1
|
Gandikota M, Krishnakanth Yadav T, Maram RR, Kalluru S, Sena MB, Siddiq EA, Kalinati Narasimhan Y, Vemireddy LR, Ghanta A. Development of activation-tagged gain-of-functional mutants in indica rice line (BPT 5204) for sheath blight resistance. Mol Biol Rep 2024; 51:381. [PMID: 38430361 DOI: 10.1007/s11033-023-09194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024]
Abstract
BACKGROUND The development of sheath blight (ShB) resistance varieties has been a challenge for scientists for long time in rice. Activation tagging is an efficient gain-of-function mutation approach to create novel phenotypes and to identify their underlying genes. In this study, a mutant population was developed employing activation tagging in the recalcitrant indica rice (Oryza sativa L.) cv. BPT 5204 (Samba Mahsuri) through activation tagging. METHODS AND RESULTS In this study, we have generated more than 1000 activation tagged lines in indica rice, from these mutant population 38 (GFP- RFP+) stable Ds plants were generated through germinal transposition at T2 generation based on molecular analysis and seeds selected on hygromycin (50 mg/L) containing medium segregation analyses confirmed that the transgene inherited as mendelian segregation ratio of 3:1 (3 resistant: 1 susceptible). Of them, five stable activation tagged Ds lines (M-Ds-1, M-Ds-2, M-Ds-3, M-Ds-4 and M-Ds-5) were selected based on phenotypic observation through screening for sheath blight (ShB) resistance caused by fungal pathogen Rhizoctonia solani (R. solani),. Among them, M-Ds-3 and M-Ds-5 lines showed significant resistance for ShB over other tagged lines and wild type (WT) plants. Furthermore, analysed for launch pad insertion through TAIL-PCR results and mapped on corresponding rice chromosomes. Flanking sequence and gene expression analysis revealed that the upregulation of glycoside hydrolase-OsGH or similar to Class III chitinase homologue (LOC_Os08g40680) in M-Ds-3 and a hypothetical protein gene (LOC_Os01g55000) in M-Ds-5 are potential candidate genes for sheath blight resistance in rice. CONCLUSION In the present study, we developed Ac-Ds based ShB resistance gain-of-functional mutants through activation tagging in rice. These activation tagged mutant lines can be excellent sources for the development of ShB resistant cultivars in rice.
Collapse
Affiliation(s)
- Mahendranath Gandikota
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - T Krishnakanth Yadav
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | | | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - M Balachandran Sena
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - E A Siddiq
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Yamini Kalinati Narasimhan
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya N.G. Ranaga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500030, India.
| |
Collapse
|
2
|
Jimmy JL, Karn R, Kumari S, Sruthilaxmi CB, Pooja S, Emerson IA, Babu S. Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes. Funct Integr Genomics 2023; 23:249. [PMID: 37474674 DOI: 10.1007/s10142-023-01167-0] [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: 04/28/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
Collapse
Affiliation(s)
- John Lilly Jimmy
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Rohit Karn
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sweta Kumari
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | | | - Singh Pooja
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Isaac Arnold Emerson
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, India
| |
Collapse
|
3
|
Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [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: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
Collapse
Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| |
Collapse
|
4
|
Ma W, Zhang C, Zhang W, Sheng P, Xu M, Ni Y, Chen M, Cheng B, Zhang X. TMT-Based Comparative Peptidomics Analysis of Rice Seedlings under Salt Stress: An Accessible Method to Explore Plant Stress-Tolerance Processing. J Proteome Res 2022; 21:2905-2919. [PMID: 36351196 DOI: 10.1021/acs.jproteome.2c00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rice (Oryza sativa L.) is an important staple crop, particularly in Asia, and abiotic stress conditions easily reduce its yields. Salt stress is one of the critical factors affecting rice growth and yield. In this study, a tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for peptidomics analysis. A total of 911 and 1263 nonredundant peptides were identified in two pooled shoot tissue samples, while there were 770 and 672 nonredundant peptides in two pooled root tissue samples, respectively. Compared with the control groups, dozens to hundreds of differentially expressed peptides (DEPs) were characterized in all treatment groups. To explore the potential functions of these DEPs, we analyzed the basic characteristics of DEPs and further analyzed the annotated Gene Ontology terms according to their precursor proteins. Several DEP precursor proteins were closely related to the response to salt stress, and some were derived from the functional domains of their corresponding precursors. The germination rate and cotyledon greening rate of transgenic Arabidopsis expressing two DEPs, OsSTPE2 and OsSTPE3, were significantly enhanced under salt stress. The described workflow enables the discovery of a functional pipeline for the characterization of the plant peptidome and reveals two new plant peptides that confer salinity tolerance to plants. Data are available via ProteomeXchange with identifier PXD037574.
