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Nair MM, Kumar SHK, Jyothsna S, Sundaram KT, Manjunatha C, Sivasamy M, Alagu M. Stem and leaf rust-induced miRNAome in bread wheat near-isogenic lines and their comparative analysis. Appl Microbiol Biotechnol 2022; 106:8211-8232. [PMID: 36385566 DOI: 10.1007/s00253-022-12268-4] [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: 06/23/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Wheat rusts remain a major threat to global wheat production and food security. The R-gene-mediated resistance has been employed as an efficient approach to develop rust-resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel molecular players, including non-coding RNAs for plant response. This study identified microRNAs associated with Sr36 and Lr45 disease resistance genes in response to stem and leaf rust, respectively. Here, small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem and leaf rust pathotypes. microRNA mining in stem rust-inoculated cultivars revealed a total of distinct 26 known and 7 novel miRNAs, and leaf rust libraries culminated with 22 known and 4 novel miRNAs. The comparative analysis between two disease sets provides a better understanding of altered miRNA profiles associated with respective R-genes and infections. Temporal differential expression pattern of miRNAs pinpoints their role during the progress of infection. Differential expression pattern of miRNAs among various treatments as well as time-course expression of miRNAs revealed stem and leaf rust-responsive miRNAs and their possible role in balancing disease resistance/susceptibility. Disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 from different subgenome origins might serve as a potential link between stem and leaf rust defence mechanisms downstream to respective R-genes. The outcome from the analysis of microRNA dynamics among two rust diseases and further characterization of identified microRNAs can contribute to significant novel insights on wheat-rust interactions and rust management. KEY POINTS: • Identification and comparative analysis of stem and leaf rust-responsive miRNAs. • Chromosomal location and functional prediction of miRNAs. • Time-course expression analysis of pathogen-responsive miRNAs.
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Affiliation(s)
- Minu M Nair
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Jyothsna
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South Asia Hub, Patancheru, 502324, Telangana, India
| | - C Manjunatha
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560024, Karnataka, India
| | - M Sivasamy
- ICAR-Indian Agricultural, Research Institute, Regional Station, Wellington, 643231, Tamil Nadu, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India.
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Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass. Genes (Basel) 2021; 13:genes13010020. [PMID: 35052360 PMCID: PMC8774571 DOI: 10.3390/genes13010020] [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: 12/01/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h2SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r2 value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.
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Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, Dandekar AM, Stevens KA, Wegrzyn JL. Comparative genomics of six Juglans species reveals disease-associated gene family contractions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:410-423. [PMID: 31823432 DOI: 10.1111/tpj.14630] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.
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Affiliation(s)
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Caballero
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - David B Neale
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- Department of Computer Science, University of California Davis, Davis, CA, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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4
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Zhang J, Wang F, Liang F, Zhang Y, Ma L, Wang H, Liu D. Functional analysis of a pathogenesis-related thaumatin-like protein gene TaLr35PR5 from wheat induced by leaf rust fungus. BMC PLANT BIOLOGY 2018; 18:76. [PMID: 29728059 PMCID: PMC5935958 DOI: 10.1186/s12870-018-1297-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/26/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plants have evolved multifaceted defence mechanisms to resist pathogen infection. Production of the pathogenesis-related (PR) proteins in response to pathogen attack has been implicated in plant disease resistance specialized in systemic-acquired resistance (SAR). Our earlier studies have reported that a full length TaLr35PR5 gene, encoding a protein exhibiting amino acid and structural similarity to a sweet protein thaumatin, was isolated from wheat near-isogenic line TcLr35. The present study aims to understand the function of TaLr35PR5 gene in Lr35-mediated adult resistance to Puccinia triticina. RESULTS We determined that the TaLr35PR5 protein contained a functional secretion peptide by utilizing the yeast signal sequence trap system. Using a heterologous expression assay on onion epidermal cells we found that TaLr35PR5 protein was secreted into the apoplast of onion cell. Expression of TaLr35PR5 was significantly reduced in BSMV-induced gene silenced wheat plants, and pathology test on these silenced plants revealed that Lr35-mediated resistance phenotype was obviously altered, indicating that Lr35-mediated resistance was compromised. CONCLUSIONS All these findings strongly suggest that TaLr35PR5 is involved in Lr35-mediated adult wheat defense in response to leaf rust attack.
