Isolation, characterisation and expression of Ty1-copia retrotransposons in Agave tequilana

Agave tequilana is native to Mexico and famous for its use in the production of alcoholic beverage tequila. Due to the growing demands of tequila it has been intensively cultivated through asexual means resulting in a narrow genetic variability. The crop is extremely prone to insects and diseases and a breeding programme for selection and conservation of the crop is required. However poorly understood classification of agave and limited availability of molecular data is a big hurdle in establishing a useful breeding programme. Retrotransposons are mobile genetic elements that can replicate through a copy and paste mechanism occupying large proportions of genomes in short periods of time. They can play a vital role in the organisation and evolution of plant genomes and retrotransposon based molecular markers can be used as powerful molecular tools. Retrotransposons can play a key role in understanding Agave tequilana genetics as well as its relationship with other agave species and cultivars. In the work described here Ty1-copia retrotransposon have been isolated and characterised, retrotransposon based molecular markers have been used to evaluate the asexual genetic diversity in different vegitatively propagated mother and daughter plants. The phylogenetic relationship of these sequences revealed that Ty1-copia retrotransposons are heterogeneous in nature and they might have been actively replicating in recent past. The copy number of Ty1- copia retreotransposon was also evaluated and it was found that a large proportion of agave genome is occupied by these elements. Ty1-copia retrotransposons were also found to be polymorphic in agave tissue culture lines suggesting that they might be activated under the effect of stressed conditions. The findings of this study will help in understanding the genetics of Agave tequilana, and will provide a basis for further research on retrotransposon mediated asexual genetic variability in agave and other clonally propagated plants in general. It will also help us understand the activity of retrotransposons in the genome of agave in unusual environmental conditions.