, Shi X, Wang C, Li Q, Lu J, Zeng D, Xie J, Shi Y, Zhai W, Zhou Y. Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm. Int J Mol Sci 2023; 24:ijms24108810. [PMID: 37240156 DOI: 10.3390/ijms24108810] [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: 03/24/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.
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Affiliation(s)
- Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xiaorong Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanlin Li
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junping Xie
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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11
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Hou Y, Liang Y, Yang C, Ji Z, Zeng Y, Li G, E Z. Complete Genomic Sequence of Xanthomonas oryzae pv. oryzae Strain, LA20, for Studying Resurgence of Rice Bacterial Blight in the Yangtze River Region, China. Int J Mol Sci 2023; 24:ijms24098132. [PMID: 37175839 PMCID: PMC10179132 DOI: 10.3390/ijms24098132] [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: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a causative agent of rice bacterial blight (BB). In 2020-2022, BB re-emerged, and there was a break out in the Yangtze River area, China. The pandemic Xoo strain, LA20, was isolated and identified from cultivar Quanyou1606 and demonstrated to be the Chinese R9 Xoo strain, which is able to override the widely adopted xa5-, Xa7- and xa13-mediated resistance in rice varieties in Yangtze River. Here, we report the complete genome of LA20 by PacBio and Illumina sequencing. The assembled genome consists of one circular chromosome of 4,960,087 bp, sharing 99.65% sequence identity with the traditional representative strain, YC11 (R5), in the Yangtze River. Comparative genome analysis of LA20 and YC11 revealed the obvious variability in Tal genes (the uppermost virulence determinants) in numbers and sequences. Particularly, six Tal genes were only found in LA20, but not in YC11, among which Tal1b (pthXo1)/Tal4 (pthXo6), along with the lost one, pthXo3 (avrXa7), might be the major factors for LA20 to overcome xa5-, Xa7- and xa13-mediated resistance, thus, leading to the resurgence of BB. This complete genome of the new pandemic Xoo strain will provide novel insights into pathogen evolution, the traits of pathogenicity on genomic level and the epidemic disease status in China.
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Affiliation(s)
- Yuxuan Hou
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yan Liang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Changdeng Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhijuan Ji
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yuxiang Zeng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Guanghao Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiguo E
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
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12
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Islam MR, Chowdhury R, Roy AS, Islam MN, Mita MM, Bashar S, Saha P, Rahat RA, Hasan M, Akter MA, Alam MZ, Latif MA. Native Trichoderma Induced the Defense-Related Enzymes and Genes in Rice against Xanthomonas oryzae pv. oryzae ( Xoo). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091864. [PMID: 37176922 PMCID: PMC10180545 DOI: 10.3390/plants12091864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 05/15/2023]
Abstract
The application of Trichoderma is a form of biological control that has been effective in combating Xanthomonas oryzae pv. oryzae, the causative agent of the devastating disease known as bacterial blight of rice. In this present study, four strains of Trichoderma, viz., T. paraviridescens (BDISOF67), T. erinaceum (BDISOF91), T. asperellum (BDISOF08), and T. asperellum (BDISOF09), were collected from the rice rhizosphere and used to test their potentiality in reducing bacterial blight. The expression patterns of several core defense-related enzymes and genes related to SA and JA pathways were studied to explore the mechanism of induced resistance by those Trichoderma strains. The results primarily indicated that all Trichoderma were significantly efficient in reducing the lesion length of the leaf over rice check variety (IR24) through enhancing the expression of core defense-related enzymes, such as PAL, PPO, CAT, and POD activities by 4.27, 1.77, 3.53, and 1.57-fold, respectively, over control. Moreover, the results of qRT-PCR exhibited an upregulation of genes OsPR1, OsPR10, OsWRKY45, OsWRKY62, OsWRKY71, OsHI-LOX, and OsACS2 after 24 h of inoculation with all tested Trichoderma strains. However, in the case of RT-PCR, no major changes in OsPR1 and OsPR10 expression were observed in plants treated with different Trichoderma strains during different courses of time. Collectively, Trichoderma induced resistance in rice against X. oryzae pv. oryzae by triggering these core defense-related enzymes and genes associated with SA and JA pathways.
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Affiliation(s)
- Md Rashidul Islam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Rabin Chowdhury
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Arpita Saha Roy
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Nazmul Islam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mamuna Mahjabin Mita
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Samrin Bashar
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Plabon Saha
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Ridwan Ahmed Rahat
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mehedi Hasan
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mst Arjina Akter
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Zahangir Alam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Abdul Latif
- Plant Pathology Division, Bangladesh Rice Research Institute, Joydebpur, Gazipur 1701, Bangladesh
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13
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Kumar M, Singh RP, Jena D, Singh V, Rout D, Arsode PB, Choudhary M, Singh P, Chahar S, Samantaray S, Mukherjee AK, Mohan C, Bohra A, Das G, Balo S, Singh ON, Verma R. Marker-Assisted Improvement for Durable Bacterial Blight Resistance in Aromatic Rice Cultivar HUR 917 Popular in Eastern Parts of India. PLANTS (BASEL, SWITZERLAND) 2023; 12:1363. [PMID: 36987051 PMCID: PMC10058408 DOI: 10.3390/plants12061363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 06/19/2023]
Abstract
Bacterial blight (BB) is a devastating disease of rice in the tropics of Indian sub-continent, where the presence of Xoo races with varying levels of genetic diversity and virulence renders disease management extremely challenging. In this context, marker-assisted improvement of plant resistance has been proven as one of the most promising approaches for the development of sustainable rice cultivars. The present study demonstrates the marker-assisted introgression of the three BB resistant genes (Xa21 + xa13 + xa5) into the background of HUR 917, a popular aromatic short grain (ASG) rice cultivar in India. The performance of the resulting improved products (near isogenic lines (NILs), HR 23-5-37-83-5, HR 23-5-37-121-10, HR 23-5-37-121-14, HR 23-65-6-191-13, HR 23-65-6-237-2, HR 23-65-6-258-10 and HR 23-65-6-258-21) establishes the utility of marker-assisted selection (MAS) approach for accelerated trait introgression in rice. The MAS-bred lines carrying three introgressed genes showed broad spectrum BB resistance (lesion length, LL of 1.06 ± 1.35 cm to 4.61 ± 0.87 cm). Besides, these improved lines showed the complete product profile of recurrent parent HUR 917 along with the enhanced level of durable BB resistance. The improved introgression lines with durable BB resistance would contribute to sustainable rice production in India, particularly in the Indo-Gangetic plane that has substantial acreage under HUR 917.
