^{Department of Plant Molecular Biology & Biotechnology, College of Agriculture, RVS Agricultural University, Gwalior- 474002, India}

Pearl millet (Pennisetum glaucum (L.) is nutritionally superior to principal cereals for instance rice or wheat owing to the presence of all the essential nutrients together with protein, minerals and energy. Crop losses due to plant diseases are economically important.  Among the disease affecting, downy mildew, also known as green ear disease, is one of the most extensively spread and destructive disease of pearl millet, potentially resulting decline in production of crop in India and Western Africa. The present investigation was commenced with the objectives of disease indexing under field conditions and molecular characterization with gene-linked ISSR marker(s)of pearl millet germplasm line(s) against downy mildew. Under field condition, out of 48 germplasm lines, seven i.e., DMRBL2, ICHPR 18-4, ICMB-98222, ICMB-92888, DHLB-33, ICMB-02444 and ICMR-06222 were found highly resistant, 34 resistant, 4 susceptible and 3 were found to be highly susceptible. Among 5 downy mildew resistant gene-based ISSR markers the gene diversity varied from 0.6137 to 0.6997 for ISSR markers UBC-873 and UBC-807 respectively with an average of 0.6628. While Polymorphic Information Content (PIC) values ranged between 0.5317 to 0.6401 for the markers UBC-873 and UBC-807 correspondingly with a mean worth of 0.5932. Categorically, our findings of ISSR revealed existence of marker loci associated with the presence of disease resistance or susceptible genes in the set of pearl millet genotypes under investigation. The results may be further employed for marker assisted breeding for the improvement of crop against downy mildew disease.