Collapse
Affiliation(s)
- Wanlu Ma
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Chenchen Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Wei Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Pijie Sheng
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Minyan Xu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Ying Ni
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Meng Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Beijiu Cheng
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China.,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Xin Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China.,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| |
Collapse
|
5
|
Samal P, Molla KA, Bal A, Ray S, Swain H, Khandual A, Sahoo P, Behera M, Jaiswal S, Iquebal A, Chakraborti M, Behera L, Kar MK, Mukherjee AK. Comparative transcriptome profiling reveals the basis of differential sheath blight disease response in tolerant and susceptible rice genotypes. PROTOPLASMA 2022; 259:61-73. [PMID: 33811539 DOI: 10.1007/s00709-021-01637-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/17/2021] [Indexed: 05/27/2023]
Abstract
Rice sheath blight (ShB) disease, caused by the fungal pathogen Rhizoctonia solani AG1-IA, is one of the devastating diseases and causes severe yield losses all over the world. No completely resistant germplasm is known till now, and as a result, the progress in resistance breeding is unsatisfactory. Basic studies to identify candidate genes, QTLs, and to better understand the host-pathogen interaction are also scanty. In this study, we report the identification of a new ShB-tolerant rice germplasm, CR 1014. Further, we investigated the basis of tolerance by exploring the disease responsive differentially expressed transcriptome and comparing them with that of a susceptible variety, Swarna-Sub1. A total of 815 and 551 genes were found to be differentially regulated in CR 1014 and Swarna-Sub1, respectively, at two different time points. The result shows that the ability to upregulate genes for glycosyl hydrolase, secondary metabolite biosynthesis, cytoskeleton and membrane integrity, the glycolytic pathway, and maintaining photosynthesis make CR 1014 a superior performer in resisting the ShB pathogen. We discuss several putative candidate genes for ShB resistance. The present study, for the first time, revealed the basis of ShB tolerance in the germplasm CR1014 and should prove to be particularly valuable in understanding molecular response to ShB infection. The knowledge could be utilized to devise strategies to manage the disease better.
Collapse
Affiliation(s)
| | | | - Archana Bal
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Soham Ray
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
- ICAR-Central Research Institute for Jute and Allied Fibers, Barrackpore, Kolkata, West Bengal, India
| | - Harekrushna Swain
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Ansuman Khandual
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Pritiranjan Sahoo
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Motilal Behera
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistical Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Asif Iquebal
- ICAR-Indian Agricultural Statistical Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Mridul Chakraborti
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Meera K Kar
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Arup K Mukherjee
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India.
| |
Collapse
|
6
|
Taranto F, Mangini G, Miazzi MM, Stevanato P, De Vita P. Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat. Genomics 2021; 113:2989-3001. [PMID: 34182080 DOI: 10.1016/j.ygeno.2021.06.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/14/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023]
Abstract
Studying and understanding the genetic basis of polyphenol oxidases (PPO)-related traits plays a crucial role in genetic improvement of crops. A tetraploid wheat collection (T. turgidum ssp., TWC) was analyzed using the 90K wheat SNP iSelect assay and phenotyped for PPO activity. A total of 21,347 polymorphic SNPs were used to perform genome-wide association analysis (GWA) in TWC and durum wheat sub-groups, detecting 23 and 85 marker-trait associations (MTA). In addition, candidate genes responsible for PPO activity were predicted. Based on the 23 MTAs detected in TWC, two haplotypes associated with low and high PPO activity were identified. Four SNPs were developed and validated providing one reliable marker (IWB75732) for marker assisted selection. The 23 MTAs were used to evaluate the genetic divergence (FST > 0.25) between the T. turgidum subspecies, providing new information important for understanding the domestication process of Triticum turgidum ssp. and in particular of ssp. carthlicum.
Collapse
Affiliation(s)
- Francesca Taranto
- National Research Council (CNR), Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, NA, Italy.
| | - Giacomo Mangini
- National Research Council (CNR), Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, BA, Italy.
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
| | | | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy
| |
Collapse
|
7
|
H. D. Sagawa C, de A. B. Assis R, Zaini PA, Wilmarth PA, Phinney BS, Moreira LM, Dandekar AM. Proteome Analysis of Walnut Bacterial Blight Disease. Int J Mol Sci 2020; 21:E7453. [PMID: 33050347 PMCID: PMC7593943 DOI: 10.3390/ijms21207453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
The interaction between the plant host, walnut (Juglans regia; Jr), and a deadly pathogen (Xanthomonas arboricola pv. juglandis 417; Xaj) can lead to walnut bacterial blight (WB), which depletes walnut productivity by degrading the nut quality. Here, we dissect this pathosystem using tandem mass tag quantitative proteomics. Walnut hull tissues inoculated with Xaj were compared to mock-inoculated tissues, and 3972 proteins were identified, of which 3296 are from Jr and 676 from Xaj. Proteins with differential abundance include oxidoreductases, proteases, and enzymes involved in energy metabolism and amino acid interconversion pathways. Defense responses and plant hormone biosynthesis were also increased. Xaj proteins detected in infected tissues demonstrate its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Secreted proteases and extracellular secretion apparatus such as type IV pilus for twitching motility and type III secretion effectors indicate putative factors recognized by the host. Taken together, these results suggest intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Our results provide insights into molecular mechanisms and highlight potential molecular tools for early detection and disease control strategies.
Collapse
Affiliation(s)
- Cíntia H. D. Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA;
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| |
Collapse
|