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Affiliation(s)
- Jiarui Zhang
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Fei Wang
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Fang Liang
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Yanjun Zhang
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Lisong Ma
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
- Division of Plant Science, Research School of Biology, Australian National University, ACT, Acton, 2601, Australia.
| | - Haiyan Wang
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
| | - Daqun Liu
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Goyal RK, Tulpan D, Chomistek N, González-Peña Fundora D, West C, Ellis BE, Frick M, Laroche A, Foroud NA. Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species. BMC Genomics 2018; 19:178. [PMID: 29506469 PMCID: PMC5838963 DOI: 10.1186/s12864-018-4545-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/13/2018] [Indexed: 12/16/2022] Open
Abstract
Background The mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress responses. To date this class of enzymes has received little attention in Triticeae species, which include important cereal crops (wheat, barley, rye and triticale) that represent over 20% of the total protein food-source worldwide. Results The work presented here focuses on two subfamilies of Triticeae MAPKs, the MAP kinases (MPKs), and the MAPK kinases (MKKs) whose members phosphorylate the MPKs. In silico analysis of multiple Triticeae sequence databases led to the identification of 152 MAPKs belonging to these two sub-families. Some previously identified MAPKs were renamed to reflect the literature consensus on MAPK nomenclature. Two novel MPKs, MPK24 and MPK25, have been identified, including the first example of a plant MPK carrying the TGY activation loop sequence common to mammalian p38 MPKs. An EF-hand calcium-binding domain was found in members of the Triticeae MPK17 clade, a feature that appears to be specific to Triticeae species. New insights into the novel MEY activation loop identified in MPK11s are offered. When the exon-intron patterns for some MPKs and MKKs of wheat, barley and ancestors of wheat were assembled based on transcript data in GenBank, they showed deviations from the same sequence predicted in Ensembl. The functional relevance of MAPKs as derived from patterns of gene expression, MPK activation and MKK-MPK interaction is discussed. Conclusions A comprehensive resource of accurately annotated and curated Triticeae MPK and MKK sequences has been created for wheat, barley, rye, triticale, and two ancestral wheat species, goat grass and red wild einkorn. The work we present here offers a central information resource that will resolve existing confusion in the literature and sustain expansion of MAPK research in the crucial Triticeae grains. Electronic supplementary material The online version of this article (10.1186/s12864-018-4545-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravinder K Goyal
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dan Tulpan
- Information and Communication Technologies, National Research Council of Canada, 100 des Aboiteaux Street, Moncton, New Brunswick, E1A 7R1, Canada
| | - Nora Chomistek
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dianevys González-Peña Fundora
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Connor West
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Brian E Ellis
- Michael Smith Laboratories, University of British Columbia, #301 - 2185 East Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Michele Frick
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada.
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Satapathy L, Kumar D, Kumar M, Mukhopadhyay K. Functional and DNA-protein binding studies of WRKY transcription factors and their expression analysis in response to biotic and abiotic stress in wheat ( Triticum aestivum L.). 3 Biotech 2018; 8:40. [PMID: 29291153 PMCID: PMC5746482 DOI: 10.1007/s13205-017-1064-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/21/2017] [Indexed: 12/16/2022] Open
Abstract
WRKY, a plant-specific transcription factor family, plays vital roles in pathogen defense, abiotic stress, and phytohormone signalling. Little is known about the roles and function of WRKY transcription factors in response to rust diseases in wheat. In the present study, three TaWRKY genes encoding complete protein sequences were cloned. They belonged to class II and III WRKY based on the number of WRKY domains and the pattern of zinc finger structures. Twenty-two DNA-protein binding docking complexes predicted stable interactions of WRKY domain with W-box. Quantitative real-time-PCR using wheat near-isogenic lines with or without Lr28 gene revealed differential up- or down-regulation in response to biotic and abiotic stress treatments which could be responsible for their functional divergence in wheat. TaWRKY62 was found to be induced upon treatment with JA, MJ, and SA and reduced after ABA treatments. Maximum induction of six out of seven genes occurred at 48 h post inoculation due to pathogen inoculation. Hence, TaWRKY (49, 50, 52, 55, 57, and 62) can be considered as potential candidate genes for further functional validation as well as for crop improvement programs for stress resistance. The results of the present study will enhance knowledge towards understanding the molecular basis of mode of action of WRKY transcription factor genes in wheat and their role during leaf rust pathogenesis in particular.
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Affiliation(s)
- Lopamudra Satapathy
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dhananjay Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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Singh D, Kumar D, Satapathy L, Pathak J, Chandra S, Riaz A, Bhaganagre G, Dhariwal R, Kumar M, Prabhu KV, Balyan HS, Gupta PK, Mukhopadhyay K. Insights of Lr28 mediated wheat leaf rust resistance: Transcriptomic approach. Gene 2017; 637:72-89. [DOI: 10.1016/j.gene.2017.09.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 01/09/2023]
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Dutta S, Kumar D, Jha S, Prabhu KV, Kumar M, Mukhopadhyay K. Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L.). PLANTA 2017; 246:939-957. [PMID: 28710588 DOI: 10.1007/s00425-017-2744-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/11/2017] [Indexed: 05/09/2023]
Abstract
A novel leaf rust responsive ta-siRNA-producing locus was identified in wheat showing similarity to 28S rRNA and generated four differentially expressing ta-siRNAs by phasing which targeted stress responsive genes. Trans-acting-small interfering RNAs (Ta-siRNAs) are plant specific molecules generally involved in development and are also stress responsive. Ta-siRNAs identified in wheat till date are all responsive to abiotic stress only. Wheat cultivation is severely affected by rusts and leaf rust particularly affects grain filling. This study reports a novel ta-siRNA producing locus (TAS) in wheat which is a segment of 28S ribosomal RNA but shows differential expression during leaf rust infestation. Four small RNA libraries prepared from wheat Near Isogenic Lines were treated with leaf rust pathogen and compared with untreated controls. A TAS with the ability to generate four ta-siRNAs by phasing events was identified along with the microRNA TamiR16 as the phase initiator. The targets of the ta-siRNAs included α-gliadin, leucine rich repeat, trans-membrane proteins, glutathione-S-transferase, and fatty acid desaturase among others, which are either stress responsive genes or are essential for normal growth and development of plants. Expression of the TAS, its generated ta-siRNAs, and their target genes were profiled at five different time points after pathogen inoculation of susceptible and resistant wheat isolines and compared with mock-inoculated controls. Comparative analysis of expression unveiled differential and reciprocal relationship as well as discrete patterns between susceptible and resistant isolines. The expression profiles of the target genes of the identified ta-siRNAs advocate more towards effector triggered susceptibility favouring pathogenesis. The study helps in discerning the functions of wheat genes regulated by ta-siRNAs in response to leaf rust.
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Affiliation(s)
- Summi Dutta
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Dhananjay Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Botany, PDM University, Bahadurgarh, Haryana, 124507, India
| | - Shailendra Jha
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Chandra S, Kazmi AZ, Ahmed Z, Roychowdhury G, Kumari V, Kumar M, Mukhopadhyay K. Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. PLANT CELL REPORTS 2017; 36:1097-1112. [PMID: 28401336 DOI: 10.1007/s00299-017-2141-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/04/2017] [Indexed: 05/06/2023]
Abstract
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Andaleeb Z Kazmi
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Zainab Ahmed
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Gargi Roychowdhury
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Veena Kumari
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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10
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Kumar D, Dutta S, Singh D, Prabhu KV, Kumar M, Mukhopadhyay K. Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis. PLANTA 2017; 245:161-182. [PMID: 27699487 DOI: 10.1007/s00425-016-2600-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/27/2016] [Indexed: 05/09/2023]
Abstract
Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust resistance breeding programs.
