Development of molecular markers and probes based on TEF-1α, β-tubulin and ITS gene sequences for quantitative detection of Fusarium oxysporum f. sp ciceris by using real-time PCR

Fusarium wilt (Fusarium oxysporum f. sp. ciceris) causes significant yield losses in chickpea worldwide. Faster, reliable and more specific molecular detection techniques were developed for the detection of Fusarium oxysporum f. sp. ciceris (Foc). The sequences obtained from multiple alignments of target genes, namely, translation elongation factor-1 alpha (TEF-1 alpha), beta-tubulin, and internal transcribed spacer (ITS), were used to design Foc-specific markers/probes. One set of TEF-1 alpha-based molecular marker, namely, SP alpha-F and R, two sets of beta-tubulin-based markers, namely, SP beta 1-F and R, and SP beta 2-F and R, and one set of ITS gene, namely, SPT-F and R, were developed for the detection and quantification of Foc from diverse samples. The specificity and sensitivity of the designed molecular markers were evaluated through conventional and real-time PCR assays which differentiated the Foc from closely related species of Fusarium and other plant pathogens. In conventional PCR, the minimum detection limits of the markers ranged from 12.5 pg to 100 pg for genomic DNA of Foc and 0.5 ng to 10 ng for infected plant samples. In real-time PCR assay, the minimum detection limits of the markers ranged from 0.001 pg to 0.25 pg for genomic DNA of Foc and from 0.04 pg to 1.5 pg for the infected plant samples. Thus, the markers designed in the present study were found to be specific for Foc and can be used consistently for the detection and identification of Foc isolates. The probes developed from the two sets of markers, namely, SP alpha and SP beta 2, also showed specificity with Foc.