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Development and characterization of genomic SSR marker for virulent strain specific Colletotrichum falcatum infecting sugarcane

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Title Development and characterization of genomic SSR marker for virulent strain specific Colletotrichum falcatum infecting sugarcane
Not Available
 
Creator Prasanth C.N., R. Viswanathan, P. Malathi, A. Ramesh Sundar
 
Subject SSR or microsatellites, Protein classifcations, Species specifc marker, Genome and transcriptome
 
Description Not Available
Colletotrichum 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 48.1Mb 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 super families, 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 foundation for development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence
Not Available
 
Date 2021-09-20T04:26:01Z
2021-09-20T04:26:01Z
2021-01-01
 
Type Research Paper
 
Identifier Not Available
2190-572X
http://krishi.icar.gov.in/jspui/handle/123456789/64534
 
Language English
 
Relation Not Available;
 
Publisher Springer International Publishing