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Affiliation(s)
- Manish Kumar
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ravi Pratap Singh
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Debarchana Jena
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Vineeta Singh
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Diptibala Rout
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | | | - Madhu Choudhary
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Prakash Singh
- Veer Kunwar Singh College of Agriculture, Bihar Agricultural University-BAU, Sabaur, Dumraon, Buxar 802136, Bihar, India
| | - Suman Chahar
- Central State Farm, National Seeds Corporation, Sirsa Road, Hisar 125001, Haryana, India
| | | | | | - Chander Mohan
- Department of Agriculture, Cooperation and Farmers Welfare, Government of India, New Delhi 110001, Delhi, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre (SABC) and Centre for Crop and Food Innovation (CCFI), Murdoch University, Perth, WA 6150, Australia
| | - Goutam Das
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Sumana Balo
- Department of Soil Science and Agricultural Chemistry, Uttar Banga Krishi Vishwavidyalaya, Coochbehar 736165, West Bengal, India
| | - Onkar Nath Singh
- Birsa Agricultural University (BAU), Ranchi 834006, Jharkhand, India
| | - Ramlakhan Verma
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
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14
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Jain L, Kumar V, Jain SK, Kaushal P, Ghosh PK. Isolation of bacteriophages infecting Xanthomonas oryzae pv. oryzae and genomic characterization of novel phage vB_XooS_NR08 for biocontrol of bacterial leaf blight of rice. Front Microbiol 2023; 14:1084025. [PMID: 37007514 PMCID: PMC10061587 DOI: 10.3389/fmicb.2023.1084025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/27/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases worldwide in rice-growing regions. The Ineffectiveness of chemicals in disease management has increased the interest in phage therapy. In this study, we isolated 19 bacteriophages, infecting Xoo, from a rice field, which belonged to phage families Siphoviridae, Myoviridae, and Podoviridae on the basis of electron microscopy. Among 19 phages, Phage vB_XooS_NR08, a member of the Siphoviridae family, expressed antibacterial activity against all Xoo strains tested and did not lyse X. campestris and other unrelated bacterial hosts. Phage NR08 showed more than 80% viability at a temperature range of 4°C–40°C, pH range of 5–9, and direct exposure to sunlight for 2 h, whereas UV light and chemical agents were highly detrimental. In a one-step growth curve, NR08 has a 40-min latent period, followed by a 30-min burst period with a burst size of 250 particle/bacterium. The genome of NR08 is double-stranded DNA, linear having a size of 98,812 bp with a G + C content of 52.9%. Annotation of the whole-genome sequence indicated that NR08 encodes 142 putative open reading frames (ORFs), including one ORF for tRNA, namely, trna1-GlnTTG. Comparative genome analysis of NR08 showed that it shares maximum similarity with Pseudomonas phage PaMx42 (40% query coverage, 95.39% identity, and acc. Length 43,225) and Xanthomonas phage Samson (40% query coverage, 96.68% identity, and acc. Length 43,314). The average alignment percentage (AP) of NR08 with other Xoophages was only 0.32 to 1.25 since the genome of NR08 (98.8 kb) is almost double of most of the previously reported Xoophages (43–47 kb), thus indicating NR08 a novel Xoophage. In in vitro bacterial challenge assay, NR08 showed bacteriostasis up to 24 h and a 99.95% reduction in bacterial growth in 48 h. In rice pot efficacy trials, single-dose treatment of NR08 showed a significant reduction in disease up to 90.23% and 79.27% on 7 and 21 dpi, respectively. However, treatment using 2% skim milk-supplemented phage preparation was significantly less effective as compared to the neat phage preparation. In summary, this study characterized a novel Xoophage having the potential as a biocontrol agent in the mitigation of BLB in rice.
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15
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Bai X, Fang H, He Y, Zhang J, Tao M, Wu Q, Yang G, Wei Y, Tang Y, Tang L, Lou B, Deng S, Yang Y, Feng X. Dynamic UAV Phenotyping for Rice Disease Resistance Analysis Based on Multisource Data. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0019. [PMID: 37040287 PMCID: PMC10076055 DOI: 10.34133/plantphenomics.0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/09/2022] [Indexed: 05/27/2023]
Abstract
Bacterial blight poses a threat to rice production and food security, which can be controlled through large-scale breeding efforts toward resistant cultivars. Unmanned aerial vehicle (UAV) remote sensing provides an alternative means for the infield phenotype evaluation of crop disease resistance to relatively time-consuming and laborious traditional methods. However, the quality of data acquired by UAV can be affected by several factors such as weather, crop growth period, and geographical location, which can limit their utility for the detection of crop disease and resistant phenotypes. Therefore, a more effective use of UAV data for crop disease phenotype analysis is required. In this paper, we used time series UAV remote sensing data together with accumulated temperature data to train the rice bacterial blight severity evaluation model. The best results obtained with the predictive model showed an R p 2 of 0.86 with an RMSEp of 0.65. Moreover, model updating strategy was used to explore the scalability of the established model in different geographical locations. Twenty percent of transferred data for model training was useful for the evaluation of disease severity over different sites. In addition, the method for phenotypic analysis of rice disease we built here was combined with quantitative trait loci (QTL) analysis to identify resistance QTL in genetic populations at different growth stages. Three new QTLs were identified, and QTLs identified at different growth stages were inconsistent. QTL analysis combined with UAV high-throughput phenotyping provides new ideas for accelerating disease resistance breeding.
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Affiliation(s)
- Xiulin Bai
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Hui Fang
- Huzhou Institute of Zhejiang University, Huzhou 313000, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Mingzhu Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Qingguan Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Guofeng Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yuzhen Wei
- School of Information Engineering, Huzhou University, Huzhou 313000, China
| | - Yu Tang
- Academy of Interdisciplinary Studies, Guangdong Polytechnic Normal University, Guangzhou 510665, China
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011-3270, USA
| | - Binggan Lou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou 31002, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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16
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Ullah I, Ali H, Mahmood T, Khan MN, Haris M, Shah H, Mihoub A, Jamal A, Saeed MF, Mancinelli R, Radicetti E. Pyramiding of Four Broad Spectrum Bacterial Blight Resistance Genes in Cross Breeds of Basmati Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:46. [PMID: 36616174 PMCID: PMC9824772 DOI: 10.3390/plants12010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Pyramiding of major resistance (R) genes through marker-assisted selection (MAS) is a useful way to attain durable and broad-spectrum resistance against Xanthomonas oryzae pv. oryzae pathogen, the causal agent of bacterial blight (BB) disease in rice (Oryza sativa L.). The present study was designed to pyramid four broad spectrum BB-R genes (Xa4, xa5, xa13 and Xa21) in the background of Basmati-385, an indica rice cultivar with much sought-after qualitative and quantitative grain traits. The cultivar, however, is susceptible to BB and was therefore, crossed with IRBB59 which possesses R genes xa5, xa13 and Xa21, to attain broad and durable resistance. A total of 19 F1 plants were obtained, some of which were backcrossed with Basmati-385 and large number of BC1F1 plants were obtained. In BC1F2 generation, 31 phenotypically superior genotypes having morphological features of Basmati-385, were selected and advanced up to BC1F6 population. Sequence-tagged site (STS)-based MAS was carried out and phenotypic selection was made in each successive generation. In BC1F6 population, potentially homozygous recombinant inbred lines (RILs) from each line were selected and evaluated on the bases of STS evaluation and resistance to local Xanthomonas oryzae pv. oryzae (Xoo) isolates. Line 23 was found pyramided with all four BB-R genes i.e., Xa4, xa5, xa13 and Xa21. Five genotypes including line 8, line 16, line 21, line 27 and line 28 were identified as pyramided with three R genes, Xa4, xa5 and xa13. Pathological study showed that rice lines pyramided with quadruplet or triplet R genes showed the highest level of resistance compared to doublet or singlet R genes. Thus, line 23 with quadruplet, and lines 8, 16, 21, 27, and 28 with triplet R genes, are recommended for replicated yield and resistance trials before release as new rice varieties. Further, traditional breeding coupled with MAS, is a solid way to attain highly effective BB-resistant rice lines with no yield cost.
