An understanding of genetic diversity among the parental lines is useful in hybrid rice breeding through informed selection of the parental lines to maximize heterosis. Present investigation was carried out to estimate genetic divergence among the 51 restorer and five CMS lines by using 16 simple sequence repeats (SSR) markers co-segregating with fertility restorer genes (Rf3, Rf4and Rf7) of hybrid rice. Among them, 10 SSRs were found to be polymorphic and the number of amplified fragments ranged from one to five. The highest PIC value (more than 0.60) was observed for eight primers viz., AB 443, RM 3, RM 29, RM 226, RM 228, RM 304, RM 1812 and RM 3873 with average PIC value of 0.444. Cluster analysis using NTSYS generated dendrogram divided all the 56 parental lines into thirteen different clusters 80 % coefficient of similarity. With greater polymorphism revealed by SSR markers, parental lines having the similar genetic background from pedigree information were grouped into different clusters. The combination of pedigree analysis and SSR markers could be a more reliable method to study the diversity and grouping of parental lines of hybrid rice.
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