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Sudhagar R, Saravanan NA, Kanchanarani R, Shanmuganathan M, Ganapathy S, Babu C, Thirumurugan A, Ravichandran V, Appunu C, Anna Durai A. Evolution, identification, evaluation, and characterization of a stable salinity tolerant sugarcane variety CoG 7. Sci Rep 2024; 14:20448. [PMID: 39242602 PMCID: PMC11379855 DOI: 10.1038/s41598-024-70756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 08/20/2024] [Indexed: 09/09/2024] Open
Abstract
From the fluff generated during 2005, after the preliminary experiments (2005-2007), a promising clone G2005047 has been identified. It showed moderate resistance to red rot (3.6 on a 9-scale scoring system), less susceptibility to shoot borer (13.25%) and internode borers (25.35%), and resistance to woolly aphid (0%). In the Advanced Yield Trials (2008-2011), it showed advantages over check for cane yield (CY) (11.79%), commercial cane sugar percent (CCSP) (0.35%), and sugar yield (SY) (20.33%). To ascertain its large-scale cultivation suitability, it has experimented under adaptive research trials (2012-2014) at farmers' fields. It exhibited 18.04%, 1.27%, and 19.55% supremacy over the check Co 86032 for CY, CCSP, and SY respectively. The stability of G2005047 under salinity was ascertained through a multi-environment-based experiment (2015-2017). AMMI (Additive Main-effects and Multiplicative Interactions) and GGE (Genotype × Genotype-Environment interaction) biplots were utilized. ANOVA revealed that the genotypic variation exerted the most significant effect followed by genotype × environment interaction and environment. G2005047 had the highest mean values for yield and quality traits with minimal ASV (AMMI stability value) (2.38:CY; 0.57: CCSP; & 0.58:SY) indicating its good-yielding ability and stability. AMMI I, AMMI II, and GGE biplots confirmed the stability of G2005047. In the jaggery quality assessment trials (2018 and 2019), it yielded 37.1% increased jaggery over the check. Also, the clone G2005047, exhibited moderate resistance to red rot disease, less susceptibility to shoot borer (13.25%) and internode borer (25.35%), and resistance against sugarcane woolly aphid (SWA). Due to supremacy for yield, quality, better performance under salinized situations, and tolerance to disease and pests, the clone G2005047 was released as a variety CoG 7 in 2022.
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Affiliation(s)
- Rajaprakasam Sudhagar
- Office of the Dean (Agriculture), Tamil Nadu Agricultural University (TNAU), Coimbatore, India.
| | | | | | - Murugappan Shanmuganathan
- Department of Genetics and Plant Breeding, Agricultural College and Research Institute, TNAU, Kudumiyanmalai, India
| | - Subbarayan Ganapathy
- Indian Council of Agricultural Research-Krishi Vigyan Kendra, TNAU, Tindivanam, Villupuram, India
| | | | | | | | - Chinnaswamy Appunu
- Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore, India
| | - Ayyadurai Anna Durai
- Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore, India
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Gujjar RS, Kumar R, Goswami SK, Srivastava S, Kumar S. MAPK signaling pathway orchestrates and fine-tunes the pathogenicity of Colletotrichum falcatum. J Proteomics 2024; 292:105056. [PMID: 38043863 DOI: 10.1016/j.jprot.2023.105056] [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: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/18/2023] [Indexed: 12/05/2023]
Abstract
Colletotrichum falcatum is the causal organism of red rot, the most devastating disease of sugarcane. Mitogen-activated protein kinase (MAPK) signaling pathway plays pivotal role in coordinating the process of pathogenesis. We identified eighteen proteins implicated in MAPK signaling pathway in C. falcatum, through nanoLCMS/MS based proteomics approach. Twelve of these proteins were the part of core MAPK signaling pathway, whereas remaining proteins were indirectly implicated in MAPK signaling. Majority of these proteins had enhanced abundance in C. falcatum samples cultured with host sugarcane stalks. To validate the findings, core MAPK pathway genes (MAPKKK-NSY1, MAPK 17-MAPK17, MAPKKK 5-MAPKKK5, MAPK-HOG1B, MAPKKK-MCK1/STE11, MAPK-MST50/STE50, MAPKK-SEK1, MAPKK-MEK1/MST7/STE7, MAPKK-MKK2/STE7, MAPKKK-MST11/STE11, MAPK 5-MPK5, and MAPK-MPK-C) were analyzed by qPCR to confirm the real-time expression in C. falcatum samples cultured with host sugarcane stalks. The results of qPCR-based expression of genes were largely in agreement with the findings of proteomics. String association networks of MAPKK- MEK1/MST7/STE7, and MAPK- MPK-C revealed strong association with plenty of assorted proteins implicated in the process of pathogenesis/virulence. This is the novel and first large scale study of MAPK proteins in C. falcatum, responsible for red rot epidemics of sugarcane various countries. KEY MESSAGE: Our findings demonstrate the pivotal role of MAPK proteins in orchestrating the pathogenicity of Colletotrichum falcatum, responsible devastating red rot disease of sugarcane. SIGNIFICANCE: Our findings are novel and the first large scale study demonstrating the pivotal role of MAPK proteins in C. falcatum, responsible devastating red rot disease of sugarcane. The study will be useful for future researchers in terms of manipulating the fungal pathogenicity through genome editing.
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Affiliation(s)
- Ranjit Singh Gujjar
- Indian Institute of Sugarcane Research, Raibareli Road, Lucknow 226002, India.
| | - Rajeev Kumar
- Indian Institute of Sugarcane Research, Raibareli Road, Lucknow 226002, India
| | | | - Sangeeta Srivastava
- Indian Institute of Sugarcane Research, Raibareli Road, Lucknow 226002, India
| | - Sanjeev Kumar
- Indian Institute of Sugarcane Research, Raibareli Road, Lucknow 226002, India
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Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [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: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
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Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
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O’Connell A, Deo J, Deomano E, Wei X, Jackson P, Aitken KS, Manimekalai R, Mohanraj K, Hemaprabha G, Ram B, Viswanathan R, Lakshmanan P. Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane. FRONTIERS IN PLANT SCIENCE 2022; 13:1021182. [DOI: 10.3389/fpls.2022.1021182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022]
Abstract
Red rot caused by the fungus Colletotrichum falcatum is the main disease limiting sugarcane productivity in several countries including the major producer India. The genetic basis for red rot resistance is unclear. We studied a panel of 305 sugarcane clones from the Australian breeding program for disease response phenotype and genotype using an Affymetrix® Axiom® array, to better understand the genetic basis of red rot resistance. SNP markers highly significantly associated with red rot response (≤ 10-8) were identified. Markers with largest effect were located in a single 14.6 Mb genomic region of sorghum (the closest diploid relative of sugarcane with a sequenced genome) suggesting the presence of a major-effect QTL. By genomic selection, the estimated selection accuracy was ~0.42 for red rot resistance. This was increased to ~0.5 with the addition of 29 highly significant SNPs as fixed effects. Analysis of genes nearby the markers linked to the QTL revealed many biotic stress responsive genes within this QTL, with the most significant SNP co-locating with a cluster of four chitinase A genes. The SNP markers identified here could be used to predict red rot resistance with high accuracy at any stage in the sugarcane breeding program.
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Sathyabhama M, Viswanathan R, Prasanth CN, Malathi P, Sundar AR. Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses. PLANT CELL REPORTS 2022; 41:1461-1476. [PMID: 35415786 DOI: 10.1007/s00299-022-02870-1] [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] [Received: 11/25/2021] [Accepted: 03/22/2022] [Indexed: 02/05/2023]
Abstract
KEY MESSAGE The differential compatibility responses of sugarcane to Colletotrichum falcatum pathotypes depend on the nature of both host primary defence signalling cascades and pathogen virulence. The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from ~ 54,699,263 raw reads, while 4022 contigs were assembled from ~ 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+, BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest clade to the perfect stage of C. falcatum (G. tucumanensis).
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Affiliation(s)
- M Sathyabhama
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
- Department of Biotechnology, PSG College of Arts and Science, Coimbatore, 641014, India
| | - R Viswanathan
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - C N Prasanth
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - P Malathi
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - A Ramesh Sundar
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. 3 Biotech 2022; 12:48. [PMID: 35127303 PMCID: PMC8787009 DOI: 10.1007/s13205-022-03113-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/08/2022] [Indexed: 02/05/2023] Open
Abstract
Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03113-6.
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Affiliation(s)
- C. Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - R. Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - P. Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - A. Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
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Viswanathan R, Singh SP, Selvakumar R, Singh D, Bharti YP, Chhabra ML, Parameswari B, Sharma A, Minnatullah M. Varietal Break Down to Red Rot in the Sugarcane Variety Co 0238 Mimics Vertifolia Effect: Characterizing New Colletotrichum falcatum Pathotype CF13. SUGAR TECH 2022. [DOI: 10.1007/s12355-021-01070-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Viswanathan R, Rao GP, Solomon S. Measures to Minimize the Growing Menace of Red Rot of Sugarcane in Subtropical India. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-01013-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Parameswari B, Nithya K, Kumar S, Holkar SK, Chabbra ML, Kumar P, Viswanathan R. Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-021-00323-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Controlled Condition Testing (CCT): An Ideal High-Throughput Method for Screening of Pre-Release Clones and Progenies for Red Rot Resistance in Sugarcane. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-00970-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Expression Analyses of Resistance-Associated Candidate Genes During Sugarcane-Colletotrichum falcatum Went Interaction. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-00976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Exploring the Sources of Red Rot Resistance Available in National Breeding Gene Pool and their Potential Utilization for Sugarcane Improvement in India. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-00959-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Host-pathogen interaction in sugarcane and red rot pathogen: exploring expression of phytoalexin biosynthesis pathway genes. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-020-00306-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Development and characterization of genomic SSR marker for virulent strain-specific Colletotrichum falcatum infecting sugarcane. 3 Biotech 2021; 11:20. [PMID: 33442518 DOI: 10.1007/s13205-020-02572-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/28/2020] [Indexed: 02/05/2023] Open
Abstract
Colle totrichum falcatum, an intriguing pathogen causing red rot in sugarcane, exhibits enormous variation for pathogenicity under field conditions. A species-specific marker is very much needed to classify the virulence among the varying population and to identify the potential of a pathotype by mining the microsatellites, which are considered to be the largest genetic source to develop molecular markers for an organism. In this study, we have mined the C. falcatum genome using MISA database which yielded 12,121 SSRs from 48.1 Mb and 2745 SSRs containing sequences. The most frequent SSR types from the genome of C. falcatum was di-nucleotide which constitutes 50.89% followed by tri-nucleotide 39.60%, hepta-nucleotide 6.7%, hexa-nucleotide 1.38% and penta-nucleotide 1.3%. Over 90 SSR containing sequences from the genome were predicted using BlastX which are found to be non-homologs. Most of the annotated SSR containing sequences fell in CAZy superfamilies, proteases, peptidases, plant cell wall degrading enzymes (PCDWE) and membrane transporters which are considered to be pathogenicity gene clusters. Among them, glycosyl hydrolases (GH) were found to be abundant in SSR containing sequences which again proved our previous transcriptome results. Our in-silico results suggested that the mined microsatellites from C. falcatum genome show absence of homolog sequences which suggests that these markers could be used as an ideal species-specific molecular marker. Two virulence specific markers were characterized using conventional PCR assays from C. falcatum along with virulent species-specific (VSS) marker developed for C. gloeosporioides. The study lays the foundation for the development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence.
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Affiliation(s)
- C Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - R Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - P Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - A Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
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