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Affiliation(s)
- Irfan Ullah
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Hamid Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Tariq Mahmood
- Department of Agriculture, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Mudassar Nawaz Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Muhammad Haris
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Hussain Shah
- Plant Sciences Division, Pakistan Agricultural Research Council Islamabad, Islamabad 45500, Pakistan
| | - Adil Mihoub
- Center for Scientific and Technical Research on Arid Regions, Biophysical Environment Station, Toug-gourt 30240, Algeria
| | - Aftab Jamal
- Department of Soil and Environmental Sciences, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar 25130, Pakistan
| | - Muhammad Farhan Saeed
- Department of Environmental Sciences, Vehari-Campus, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Roberto Mancinelli
- Department of Agricultural and Forestry Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Emanuele Radicetti
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DOCPAS), University of Ferrara, 44121 Ferrara, Italy
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17
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Javed MA, Ali SW, Ashfaq M, Tabassam J, Ali M, IhsanUllah M, Nayab SF, Kaya Y, Khalili E, Ali Q, Yau TE. Molecular profiling of bacterial blight resistance in Malaysian rice cultivars. BRAZ J BIOL 2022; 82:e256189. [PMID: 36541981 DOI: 10.1590/1519-6984.256189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022] Open
Abstract
Bacteria blight is one of the most serious bacterial diseases of rice worldwide. The identification of genetic potential against bacterial blight in the existing rice resources is a prerequisite to develop multigenic resistance to combat the threat of climate change. This investigation was conducted to evaluate alleles variation in 38 Malaysian cultivars using thirteen Simple Sequences Repeats markers and one Sequence Tagged Sites (STS) marker which were reported to be linked with the resistance to bacterial blight. Based on molecular data, a dendrogram was constructed which classified the rice cultivars into seven major clusters at 0.0, 0.28 and 0.3 of similarity coefficient. Cluster 5 was the largest group comprised of ten rice cultivars where multiple genes were identified. However, xa13 could not be detected in the current rice germplasm, whereas xa2 was detected in 25 cultivars. Molecular analysis revealed that Malaysian rice cultivars possess multigenic resistance.
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Affiliation(s)
- M A Javed
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan.,Universiti Teknologi Malaysia - UTM Skudai, Faculty of Science, Department of Biosciences, Johor Bahru, Malaysia
| | - S W Ali
- University of the Punjab, Department of Food Science and Technology, Faculty of Agricultural Sciences, Lahore, Pakistan
| | - M Ashfaq
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - J Tabassam
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - M Ali
- University of the Punjab, Faculty of Agricultural Sciences, Department of Entomology, Lahore, Pakistan
| | - M IhsanUllah
- Cotton Research Institute Multan, Multan, Pakistan
| | - S F Nayab
- Sorghum Research Sub Station, Dera Ghazi Khan, Pakistan
| | - Y Kaya
- Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - E Khalili
- Tarbiat Modarres University, Faculty of Science, Department of Plant Science, Tehran, Iran
| | - Q Ali
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - T E Yau
- Universiti Teknologi Malaysia - UTM Skudai, Faculty of Science, Department of Biosciences, Johor Bahru, Malaysia
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18
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Haridasan A, Thomas J, Raj ED. Deep learning system for paddy plant disease detection and classification. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:120. [PMID: 36399232 DOI: 10.1007/s10661-022-10656-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/15/2022] [Indexed: 06/16/2023]
Abstract
Automatic detection and analysis of rice crop diseases is widely required in the farming industry, which can be utilized to avoid squandering financial and other resources, reduce yield losses, and improve treatment efficiency, resulting in healthier crop output. An automated approach was proposed for accurately detecting and classifying diseases from a supplied photograph. The proposed system for the recognition of rice plant diseases adopts a computer vision-based approach that employs the techniques of image processing, machine learning, and deep learning, reducing the reliance on conventional methods to protect paddy crops from diseases like bacterial leaf blight, false smut, brown leaf spot, rice blast, and sheath rot, the five primary diseases that frequently plague the Indian rice fields. Following image pre-processing, image segmentation is employed to determine the diseased section of the paddy plant, with the diseases listed above being identified purely on the basis of their visual contents. An integration of a support vector machine classifier and convolutional neural networks are used to recognize and classify specific varieties of paddy plant diseases. With ReLU and softmax functions, the suggested deep learning-based strategy attained the highest validation accuracy of 0.9145. Following recognition, a predictive remedy is recommended, which can assist agriculture-related individuals and organizations in taking suitable measures to combat these diseases.
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Affiliation(s)
- Amritha Haridasan
- Department of Computer Science and Engineering, Indian Institute of Information Technology, Kottayam, Kerala, India
| | - Jeena Thomas
- Department of Computer Science and Engineering, Indian Institute of Information Technology, Kottayam, Kerala, India
| | - Ebin Deni Raj
- Department of Computer Science and Engineering, Indian Institute of Information Technology, Kottayam, Kerala, India.
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19
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Photodynamic antibacterial and antibiofilm activity of riboflavin against Xanthomonas oryzae pv oryzae: an ecofriendly strategy to combat bacterial leaf blight (BLB) rice disease. Arch Microbiol 2022; 204:566. [PMID: 35982196 DOI: 10.1007/s00203-022-03183-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 11/02/2022]
Abstract
Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv oryzae (Xoo), is one of the most damaging rice diseases, causing severe production losses depending on the rice variety. The purpose of this study was to develop an antibacterial photodynamic treatment (aPDT) using riboflavin for the treatment of BLB disease. Combining light and riboflavin (RF) therapy significantly reduced bacterial planktonic cells compared to RF alone. Photoactivated riboflavin also decreased biofilm biomass by reducing the number of viable sessile cells and the production of extracellular polymeric substances (EPS). Reactive oxygen species (ROS) levels in Xoo cells treated with photoactivated riboflavin were found to be significantly higher than in cells treated with riboflavin and light individually. Malondialdehyde (MDA) increased greatly in photoactivated riboflavin treated cells, indicating that severe oxidative damage was induced. Subsequently, a reduction in lactate dehydrogenase (LDH) activity in photoactivated riboflavin treated Xoo cells indicates that oxidative stress has disrupted the respiratory system, leading to bacterial cell death. In an ex vivo aPDT assay, photoactivated riboflavin successfully eradicated Xoo on the surface of rice leaves. Photoactivated riboflavin had no side effects on rice seed germination in subsequent trials, indicating that it is safe for agricultural applications. Therefore, all these findings suggest that aPDT is a potential alternative management strategy for BLB disease.
