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Transposon variation by order during allopolyploidisation between B rassica oleracea and B rassica rapa
Author(s) -
An Z.,
Tang Z.,
Ma B.,
Mason A. S.,
Guo Y.,
Yin J.,
Gao C.,
Wei L.,
Li J.,
Fu D.
Publication year - 2014
Publication title -
plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.871
H-Index - 87
eISSN - 1438-8677
pISSN - 1435-8603
DOI - 10.1111/plb.12121
Subject(s) - transposable element , biology , gene , genetics , genome
Although many studies have shown that transposable element ( TE ) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE ‐associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE , and determined the impact of TE ‐associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the I nter‐ R etrotransposon A mplified P olymorphism ( IRAP ) method to detect variation in TE ‐associated sequences during the process of allopolyploidisation between B rassica rapa ( AA ) and B rassica oleracea ( CC ), and in successive generations of self‐pollinated progeny. In addition, fragments with TE insertions were used to perform B last2 GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety‐two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TE s could be classed in ascending frequency into LTR ‐ RE s, TIR s, LINE s, SINE s and unknown TE s. The frequency of novel variation (putative activation) detected for the four orders of TE s was highest from the F 1 to F 2 generations, and lowest from the F 2 to F 3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.