| Summary: | Intergeneric crosses between <i>Brassica</i> species and <i>Raphanus sativus</i> have produced crops with prominent shoot and root systems of <i>Brassica</i> and <i>R. sativus</i>, respectively. It is necessary to discriminate donor genomes when studying cytogenetic stability in distant crosses to identify homologous chromosome pairing, and microsatellite repeats have been used to discriminate subgenomes in allopolyploids. To identify genome-specific microsatellites, we explored the microsatellite content in three <i>Brassica</i> species (<i>B. rapa</i>, AA, <i>B. oleracea</i>, CC, and <i>B. nigra</i>, BB) and <i>R. sativus</i> (RR) genomes, and validated their genome specificity by fluorescence in situ hybridization. We identified three microsatellites showing A, C, and B/R genome specificity. ACBR_msat14 and ACBR_msat20 were detected in the A and C chromosomes, respectively, and ACBR_msat01 was detected in B and R genomes. However, we did not find a microsatellite that discriminated the B and R genomes. The localization of ACBR_msat20 in the 45S rDNA array in ×<i>Brassicoraphanus</i> 977 corroborated the association of the 45S rDNA array with genome rearrangement. Along with the rDNA and telomeric repeat probes, these microsatellites enabled the easy identification of homologous chromosomes. These data demonstrate the utility of microsatellites as probes in identifying subgenomes within closely related <i>Brassica</i> and <i>Raphanus</i> species for the analysis of genetic stability of new synthetic polyploids of these genomes.
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