The present investigation was undertaken to find molecular markers linked to leaf rust resistance genes, <i>Lr</i>9 and Kharchia local mutant KLM4-3B. Preliminary AFLP analysis was carried out with different stocks, a survey of primer combinations with different selective nucleotide indicated that for each primer combination, the number of scorable loci ranged from 34 to 123. Only a limited primer combination used in the set of parental and near isogenic lines showed a high level of polymorphism for AFLP marker. Putative AFLP marker were found to be linked to <i>Lr</i>9, <i>Lr</i>19 and KLM4-3B. The alien genes were readily identified.
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