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20
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Chen Y, Li T, Jin Z, Chi YR. New Axially Chiral Molecular Scaffolds with Antibacterial Activities against Xanthomonas oryzae pv. oryzae for Protection of Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6050-6058. [PMID: 35544385 DOI: 10.1021/acs.jafc.2c01407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new class of axially chiral thiazine molecules were constructed and showed promising antibacterial activities against the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo). The axial chiralities of these compounds (R- or S-atropisomer) showed clear impacts on the in vitro inhibitory activities against Xoo. An optimal molecule of this class with the (S)-axially chiral configuration was identified to exhibit inhibitory activity against Xoo with an EC50 value of 4.18 μg/mL. This inhibition efficiency is superior to that of two commercial antibacterial agrochemicals, thiodiazole-copper and bismerthiazol, as the positive controls. This hit compound also performed better than the controls in our in vivo studies. Preliminary mechanistic studies via scanning electron microscopy images showed that our hit compound at a concentration of 10 μg/mL destroyed the bacterial integrity of Xoo. Label-free quantitative proteomics analysis indicated that a total of 366 differentially expressed proteins of the rice plants were significantly influenced in the presence of our hit molecule.
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Affiliation(s)
- Yanlin Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Tingting Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhichao Jin
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Yonggui Robin Chi
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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21
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Park JR, Lee CM, Ji H, Baek MK, Seo J, Jeong OY, Park HS. Characterization and QTL Mapping of a Major Field Resistance Locus for Bacterial Blight in Rice. PLANTS 2022; 11:plants11111404. [PMID: 35684177 PMCID: PMC9182613 DOI: 10.3390/plants11111404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
Bacterial blight (BB) disease, caused by Xanthomonas oryzae pv. oryzae (Xoo), is among the major factors that can cause rice yields to decrease. To address BB disease, researchers have been looking for ways to change pesticides and cultivation methods, but developing resistant cultivars is the most effective method. However, the resistance and genetic factors of cultivars may be destroyed due to the emergence of new Xoo species caused by recent and rapid climate changes. Therefore, breeders need to identify resistance genes that can be sustained during unpredictable climate changes and utilized for breeding. Here, qBBR11, a quantitative trait locus (QTL) for resistance to BB disease, was detected in KJ (Korea Japonica varieties) 11_067 to KJ11_068 on chromosome 11 in a population derived by crossing JJ (Jeonju) 623 and HR(High resistant)27,195, which possess similar genetic backgrounds but different degrees of resistance to BB disease. qBBR11 was reduced from 18.49–18.69 Mbp of chromosome 11 to 200 kbp segment franked. In this region, 16 candidate genes were detected, and we identified 24 moderate-impact variations and four high-impact variations. In particular, high-impact variations were detected in Os11g0517800 which encode the domain region of GCN2 which is the eIF-2-alpha kinase associated with the resistance of abiotic/biotic stress in rice. In JJ623, which is moderately resistant to BB disease, a stop codon was created due to single nucleotide polymorphism (SNP). Therefore, compared with HR27195, JJ623 has weaker resistance to BB disease, though the two have similar genetic backgrounds. The results suggest that variation in the qBBR11 region regulates an important role in improving resistance to BB diseases, and qBBR11 is useful in providing an important resource for marker-assisted selection to improve mechanisms of resistance to BB disease.
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Affiliation(s)
- Jae-Ryoung Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Jeonghwan Seo
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - O-Young Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
- Correspondence: ; Tel.: +82-63-238-5214
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22
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Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices. Genes (Basel) 2022; 13:genes13050830. [PMID: 35627215 PMCID: PMC9141261 DOI: 10.3390/genes13050830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland rice varieties were collected as the initial genetic resource in our breeding program to improve the pathogen resistance and eating and cooking qualities. These varieties were analyzed using a whole-genome SNP array and were clustered into three groups. Further analysis revealed that the favorable alleles of pathogen resistance genes are mostly absent in our collected varieties. However, it showed that most varieties possess favorable alleles of Waxy (Wx) and ALKALI DEGENERATION (ALK), which are able to enhance the eating and cooking qualities. Moreover, only about one fifth of all varieties harbors favorable the allele of fragrance gene Betainealdehyde dehydrogenase (BADH2). Together, these results give an overall view of the genetic constitution of the target traits, which provide useful information for future genetic improvement in breeding practices.
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23
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Shin NH, Han JH, Vo KTX, Seo J, Navea IP, Yoo SC, Jeon JS, Chin JH. Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. RICE (NEW YORK, N.Y.) 2022; 15:22. [PMID: 35397732 PMCID: PMC8994804 DOI: 10.1186/s12284-022-00568-2] [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: 07/12/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC2F5 breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.
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Affiliation(s)
- Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea
| | - Jeonghwan Seo
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Korea
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong, Gyeonggi-do, 17579, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea.
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea.
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24
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Shah S, Tsuneyoshi H, Ichitani K, Taura S. QTL Analysis Revealed One Major Genetic Factor Inhibiting Lesion Elongation by Bacterial Blight (Xanthomonas oryzae pv. oryzae) from a japonica Cultivar Koshihikari in Rice. PLANTS 2022; 11:plants11070867. [PMID: 35406847 PMCID: PMC9003242 DOI: 10.3390/plants11070867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/19/2022]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen that has ravaged the rice industry as the causal agent of bacterial blight (BB) diseases in rice. Koshihikari (KO), an elite japonica cultivar, and ARC7013 (AR), an indica cultivar, are both susceptible to Xoo. Their phenotypic characteristics reveal that KO has shorter lesion length than that of AR. The F2 population from KO × AR results in continuous distribution of lesion length by inoculation of an Xoo race (T7147). Consequently, quantitative trait loci (QTL) mapping of the F2 population is conducted, covering 12 chromosomes with 107 simple sequence repeat (SSR) and insertion/deletion (InDel) genetic markers. Three QTLs are identified on chromosomes 2, 5, and 10. Of them, qXAR5 has the strongest resistance variance effect of 20.5%, whereas qXAR2 and qXAR10 have minor QTL effects on resistance variance, with 3.9% and 2.3%, respectively, for a total resistance variance of 26.7%. The QTLs we examine for this study differ from the loci of BB resistance genes from earlier studies. Our results can help to facilitate understanding of genetic and morphological fundamentals for use in rice breeding programs that are more durable against evolving Xoo pathogens and uncertain climatic temperature.
