Multiplex SSR–PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice

In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5′-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR–PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi2 test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes.