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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, Bst 6I, and Dra RI 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. • Plant pathogens damage crop quality and yield; lead to economic losses. • Molecular markers have potential for early and accurate detection of various pathogens of cotton. • Mmarkers were designed to detect cotton's significant fungal, bacterial and viral pathogens. • Multiplexed analysis of various cotton pathogens is performed. [ABSTRACT FROM AUTHOR]

A new method of transgenic development called “ In-planta ” transformation method, where Agrobacterium is used to infect the plantlets but the steps of in vitro regeneration of plants is totally avoided. In this study, we have reported a simple In-planta method for efficient transformation of diploid cotton Gossypium hirsutum cv LRK-516 Anjali using Agrobacterium tumefaciens EHA-105 harbouring recombinant binary vector plasmid pBinAR with Arabidopsis At-NPR1 gene. Four day old plantlets were used for transformation. A vertical cut was made at the junction of cotyledonary leaves, moderately bisecting the shoot tip and exposing meristem cells at apical meristem. This site was infected with Agrobacterium inoculum. The transgenic events obtained were tested positive for the presence of At-NPR1 gene with promoter nptII gene. They are also tested negative for vector backbone integration and Agrobacterium contamination in T0 events. With this method a transformation frequency of 6.89% was reported for the cv LRK-516. [ABSTRACT FROM AUTHOR]