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Affiliation(s)
- Shameel Shah
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
| | - Hiroaki Tsuneyoshi
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan;
| | - Katsuyuki Ichitani
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan;
- The United Graduate School of Agriculture Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Satoru Taura
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
- Division of Gene Research, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: ; Tel.: +81-0992853590
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25
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Sharma A, Chouhan A, Bhatt T, Kaur A, Minhas AP. Selectable Markers to Marker-Free Selection in Rice. Mol Biotechnol 2022; 64:841-851. [DOI: 10.1007/s12033-022-00460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
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26
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Anik TR, Nihad SAI, Hasan MAI, Hossain MA, Rashid MM, Khan MAI, Halder KP, Latif MA. Exploring of bacterial blight resistance in landraces and mining of resistant gene(s) using molecular markers and pathogenicity approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:455-469. [PMID: 35400880 PMCID: PMC8943093 DOI: 10.1007/s12298-022-01139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Bacterial blight, one of the oldest and most severe diseases of rice poses a major threat to global rice production and food security. Thereafter, sustainable management of this disease has given paramount importance globally. In the current study, we explored 792 landraces to evaluate their disease reaction status against three highly virulent strains (BXo69, BXo87 and BXo93) of Xanthomonas oryzae pv. oryzae (Xoo). Subsequently, we intended to identify the possible candidate resistant (R) genes responsible for the resistant reaction using six STS (Sequence Tagged Site) markers correspond to Xa4, xa5, Xa7, xa13, Xa21 and Xa23 genes and finally, we evaluated morphological variability of the potential bacterial blight resistant germplasm using quantitative traits. Based on pathogenicity test, a single germplasm was found as highly resistant while, 33 germplasm were resistant and 40 were moderately resistant. Further molecular study on these 74 germplasm divulged that 41 germplasm carried Xa4 gene, 15 carried xa5 gene, 62 carried Xa7 gene, 33 carried xa13 gene, and 19 carried Xa23 gene. Only a single germplasm found to carry Xa21 gene. Interestingly, we found a wide range of gene combinations ranged from 2 to 4 genes among the germplasm, where 10 germplasm carried 4 genes, 15 germplasm carried 3 genes and 38 germplasm carried 2 genes of various combinations. Notably, G3 genotype (Acc. No. 4216; highly resistant) having Xa4, Xa7, xa13, Xa21 and G43 genotype (Acc.No. 1523; resistant) having Xa4, xa5, xa13 and Xa23 gene combination being the most effective against all the Xoo strains. Nonetheless, UPGMA dendrogram and heatmap analysis based on quantitative traits identified two clusters viz. cluster-III and cluster-VIII with multiple desired traits. The outcome of this study would enrich and diversify the rice gene pool and would be useful for the development of durable bacterial blight resistant varieties. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01139-x.
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Affiliation(s)
- Touhidur Rahman Anik
- Plant Pathology Division, Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
| | | | - Md. Al-Imran Hasan
- Plant Pathology Division, Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
| | | | - Md. Mamunur Rashid
- Plant Pathology Division, Bangladesh Rice Research Institute, Regional Station, Cumilla, Bangladesh
| | | | - Krishna Pada Halder
- Office of Director Research, Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
| | - Mohammad Abdul Latif
- Plant Pathology Division, Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
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27
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Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools. Mol Biol Rep 2022; 49:5787-5803. [PMID: 35064401 DOI: 10.1007/s11033-021-06815-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/06/2021] [Indexed: 10/19/2022]
Abstract
Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.
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28
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Vishakha K, Das S, Das SK, Banerjee S, Ganguli A. Antibacterial, anti-biofilm, and anti-virulence potential of tea tree oil against leaf blight pathogen Xanthomonas oryzae pv. oryzae instigates disease suppression. Braz J Microbiol 2022; 53:19-32. [PMID: 35001350 PMCID: PMC8882498 DOI: 10.1007/s42770-021-00657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
Abstract
Bacterial leaf blight (BLB) disease, caused by Xanthomonas oryzae pv. oryzae (Xoo), causes major annual economic losses around the world. Inorganic copper compounds and antibiotics are conventionally used to control BLB disease. They often cause environmental pollution, contributing to adverse effects on human health. Therefore, research is now leading to the search for alternative control methods. Tea tree oil (TTO) is obtained from a traditional medicinal plant, Melaleuca alternifolia, with antibacterial properties. In this study, we found that TTO showed antibacterial activity against Xoo with a minimum inhibitory concentration (MIC) of 18 mg/ml. These antagonistic activities were not limited only to planktonic cells, as further studies have shown that TTO effectively eradicated sessile cells of Xoo in both initial and mature biofilms. Furthermore, it was also observed that TTO reduced various key virulence properties of Xoo, such as swimming, swarming motility, and the production of extracellular polymeric substances, xanthomonadin, and exoenzymes. TTO triggered ROS generation with cell membrane damage as an antibacterial mode of action against Xoo. The in silico study revealed that 1,8-cineole of TTO was effectively bound to two essential proteins, phosphoglucomutase and peptide deformylase, responsible for the synthesis of EPS and bacterial survival, respectively. These antibacterial and anti-virulence activities of TTO against Xoo were further confirmed by an ex vivo virulence assay where TTO significantly reduced the lesion length caused by Xoo on rice leaves. All these data concluded that TTO could be a safe, environment-friendly alternative approach for the comprehensive management of BLB disease.
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Affiliation(s)
- Kumari Vishakha
- Department of Microbiology, Techno India University, West Bengal EM-4 Sector V, Kolkata, West Bengal, 700091, India
| | - Shatabdi Das
- Department of Microbiology, Techno India University, West Bengal EM-4 Sector V, Kolkata, West Bengal, 700091, India
| | - Sudip Kumar Das
- Department of Microbiology, Techno India University, West Bengal EM-4 Sector V, Kolkata, West Bengal, 700091, India
| | - Satarupa Banerjee
- Department of Microbiology, Techno India University, West Bengal EM-4 Sector V, Kolkata, West Bengal, 700091, India
| | - Arnab Ganguli
- Department of Microbiology, Techno India University, West Bengal EM-4 Sector V, Kolkata, West Bengal, 700091, India.
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Doni F, Suhaimi NSM, Mispan MS, Fathurrahman F, Marzuki BM, Kusmoro J, Uphoff N. Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies. Int J Mol Sci 2022; 23:737. [PMID: 35054923 PMCID: PMC8775878 DOI: 10.3390/ijms23020737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/03/2022] [Accepted: 01/08/2022] [Indexed: 12/26/2022] Open
Abstract
Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.
