Multiplex molecular marker-assisted analysis of significant pathogens of cotton (Gossypium sp.)

Plant pathogens diminish crop quality and yield, leading to economic losses. Molecular markers have the potential for early and accurate detection of pathogens. DNA markers based on ITS regions, pthN gene, and CP gene were designed to detect strains of fungal, bacterial, and viral pathogens, respectively. The pRS and pRB primers were found specific to strains of R. solani and R. bataticola. Four strains of R. areola isolates from each cultivated cotton species were detected using the primer pRARE. Further, CAPS markers, Bst6I, and DraRI specific to the strains of Alternaria macrospora were developed, which could differentiate from other fungal pathogens. Furthermore, we developed a multiplexed assay to detect six pathogens simultaneously. These diagnostic markers could help assess the prevalence of cotton infecting pathogens in the field (from plant tissue or soil). Consequently, the diagnostic assay could be used for undertaking judicious disease control measures in commercial agriculture.