512 Copia-like Retrotransposon Sequences in the Ipomoea batatas Genome

in HortScience

The presence of copia-like retrotransposon sequences in sweetpotato [Ipomoea batatas (L.) Lam.] was investigated. PCR-based amplification using primers to highly conserved copia-like reverse transcriptase sequences produced several products corresponding to the expected target size (≈300 bp) that were subsequently isolated and cloned. A random sample of the clones were sequenced and all six reading frames were translated into their corresponding amino acid sequences. Sequence analysis revealed the presence of 22 copia-like reverse transcriptase sequences corresponding to various subfamilies. The presence of several sequence families in the genome is indicative of past or recent transposition activity. Southern blot analysis suggested that these copia-like sequences were present in several hundred copies in the sweetpotato genome. Data also showed retrotransposon insertion polymorphisms between a limited sample of virus-tested and virus-infected sweetpotato clones, indicating putative activity and mobility. This investigation documented the presence of copia-like retrotransposon sequences in the sweetpotato genome. This is an important step in clarifying the possible association between mobile genetic elements and the unusually high incidence of somatic mutations that may result in clonal decline in sweetpotato and other asexually propagated crops. Data presented provides information on the possible use of retrotransposons as genetic markers for sweetpotato crop improvement.

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