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Affiliation(s)
- Febri Doni
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Nurul Shamsinah Mohd Suhaimi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur 50603, Malaysia
| | - F Fathurrahman
- Department of Agrotechnology, Faculty of Agriculture, Universitas Islam Riau, Pekanbaru 28284, Indonesia;
| | - Betty Mayawatie Marzuki
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Joko Kusmoro
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Norman Uphoff
- SRI International Network and Resources Center, Cornell University, Ithaca, NY 14853, USA;
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30
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Xing J, Zhang D, Yin F, Zhong Q, Wang B, Xiao S, Ke X, Wang L, Zhang Y, Zhao C, Lu Y, Chen L, Cheng Z, Chen L. Identification and Fine-Mapping of a New Bacterial Blight Resistance Gene, Xa47(t), in G252, an Introgression Line of Yuanjiang Common Wild Rice ( Oryza rufipogon). PLANT DISEASE 2021; 105:4106-4112. [PMID: 34261357 DOI: 10.1094/pdis-05-21-0939-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F2 population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F2 progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.
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Affiliation(s)
- Jiaxin Xing
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Dunyu Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Fuyou Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Qiaofang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Bo Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Suqin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Xue Ke
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lingxian Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Yun Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Caimei Zhao
- College of Life Science, Yunnan University, Kunming, Yunnan 650091, P.R. China
| | - Yuanda Lu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Zaiquan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lijuan Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
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Dutta M, Saha A, Moin M, Kirti PB. Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:777285. [PMID: 34899804 PMCID: PMC8660974 DOI: 10.3389/fpls.2021.777285] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023]
Abstract
Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Mazahar Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - Pulugurtha Bharadwaja Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, India
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Yazid SN, Ahmad K, Razak MSFA, Rahman ZA, Ramachandran K, Mohamad SNA, Ghaffar MBA. Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach. BRAZ J BIOL 2021; 84:e248359. [PMID: 34730685 DOI: 10.1590/1519-6984.248359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/09/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.
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Affiliation(s)
- S N Yazid
- Universiti Putra Malaysia - UPM, Faculty of Agriculture, Department of Plant Protection, Serdang, Selangor, Malaysia
| | - K Ahmad
- Universiti Putra Malaysia - UPM, Faculty of Agriculture, Department of Plant Protection, Serdang, Selangor, Malaysia.,Universiti Putra Malaysia - UPM, Institute of Tropical Agriculture and Food Security - ITAFoS, Serdang, Selangor, Malaysia
| | - M S F A Razak
- Malaysia Agricultural Research and Development Institute - MARDI, Centre for Marker Discovery and Validation - CMDV, Serdang, Selangor, Malaysia
| | - Z A Rahman
- Malaysia Agricultural Research and Development Institute - MARDI, Centre for Marker Discovery and Validation - CMDV, Serdang, Selangor, Malaysia
| | - K Ramachandran
- Malaysia Agricultural Research and Development Institute - MARDI, Paddy and Rice Research Centre, Kepala Batas, Pulau Pinang, Malaysia
| | - S N A Mohamad
- Universiti Sains Malaysia, School of Biological Science, Penang, Malaysia
| | - M B Ab Ghaffar
- Malaysia Agricultural Research and Development Institute - MARDI, Industrial Crop Research Centre, Kepala Batas, Pulau Pinang, Malaysia
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33
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Thianthavon T, Aesomnuk W, Pitaloka MK, Sattayachiti W, Sonsom Y, Nubankoh P, Malichan S, Riangwong K, Ruanjaichon V, Toojinda T, Wanchana S, Arikit S. Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice ( Oryza sativa L.) against Thai Xoc Strains. Genes (Basel) 2021; 12:1587. [PMID: 34680982 PMCID: PMC8535723 DOI: 10.3390/genes12101587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance.
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Affiliation(s)
- Tripop Thianthavon
- Plant Breeding Program, Faculty of Agriculture at Kamphaeng Saen, Kesetsart University, Nakhon Pathom 73140, Thailand;
| | - Wanchana Aesomnuk
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Mutiara K. Pitaloka
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
| | - Wannapa Sattayachiti
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Yupin Sonsom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Phakchana Nubankoh
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand;
| | - Kanamon Riangwong
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom 73000, Thailand;
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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Du XX, Park JR, Wang XH, Jang YH, Kim EG, Lee GS, Kim KM. Applying HPLC to Screening QTLs for BLB Resistance in Rice. PLANTS 2021; 10:plants10102145. [PMID: 34685953 PMCID: PMC8537431 DOI: 10.3390/plants10102145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/28/2022]
Abstract
Bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae and is a major cause of rice yield reductions around the world. When diseased, plants produce a variety of metabolites to resist pathogens. In this study, the various defense metabolites were quantified using high-performance liquid chromatography (HPLC) after Xoo inoculation in a 120 Cheongcheong/Nagdong double haploid (CNDH) population. Quantitative trait locus (QTL) mapping was conducted using the concentration of the plant defense metabolites. HPLC analyzes the concentration of substances according to the severity of disease symptoms. Searching for BLB resistance candidate genes by applying this analysis method is very effective when mapping related genes. These resistance genes can be mapped directly to the causative pathogens. A total of 17 metabolites were detected by means of HPLC analysis after Xoo inoculation in the 120 CNDH population. QTL mapping of the metabolite concentrations resulted in the detection of the BLB resistance candidate gene, OsWRKYq6, in RM3343 of chromosome 6. OsWRKYq6 has a very high homology sequence with WRKY transcription factor 39, and when inoculated with Xoo, the relative expression level of the resistant population was higher than that of the susceptible population. Resistance genes have previously been detected using only phenotypic change data. In this study, resistance candidate genes were detected using the concentration of metabolites produced in plants after inoculation with pathogens. This newly developed analysis method can be used to effectively detect and identify genes directly involved in disease resistance for future studies.
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Affiliation(s)
- Xiao-Xuan Du
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
| | - Jae-Ryoung Park
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Xiao-Han Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea;
| | - Yoon-Hee Jang
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Gang-Seob Lee
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
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Janaki Ramayya P, Vinukonda VP, Singh UM, Alam S, Venkateshwarlu C, Vipparla AK, Dixit S, Yadav S, Abbai R, Badri J, T. R, Phani Padmakumari A, Singh VK, Kumar A. Marker-assisted forward and backcross breeding for improvement of elite Indian rice variety Naveen for multiple biotic and abiotic stress tolerance. PLoS One 2021; 16:e0256721. [PMID: 34473798 PMCID: PMC8412243 DOI: 10.1371/journal.pone.0256721] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/13/2021] [Indexed: 11/18/2022] Open
Abstract
The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY1.1, qDTY2.2 and qDTY4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.
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Affiliation(s)
| | | | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Shamshad Alam
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Challa Venkateshwarlu
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research (IIRR), Rajendra Nagar, Hyderabad, India
| | - Ram T.
