Alu sequences constitute the most abundant family of short interspersed nuclear elements, SINEs, in the primate genome. The Alu-PCR method, which consists of amplification between Alu sequences, is usually applied in human genetics to provide polymorphic markers. Here we report the presence of Alu-like sequences in sugarcane and related species by applying the Alu-PCR-like method. Amplifications using a PCR primer defined in conserved regions of Alu human sequences lead to specific complex multiband profiles in all the Saccharum and related genera clones surveyed. The isolation and characterisation of the amplified genus-specific inter-Alu-like fragments allowed us to isolate repeated sequences that are specific for different genera of the Saccharum complex: MsCIR2 from Miscanthus, EaCIR6 and EaCIR7 from Erianthus. and SrCIR2 from Saccharum. Two PCR diagnostic tests were developed from the inter-Alu-like sequences MsCIR2 and EaCIR6, and proved efficient in identifying intergeneric hybrids Saccharum x Miscanthus or Saccharum x Erianthus, respectively. The present study illustrates how the Alu-PCR-like method could help investigating the origin of amphiploid species and monitoring introgression in plants.
