Development of sequence characterised amplified region (SCAR) markers in Acacia auriculiformis

This paper reports the development of sequence characterised amplified region (SCAR) markers and their multiplexing for easy, fast and robust identification in Acacia auriculiformis. A total of 44 of 48 fragments screened using random amplified polymorphic DNA (RAPD) markers were successfully converted and developed into SCAR markers. Six SCAR markers that had high discrimination ability and good fragment quality were selected and multiplexed into one set called a multiplex PCR (polymerase chain reaction) of SCAR (MuPS) marker. Results using 40 individuals of A. auriculiformis showed that the discriminatory power of each marker ranged between 0.385 and 0.512. However, when MuPS marker was used the discriminatory power increased to 0.974. When the MuPS was applied to 40 A. mangium individuals and 16 different Acacia hybrids, the discriminatory power decreased to 0.652 and 0.483 respectively