A comparative in silico analysis on frequency and distribution of microsatellites in coding regions of three formae speciales of Fusarium oxysporum and development of EST-SSR markers for polymorphism studies

Abstract

Fusarium oxysporum is a ubiquitous species complex of soil-borne plant pathogens comprising of many different formae speciales, each characterized by a high degree of host specificity. In the present investigation, we surveyed microsatellites in the available express sequence tags and transcript sequences of three formae speciales of F. oxysporum viz. melonis (Fom), cucumerium (Foc), and lycopersici (Fol). The relative abundance and density of microsatellites were higher in Fom when compared with Foc and Fol. Thirty microsatellite primers were designed, ten from each forma specialis, for genetic characterization of F. oxysporum isolates belonging to five formae speciales. Of the 30 primers, only 14 showed amplification. A total of 28 alleles were amplified by 14 primers with an average of two alleles per marker. Eight markers showed 100% polymorphism. The markers were found to be more polymorphic (47%) in Fol as compared to Fom and Foc; however, polymorphic information content was the maximum (0.899) in FocSSR-3. Nine polymorphic markers obtained in this study clearly demonstrate the utility of newly developed markers in establishing genetic relationships among different isolates of F. oxysporum.

Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici

“…Coding regions are mostly dominated by tri-and hexa-repeats, whereas di-, teta-, and hexa-nucleotide repeats are often found in non-coding regions. Similar, distribution pattern of SSR motifs and predominance of tri-and hexa-motifs in the coding region was reported by Mahfooz et al (2012). These tri-and hexa-SSR motifs in the coding regions are translated into amino acids repeats, which possibly contribute to the biological function of the protein (Kim et al, 2008).…”

“…Several studies have shown the importance of using microsatellites to understand epidemiological processes in plant pathogenic fungi (Breuillin et al, 2006;Lievens et al, 2009). Their codominance, high polymorphism, and ease of scoring allow inferences of population genetic parameters such as gene flow, effective population size, or reproductive system, to be made with high accuracy (Mahfooz et al, 2012). Most importantly, microsatellite sequences obtained through in silico mining have more or less the same utility and potential comparative with those derived from a genomic library.…”

“…These tri-and hexa-SSR motifs in the coding regions are translated into amino acids repeats, which possibly contribute to the biological function of the protein (Kim et al, 2008). Di-nucleotide motifs are often found in the exonic region of F. oxysporum (Mahfooz et al, 2012), however, (GT)n repeats were also com- um genome was higher in chromosome 1 relative to other chromosomes. Role of microsatellites in regulation of gene expression and in the evolution of gene regulation are well documented (Li et al, 2002(Li et al, , 2004.…”

“…tritici (Singh et al, 2011 b). The rationale behind the categorization of SSR motifs on the basis of length of SSR tracts (Class I, II and III) is that longer perfect repeats are highly polymorphic as noticed in case of F. graminearum (Singh et al, 2011 a) and Fusarium oxysporum (Mahfooz et al, 2012). Microsatellites in Class III tended to be less variable, representing sites where SSR expansion may occasionally occur but its probability is limited due to a smaller chance of slipped-strand impairing over the shorter SSR template (Temnykh et al, 2001).…”

“…Simple sequence repeat (SSR) or microsatellite markers have become a preferred choice in recent years for several uses due to their multi-allelic nature, co-dominant inheritance, high abundance, hyper variance, extensive genome coverage, reproducibility, and discriminatory power (Mahfooz et al, 2012). Except for some nuclear restriction fragment length polymorphism (RFLP) (Rosewich et al, 1999) and RAPD (random amplified polymorphic DNA) markers (Balmas et al, 2005), limited molecular markers were available for F. oxysporum f. sp.…”