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Singh K, Sharma P, Jaiswal S, Mishra P, Maurya R, Muthusamy SK, Saharan MS, Jasrotia RS, Kumar J, Mishra S, Sheoran S, Singh GP, Angadi UB, Rai A, Tiwari R, Iquebal MA, Kumar D. Genome and transcriptome based comparative analysis of Tilletia indica to decipher the causal genes for pathogenicity of Karnal bunt in wheat. BMC PLANT BIOLOGY 2024; 24:676. [PMID: 39009989 PMCID: PMC11251232 DOI: 10.1186/s12870-024-04959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/28/2024] [Indexed: 07/17/2024]
Abstract
Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR ( http://backlin.cabgrid.res.in/tiger/ ), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.
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Affiliation(s)
- Kalpana Singh
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Pallavi Mishra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ranjeet Maurya
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Senthilkumar K Muthusamy
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala, India
| | - M S Saharan
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jitender Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Shefali Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - U B Angadi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India.
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Manakkatt HM, Gurjar MS, Saharan MS, Aggarwal R. Expression analysis of genes involved in teliospores germination of Tilletia indica inciting Karnal bunt of wheat. Mol Biol Rep 2024; 51:726. [PMID: 38856802 DOI: 10.1007/s11033-024-09690-4] [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: 01/22/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Karnal bunt of wheat is an important quarantine disease, incited by Tilletia indica. It limits India's trade in wheat export. The teliospores are major source of inoculum to initiate and spread the Karnal bunt disease. The study aimed to identify the germination-related genes in the teliospores of T. indica. METHODS AND RESULTS The candidate genes in the teliospores germination were identified through the differential gene expression analysis with suitable bioinformatics analysis. Keeping in soil-borne nature of fungi, the teliospores of T. indica (2015 and 2018) were subjected to the qPCR analysis. 20 candidate genes were identified having role in germination of teliospores of T. indica. Twenty genes, viz. Ti9297 (9.31, 7.87-fold), Ti8696 (5.13, 6.54-fold), Ti7699 (8.9, 7.7-fold), Ti7858 (10.33, 6.21-fold), Ti7954 (7.46, 5.54-fold), Ti7739 (5.46, 6.46-fold), Ti9665 (10.74, 7.64-fold), Ti9335 (6.75, 4.36-fold), Ti8396 (9.35, 7.72-fold), Ti8126 (8.87, 11.31-fold), Ti7326 (6.04, 7.7-fold), Ti10208 (13.83, 5.81-fold), Ti12356 (7.83, 8.02-fold), Ti14271 (9.98, 6.32-fold), Ti9234 (11.2, 8.72-fold), Ti 8876 (6.47, 3.55-fold), Ti 10,606 (4.97, 2.35-fold), Ti7758 (10.33, 8.78-fold), Ti4692 (6.89, 9.88-fold), and Ti3932 (5.77, 4.5-fold) were found highly expressed in the germinating teliospores of 2015 and 2018, respectively. Eight genes (Ti508, Ti4152, Ti5346, Ti2375, Ti3739, Ti1134, Ti4399, and Ti4422) were downregulated in the germinating teliospores but these eight genes were showed higher expression in the dormant teliospores. CONCLUSIONS Twenty candidate genes were upregulated in the germinating teliospores are supposed to be involved in the process of germination. Eight genes were downregulated which were related to the process of the dormancy of teliospores. The study will be helpful to devise the newer management strategies for Karnal bunt disease of wheat.
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Affiliation(s)
- Haritha Mohan Manakkatt
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- ICAR-Mahatma Gandhi Integrated Farming Research Institute, Piprakothi, Motihari, Bihar, 845429, India
| | - Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Basak P, Gurjar MS, Kumar TPJ, Kashyap N, Singh D, Jha SK, Saharan MS. Transcriptome analysis of Bipolaris sorokiniana - Hordeum vulgare provides insights into mechanisms of host-pathogen interaction. Front Microbiol 2024; 15:1360571. [PMID: 38577688 PMCID: PMC10993733 DOI: 10.3389/fmicb.2024.1360571] [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: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Spot blotch disease incited by Bipolaris sorokiniana severely affects the cultivation of barley. The resistance to B. sorokiniana is quantitative in nature and its interaction with the host is highly complex which necessitates in-depth molecular analysis. Thus, the study aimed to conduct the transcriptome analysis to decipher the mechanisms and pathways involved in interactions between barley and B. sorokiniana in both the resistant (EC0328964) and susceptible (EC0578292) genotypes using the RNA Seq approach. In the resistant genotype, 6,283 genes of Hordeum vulgare were differentially expressed out of which 5,567 genes were upregulated and 716 genes were downregulated. 1,158 genes of Hordeum vulgare were differentially expressed in the susceptible genotype, out of which 654 genes were upregulated and 504 genes were downregulated. Several defense-related genes like resistant gene analogs (RGAs), disease resistance protein RPM1, pathogenesis-related protein PRB1-2-like, pathogenesis-related protein 1, thaumatin-like protein PWIR2 and defensin Tm-AMP-D1.2 were highly expressed exclusively in resistant genotype only. The pathways involved in the metabolism and biosynthesis of secondary metabolites were the most prominently represented pathways in both the resistant and susceptible genotypes. However, pathways involved in MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction were highly enriched in resistant genotype. Further, a higher number of pathogenicity genes of B. sorokiniana was found in response to the susceptible genotype. The pathways encoding for metabolism, biosynthesis of secondary metabolites, ABC transporters, and ubiquitin-mediated proteolysis were highly expressed in susceptible genotype in response to the pathogen. 14 and 11 genes of B. sorokiniana were identified as candidate effectors from susceptible and resistant host backgrounds, respectively. This investigation will offer valuable insights in unraveling the complex mechanisms involved in barley- B. sorokiniana interaction.
