Isolation and characterization of Ty1-copia retrotransposon sequences in the blue agave (Agave tequilana Weber var. azul) and their development as SSAP markers for phylogenetic analysis

Agave tequilana Weber variety “azul” is the only variety of blue agave which is accepted for the production of tequila, but the phylogenetic relationships between this variety and other agave germplasm is still poorly understood. Retrotransposon-based molecular markers have proven to be highly informative in determining phylogenetic relationships in other crop systems. We report the isolation of a population of Ty1-copia retrotransposon terminal sequences from A. tequilana and develop three of these as sequence-specific amplification polymorphism (SSAP) molecular genetic markers. SSAP analysis shows high levels of retrotransposon polymorphism throughout agave varieties and species and identifies the tequila agaves as a distinct phylogenetic group. The retrotransposon SSAP markers presented here represent a powerful new tool for germplasm assessment in the agaves.