Conversion of AFLP fragments tightly linked to SCMV resistance genes Scmv1 and Scmv2 into simple PCR-based markers

In a previous study, bulked segregant analysis with amplified fragment length polymorphisms (AFLPs) identified several markers closely linked to the sugarcane mosaic virus resistance genes Scmv1 on chromosome 6 and Scmv2 on chromosome 3. Six AFLP markers (E33M61-2, E33M52, E38M51, E82M57, E84M59 and E93M53) were located on chromosome 3 and two markers (E33M61-1 and E35M62-1) on chromosome 6. Our objective in the present study was to sequence the respective AFLP bands in order to convert these dominant markers into more simple and reliable polymerase chain reaction (PCR)-based sequence-tagged site markers. Six AFLP markers resulted either in complete identical sequences between the six inbreds investigated in this study or revealed single nucleotide polymorphisms within the inbred lines and were, therefore, not converted. One dominant AFLP marker (E35M62-1) was converted into an insertion/deletion (indel) marker and a second AFLP marker (E33M61-2) into a cleaved amplified polymorphic sequence marker. Mapping of both converted PCR-based markers confirmed their localization to the same chromosome region (E33M61-2 on chromosome 3; E35M62-1 on chromosome 6) as the original AFLP markers. Thus, these markers will be useful for marker-assisted selection and facilitate map-based cloning of SCMV resistance genes.