Molecular markers facilitate rapid and environment-neutral characterization of the pattern of genetic diversity. The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) at Patancheru, India, has developed a large number and diverse range of maintainer lines (B-lines) and restorer lines (R-lines) of pearl millet [Pennisetum glaucum (L.) R. Br.] in last three decades. In the present study, 213 lines (98 B-lines and 115 R-lines) were genotyped using high throughput assay and 38 polymorphic simple sequence repeat (SSR) markers, which detected 308 alleles averaging 8.1 alleles per locus. Restorer lines were genetically more diverse than B-lines, as higher average gene diversity was detected among R-lines (0.62) than among B-lines (0.50). A neighbor-joining tree based on simple matching dissimilarity distance matrix clearly differentiated B-lines from R-lines into two clusters, with further subdivision of B-lines into four subclusters and R-lines into five subclusters. Seven B-lines clustered with R-lines, and only two R-lines clustered with B-lines. Few unique alleles (1 to 3) were detected in 14 B- and 30 R-lines, which could be used to distinguish them from each other as well as from the remaining lines used in this study. The SSR alleles of each of the parental lines along with distinctness, uniformity, and stability (DUS) characterization may enable ICRISAT to protect these lines from any kind of infringement by the multiple users who have received these lines for hybrid development.
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