- ICAR-Indian Institute of Rice Research (IIRR), Rajendra Nagar, Hyderabad, India
| | | | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
- * E-mail:
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Liu J, Chia SL, Tan GH. Isolation and Characterization of Novel Phages Targeting Xanthomonas oryzae: Culprit of Bacterial Leaf Blight Disease in Rice. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:142-151. [PMID: 36161243 PMCID: PMC9041505 DOI: 10.1089/phage.2021.0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Bacterial leaf blight (BLB) disease caused 80% of disease incidence in paddy in Kedah and Selangor states of Malaysia. The pathogenic bacterium, Xanthomonas oryzae pv. oryzae (Xoo), is one of the destructive pathogens infecting lowland irrigated and rainfed paddy in Asia's tropical and temperate environments. Bacteriophages (or phages) have been proposed to control the pathogen due to their efficacy and safety aspects. Material and Methods: In this study, a total of 70 Xoo-phages were isolated from termite which living in rice-growing area. Results: 2 lytic phages NΦ-1 and NΦ-3 were selected due to the high titer of the virus. Electron microscopic analysis showed that those phages belonged to the family Podoviridae, order Caudovirales with short noncontracted tails. Moreover, these phages have a narrow host range specifically target Xoo with a higher burst size. Whole-genome sequencing showed that the Xoo-phage NΦ-1 and NΦ-3 consists of a linear double-stranded DNA molecule of length 41,151 and 38,454 bp, respectively. Conclusion: This study successfully characterized two novel Xanthomonas phages and their potential as antimicrobial agents against BLB disease in rice.
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Affiliation(s)
- Jian Liu
- Microbial Culture Collection Unit, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Suet Lin Chia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Geok Hun Tan
- Microbial Culture Collection Unit, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
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Shaw RK, Shen Y, Zhao Z, Sheng X, Wang J, Yu H, Gu H. Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower ( Brassica oleracea var. botrytis L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667757. [PMID: 34354719 PMCID: PMC8329456 DOI: 10.3389/fpls.2021.667757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis L.) is one of the important, nutritious and healthy vegetable crops grown and consumed worldwide. But its production is constrained by several destructive fungal diseases and most importantly, downy mildew leading to severe yield and quality losses. For sustainable cauliflower production, developing resistant varieties/hybrids with durable resistance against broad-spectrum of pathogens is the best strategy for a long term and reliable solution. Identification of novel resistant resources, knowledge of the genetics of resistance, mapping and cloning of resistance QTLs and identification of candidate genes would facilitate molecular breeding for disease resistance in cauliflower. Advent of next-generation sequencing technologies (NGS) and publishing of draft genome sequence of cauliflower has opened the flood gate for new possibilities to develop enormous amount of genomic resources leading to mapping and cloning of resistance QTLs. In cauliflower, several molecular breeding approaches such as QTL mapping, marker-assisted backcrossing, gene pyramiding have been carried out to develop new resistant cultivars. Marker-assisted selection (MAS) would be beneficial in improving the precision in the selection of improved cultivars against multiple pathogens. This comprehensive review emphasizes the fascinating recent advances made in the application of molecular breeding approach for resistance against an important pathogen; Downy Mildew (Hyaloperonospora parasitica) affecting cauliflower and Brassica oleracea crops and highlights the QTLs identified imparting resistance against this pathogen. We have also emphasized the critical research areas as future perspectives to bridge the gap between availability of genomic resources and its utility in identifying resistance genes/QTLs to breed downy mildew resistant cultivars. Additionally, we have also discussed the challenges and the way forward to realize the full potential of molecular breeding for downy mildew resistance by integrating marker technology with conventional breeding in the post-genomics era. All this information will undoubtedly provide new insights to the researchers in formulating future breeding strategies in cauliflower to develop durable resistant cultivars against the major pathogens in general and downy mildew in particular.
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Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Ageing Effects, Generation Means, and Path Coefficient Analyses on High Kernel Elongation in Mahsuri Mutan and Basmati 370 Rice Populations. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8350136. [PMID: 34095311 PMCID: PMC8164538 DOI: 10.1155/2021/8350136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/10/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022]
Abstract
High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.
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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10040716. [PMID: 33917162 PMCID: PMC8067883 DOI: 10.3390/plants10040716] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
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Msami JA, Kawaguchi Y, Ichitani K, Taura S. Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24. BREEDING SCIENCE 2021; 71:144-154. [PMID: 34377062 PMCID: PMC8329881 DOI: 10.1270/jsbbs.20104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 06/13/2023]
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F2 population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F2 population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F2 population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.
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Affiliation(s)
- Jessey Anderson Msami
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yoshiki Kawaguchi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Satoru Taura
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Division of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Identification of Bacterial Blight Resistance Loci in Rice ( Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study. PLANTS 2021; 10:plants10030518. [PMID: 33802191 PMCID: PMC8001028 DOI: 10.3390/plants10030518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1–6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.
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Li C, Zhang J, Ren Z, Xie R, Yin C, Ma W, Zhou F, Chen H, Lin Y. Development of 'multiresistance rice' by an assembly of herbicide, insect and disease resistance genes with a transgene stacking system. PEST MANAGEMENT SCIENCE 2021; 77:1536-1547. [PMID: 33201594 DOI: 10.1002/ps.6178] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Weeds, diseases and pests pose serious threats to rice production and cause significant economic losses. Cultivation of rice varieties with resistance to herbicides, diseases and pests is believed to be the most economical and environmentally friendly method to deal with these problems. RESULTS In this study, a highly efficient transgene stacking system was used to assembly the synthetic glyphosate-tolerance gene (I. variabilis-EPSPS*), lepidopteran pest resistance gene (Cry1C*), brown planthopper resistance genes (Bph14* and OsLecRK1*), bacterial blight resistance gene (Xa23*) and rice blast resistance gene (Pi9*) onto a transformable artificial chromosome vector. The construct was transferred into ZH11 (a widely used japonica rice cultivar Zhonghua 11) via Agrobacterium-mediated transformation and 'multiresistance rice' (MRR) with desirable agronomic traits was obtained. The results showed that MRR had significantly improved resistance to glyphosate, borers, brown planthopper, bacterial blight and rice blast relative to the recipient cultivar ZH11. Besides, under the natural occurrence of pests and diseases in the field, the yield of MRR was significantly higher than that of ZH11. CONCLUSION A multigene transformation strategy was employed to successfully develop rice lines with multiresistance to glyphosate, borers, brown planthopper, bacterial blight and rice blast, and the obtained MRR is expected to have great application potential. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Chuanxu Li
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhiyong Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rong Xie
- Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Luzhou Branch of National Rice Improvement Center, Deyang, China
| | - Changxi Yin
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weihua Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Lu J, Wang C, Zeng D, Li J, Shi X, Shi Y, Zhou Y. Genome-Wide Association Study Dissects Resistance Loci against Bacterial Blight in a Diverse Rice Panel from the 3000 Rice Genomes Project. RICE (NEW YORK, N.Y.) 2021; 14:22. [PMID: 33638765 PMCID: PMC7914325 DOI: 10.1186/s12284-021-00462-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 02/12/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL). RESULTS BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5-11.1 was validated as positively regulating resistance against strain C5. CONCLUSIONS Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.