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Affiliation(s)
- Dhananjay Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Summi Dutta
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- QAAFI, Centre of Plant Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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11
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Chandra S, Singh D, Pathak J, Kumari S, Kumar M, Poddar R, Balyan HS, Gupta PK, Prabhu KV, Mukhopadhyay K. De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection. PLoS One 2016; 11:e0148453. [PMID: 26840746 PMCID: PMC4739524 DOI: 10.1371/journal.pone.0148453] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Jyoti Pathak
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Supriya Kumari
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Puspendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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12
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Kumar D, Kapoor A, Singh D, Satapathy L, Singh AK, Kumar M, Prabhu KV, Mukhopadhyay K. Functional characterisation of a WRKY transcription factor of wheat and its expression analysis during leaf rust pathogenesis. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1295-1309. [PMID: 32481078 DOI: 10.1071/fp14077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/04/2014] [Indexed: 05/27/2023]
Abstract
WRKY proteins are a large family of plant-specific transcription factors associated with regulation of biotic and abiotic stress responses, but how they respond to cereal rust pathogens has never been explored at the molecular level. Full-length cDNA of TaWRKY1B was obtained from a wheat cultivar HD2329 derivative containing leaf rust resistance gene Lr28 based on domain characteristics. The unique feature of this WRKY transcription factor gene was the close proximity of the DNA-binding domain and consensus DNA element W-Box within the open reading frame. Infection with a virulent race of leaf rust fungus resulted in 146-fold induction of the gene in resistant plants, but only 12-fold in the susceptible plants as compared with mock-inoculated controls. Docking models of 74 amino acids DNA-binding domain and 26bp W-Box element showed that the WRKY domain, located on the β1 strand, only interacts with the W-Box at positions corresponding to W125, R126, K127 and Y128 amino acids. A truncated recombinant protein of 9.0 kD, encompassing the DNA-binding domain also showed binding specificity to the 32bp W-Box element in electrophoretic mobility shift assays. The protein-DNA ensemble was also characterised using high-resolution atomic force microscopic imaging. The results contribute to an understanding of the molecular structure and function of a previously uncharacterised WRKY transcription factor in wheat that can be manipulated to improve biotic stress tolerance.
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Affiliation(s)
- Dhananjay Kumar
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Anjali Kapoor
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Dharmendra Singh
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Lopamudra Satapathy
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Ashwini Kumar Singh
- Central Instrumentation Facility, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Manish Kumar
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Kumble Vinod Prabhu
- National Phytotron Facility, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kunal Mukhopadhyay
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, India
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13
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Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes. J Nucleic Acids 2014; 2014:570176. [PMID: 25180085 PMCID: PMC4144313 DOI: 10.1155/2014/570176] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/19/2014] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are endogenous small noncoding RNAs which play critical roles in gene regulation. Few wheat (Triticum aestivum L.) miRNA sequences are available in miRBase repertoire and knowledge of their biological functions related to biotic stress is limited. We identified 52 miRNAs, belonging to 19 families, from next-generation transcriptome sequence data based on homology search. One wheat specific novel miRNA was identified but could not be ascribed or assigned to any known miRNA family. Differentially expressed 22 miRNAs were found between susceptible and resistant wheat near-isogenic lines inoculated with leaf rust pathogen Puccinia triticina and compared with mock inoculated controls. Most miRNAs were more upregulated in susceptible NIL compared to resistant NIL. We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. A miRNA-mediated regulatory network revealed relationships among the components of the targetome. The present study provides insight into potential miRNAs with probable roles in leaf rust pathogenesis and their target genes in wheat which establish a foundation for future studies.
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14
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Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling. Mol Genet Genomics 2014; 289:1289-306. [PMID: 25098419 DOI: 10.1007/s00438-014-0890-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022]
Abstract
WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.
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