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Affiliation(s)
- Poulami Basak
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Natasha Kashyap
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Su S, Zhang Z, Shen T, Chen J, Liu Q. Kernel Transcriptome Profiles of Susceptible Wheat Genotypes in Response to Wheat Dwarf Bunt. Int J Mol Sci 2023; 24:17281. [PMID: 38139108 PMCID: PMC10744332 DOI: 10.3390/ijms242417281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/21/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Wheat dwarf bunt is caused by Tilletia controversa J. G. Kühn (TCK), which is a serious fungal diseases affecting kernels of wheat. In order to identify candidate genes involved in the abnormal development of kernels in wheat, we used RNA sequencing technology to analyze the transcriptome of the abnormal and healthy kernels of a susceptible variety (Yili053) at the mid-filling stage, late-filling stage, and maturity stage, respectively. The differentially expressed genes (DEGs) were analyzed, and there were 3930 DEGs, 28,422 DEGs, and 20,874 DEGs found at the mid-filling stage, late-filling stage, and maturity stage in Yili053, respectively. A total of 1592 DEGs (506 DEGs up-regulated) showed continuously differential expression in the three stages. Gene ontology analysis showed that these DEGs were related to biological regulation, metabolic processes, and the response to stimulus. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs play major roles in pathways including photosynthesis, carbon metabolism, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. Moreover, we predicted that 13 MADS-MIKC transcription factors, which were continuously up-regulated, were crucial for regulating the maturation and senescence of eukaryotes. Some 21 genes related to the plant hormone signaling transduction pathway and 61 genes related to the response to stimulus were analyzed. A total of 26 of them were successful validated with a qPCR analysis. These genes were thought to be involved in the abnormal development of kernels infected by TCK. A transcriptomics analysis of wheat kernels in response to TCK will contribute to understanding the interaction of TCK and wheat, and may provide a basis for knowledge of molecular events in the abnormal development of kernels, which will be helpful for more efficient TCK management.
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Affiliation(s)
- Shenqiang Su
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (S.S.); (Z.Z.); (T.S.); (J.C.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Zihao Zhang
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (S.S.); (Z.Z.); (T.S.); (J.C.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Tong Shen
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (S.S.); (Z.Z.); (T.S.); (J.C.)
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Chen
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (S.S.); (Z.Z.); (T.S.); (J.C.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Qi Liu
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (S.S.); (Z.Z.); (T.S.); (J.C.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
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Wang A, Shu X, Xu D, Jiang Y, Liang J, Yi X, Zhu J, Yang F, Jiao C, Zheng A, Yin D, Li P. Understanding the Rice Fungal Pathogen Tilletia horrida from Multiple Perspectives. RICE (NEW YORK, N.Y.) 2022; 15:64. [PMID: 36522490 PMCID: PMC9755434 DOI: 10.1186/s12284-022-00612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Rice kernel smut (RKS), caused by the fungus Tilletia horrida, has become a major disease in rice-growing areas worldwide, especially since the widespread cultivation of high-yielding hybrid rice varieties. The disease causes a significant yield loss during the production of rice male sterile lines by producing masses of dark powdery teliospores. This review mainly summarizes the pathogenic differentiation, disease cycle, and infection process of the T. horrida, as well as the decoding of the T. horrida genome, functional genomics, and effector identification. We highlight the identification and characterization of virulence-related pathways and effectors of T. horrida, which could foster a better understanding of the rice-T. horrida interaction and help to elucidate its pathogenicity molecular mechanisms. The multiple effective disease control methods for RKS are also discussed, included chemical fungicides, the mining of resistant rice germplasms/genes, and the monitoring and early warning signs of this disease in field settings.
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Affiliation(s)
- Aijun Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Xinyue Shu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Deze Xu
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Yuqi Jiang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Juan Liang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Xiaoqun Yi
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chunhai Jiao
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Aiping Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Desuo Yin
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China.
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China.
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