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Affiliation(s)
- Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaorong Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Muhammad I, Musa I, Ahmed M, Jatto MI, Yusuf BR. Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9111411. [PMID: 33105815 PMCID: PMC7690635 DOI: 10.3390/plants9111411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/28/2020] [Accepted: 10/20/2020] [Indexed: 05/30/2023]
Abstract
The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes-Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.
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Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Isma’ila Muhammad
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Ibrahim Musa
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muideen Ahmed
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muhammed Itopa Jatto
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Bashir Rini Yusuf
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
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Shobha B, Lakshmeesha TR, Ansari MA, Almatroudi A, Alzohairy MA, Basavaraju S, Alurappa R, Niranjana SR, Chowdappa S. Mycosynthesis of ZnO Nanoparticles Using Trichoderma spp. Isolated from Rhizosphere Soils and Its Synergistic Antibacterial Effect against Xanthomonas oryzae pv. oryzae. J Fungi (Basel) 2020; 6:jof6030181. [PMID: 32962271 PMCID: PMC7558757 DOI: 10.3390/jof6030181] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/22/2023] Open
Abstract
The Plant Growth Promoting Fungi (PGPF) is used as a source of biofertilizers due to their production of secondary metabolites and beneficial effects on plants. The present work is focused on the co-cultivation of Trichoderma spp. (T. harzianum (PGT4), T. reesei (PGT5) and T. reesei (PGT13)) and the production of secondary metabolites from mono and co-culture and mycosynthesis of zinc oxide nanoparticles (ZnO NPs), which were characterized by a UV visible spectrophotometer, Powder X-ray Diffraction (PXRD), Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy (SEM) with Energy Dispersive Spectroscopy (EDAX) and Transmission Electron Microscope (TEM) and Selected Area (Electron) Diffraction (SAED) patterns. The fungal secondary metabolite crude was extracted from the mono and co-culture of Trichoderma spp. And were analyzed by GC-MS, which was further subjected for antibacterial activity against Xanthomonas oryzae pv. Oryzae, the causative organism for Bacterial Leaf Blight (BLB) in rice. Our results showed that the maximum zone of inhibition was recorded from the co-culture of Trichoderma spp. rather than mono cultures, which indicates that co-cultivation of beneficial fungi can stimulate the synthesis of novel secondary metabolites better than in monocultures. ZnO NPs were synthesized from fungal secondary metabolites of mono cultures of Trichoderma harzianum (PGT4), Trichoderma reesei (PGT5), Trichoderma reesei (PGT13) and co-culture (PGT4 + PGT5 + PGT13). These ZnO NPs were checked for antibacterial activity against Xoo, which was found to be of a dose-dependent manner. In summary, the biosynthesized ZnO NPs and secondary metabolites from co-culture of Trichoderma spp. are ecofriendly and can be used as an alternative for chemical fertilizers in agriculture.
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Affiliation(s)
- Balagangadharaswamy Shobha
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru 560056, India; (B.S.); (S.B.); (R.A.)
| | - Thimappa Ramachandrappa Lakshmeesha
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru 560056, India; (B.S.); (S.B.); (R.A.)
- Correspondence: (T.R.L.); (A.A.); (S.C.)
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim, 51431 Saudi Arabia;
- Correspondence: (T.R.L.); (A.A.); (S.C.)
| | - Mohammad A. Alzohairy
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim, 51431 Saudi Arabia;
| | - Sumanth Basavaraju
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru 560056, India; (B.S.); (S.B.); (R.A.)
| | - Ramesha Alurappa
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru 560056, India; (B.S.); (S.B.); (R.A.)
| | | | - Srinivas Chowdappa
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru 560056, India; (B.S.); (S.B.); (R.A.)
- Correspondence: (T.R.L.); (A.A.); (S.C.)
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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Joshi JB, Arul L, Ramalingam J, Uthandi S. Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management. J Biosci 2020. [DOI: 10.1007/s12038-020-00085-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
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Sarif HM, Rafii MY, Ramli A, Oladosu Y, Musa HM, Rahim HA, Zuki ZM, Chukwu SC. Genetic diversity and variability among pigmented rice germplasm using molecular marker and morphological traits. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1804451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Hamidah Mohd Sarif
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Mohd Y. Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Asfaliza Ramli
- Rice Research Center, Malaysian Agriculture and Research Development Institute (MARDI), Serdang, Selangor, Malaysia
| | - Yusuff Oladosu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Hanafi M. Musa
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Harun A. Rahim
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency Bangi, Selangor, Malaysia
| | - Zakiah Mohd Zuki
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
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Li Y, Liu Y, Yang D, Jin Q, Wu C, Cui J. Multifunctional molybdenum disulfide-copper nanocomposite that enhances the antibacterial activity, promotes rice growth and induces rice resistance. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122551. [PMID: 32272326 DOI: 10.1016/j.jhazmat.2020.122551] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 06/11/2023]
Abstract
Molybdenum disulfide sheets loaded with copper nanoparticles (MoS2-CuNPs) was prepared and its antibacterial activity against phytopathogen Xanthomonas oryzae pv. oryzae (Xoo) was investigated in vitro and in vivo for the first time. In a 2 h co-incubation, MoS2-CuNPs exhibited 19.2 times higher antibacterial activity against Xoo cells than a commercial copper bactericide (Kocide 3000). In the detached leaf experiment, the disease severity decreased from 86.25 % to 7.5 % in the MoS2-CuNPs treated rice leaves. The results further demonstrated that foliar application of MoS2-CuNPs could form a protective film and increase the density of trichome on the surface of rice leaves, finally prevent the infection of Xoo cells. This was probably due to the synergistic effect of MoS2-CuNPs. Additionally, foliar application of MoS2-CuNPs (4-32 μg/mL) increased obviously the content of Mo and chlorophyll (up 30.85 %), and then improved the growth of rice seedlings. Furthermore, the obtained MoS2-CuNPs could activate the activities of the antioxidant enzymes in rice, indicating higher resistance of rice under abiotic/biotic stresses. The multifunctional MoS2-CuNPs with superior antibacterial activity provided a promising alternative to the traditional antibacterial agents and had great potential in plant protection.
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Affiliation(s)
- Yadong Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China; Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Yingliang Liu
- Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Desong Yang
- College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China; Engineering Research Center of Materials-Oriented Chemical Engineering of Xinjiang Bintuan, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Qian Jin
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Cailan Wu
- College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China; Engineering Research Center of Materials-Oriented Chemical Engineering of Xinjiang Bintuan, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Jianghu Cui
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China.
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