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Long Terminal Repeat (LTR) retrotransposons are ubiquitous in the plant kingdom and play an important role in plant genome evolution.Activation of retrotransposon is the pivotal factor for the genesis of genetic polymorphism.Retrotransposon-based molecular markers are excellent tools for detecting genetic diversity and genomic changes associated with retrotransposon activity.The scarcity of retrotransposon long terminal repeat (LTR) sequence limits the application of retrotransposon-based molecular marker systems.In this study,conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy LTR retrotransposons were amplified from masson pine using degenerate primers,3′-LTR segments were isolated and characterized from the masson pine genome using a genome walking strategy,subsequently inter-retrotransposon amplified polymorphism (IRAP) markers were explored for genetic diversity assessment.Phylogenetic analysis demonstrated that Ty1-copia and Ty3-gypsy RT sequences had considerable homology with other species,indicating that both vertical transmission and horizontal transmission may probably be the source of LTR retrotransposons in masson pine.Southern dot blot hybridization results,suggested that both types of LTR retrotransposons are present in the genome of masson pine with high copy number.IRAP were shown to have clearly distinguishable amplification bands and high levels of polymorphism for masson pine.Dendrogram of our IRAP data highlighted that IRAP markers for individual elements are distinguishable and will shed light on the usage in genetic diversity studies of the masson pine,which might also yield polymorphic banding patterns in other angiosperm species such as Hylocereus undatus and Prunus pseudocerasus.Transcription activation of Ty1-copia and Ty3-gypsy group retrotransposons in masson pine was investigated with exposure to various abiotic stresses.The insertional polymorphism and the transposition activation were detected by IRAP.Results revealed that none of the analyzed materials in course of two months trials displayed fingerprint changes.