Identification and characterization of hypervariable sequences within the Saccharum complex

Replicated Saccharum in vivo-plants from cv. Ja60-5 genealogy were evaluated for pre-existing genomic variability by AFLP. By using six different copy primer combinations, 29 bands were found polymorphic within asexually propagated plants, covering approximately 6265 bp of the Saccharum genome. A total of 14 bands were polymorphic in at least four genotypes, representing hypervariable regions of the sugarcane genome. UPGMA analysis illustrates the presence of a natural pre-existing variability in all vegetative-propagated Saccharum genotypes, which do not have a significative effect on the classification of the studied genotypes. Southern blot demonstrates that integration pattern of the variable sequences were not high-complex and its copy number ranged one to six per genome. Sequencing of hypervariable bands showed novel non-repetitive elements in Saccharum with quite low homologies to both genomic DNA sequences reported in public databases and Expressed Sequences Tags in sugarcane. Results support hypothesis about the role of natural mechanisms in plants capable of modifying genome structure, which promote a potential source of variability and could be related to the genome plasticity.