Abstract
BackgroundIt is widely recognized that interspecific hybridization may induce "genome shock", and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. A prominent component involved in the genome shock is reactivation of cryptic transposable elements (TEs) in the hybrid genome, which is often associated with alteration in the elements' epigenetic modifications like cytosine DNA methylation. We have previously reported that introgressants derived from hybridization between Oryza sativa (rice) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs, a copia retrotransposon Tos17 and a MITE mPing. It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants, their relevance to alteration in cytosine methylation, and their impact on expression of adjacent cellular genes.ResultsWe document in this study that the Dart TE family was transpositionally reactivated followed by stabilization in all three studied introgressants (RZ1, RZ2 and RZ35) derived from introgressive hybridization between rice (cv. Matsumae) and Z. latifolia, while the TEs remained quiescent in the recipient rice genome. Transposon-display (TD) and sequencing verified the element's mobility and mapped the excisions and re-insertions to the rice chromosomes. Methylation-sensitive Southern blotting showed that the Dart TEs were heavily methylated along their entire length, and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line. Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted Dart-related TE copies indicated that whereas marked difference in the expression of all four genes in both tissues (leaf and root) were detected between the introgressants and their rice parental line under both normal and various stress conditions, the difference showed little association with the presence or absence of the newly mobilized Dart-related TEs.ConclusionIntrogressive hybridization has induced transpositional reactivation of the otherwise immobile Dart-related TEs in the parental rice line (cv. Matsumae), which was accompanied with a moderate alteration in the element's cytosine methylation. Significant difference in expression of the Dart-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions, but the alteration in gene expression was not coupled with the TEs.
Highlights
It is widely recognized that interspecific hybridization may induce “genome shock”, and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants
We have demonstrated that introgression of small amount of chromatin of Zizania latifolia into rice has caused an array of genetic and epigenetic instabilities in the recipient rice genome [19,20], and in particular, rampant mobilization of a copia retrotransposon Tos17 and a MITE [21]
The Dart transposon family was transpositionally reactivated in the rice-Zizania introgressants Based on the sequence of a full-length copy of Dart1 [23], we used the same pair of primers that should be specific to all conserved Dart-related elements to amplify a 296 bp fragment within the ORF region, designed by Fujino et al [23]
Summary
It is widely recognized that interspecific hybridization may induce “genome shock”, and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. At least circumstantial evidence has indicated that for the hybridization- associated genomic shock to occur, a symmetric hybrid genome is not a prerequisite; instead, introgression or integration of “foreign” chromatin or DNA segments via introgressive hybridization or other means (e.g., transgenic) might as well produce the “shocking” effects on the recipient genome [11] It was shown in cultured animal cells that random integration of pieces of foreign DNA can cause the host genome to undergo extensive and genome-wide alterations in cytosine methylation of both cellular genes and TE-related DNA repeats [17,18]. Given the recent finding that the cellular controlling mechanisms for TE activity are likely individualized [22], it is interesting to explore whether TE reactivation in the rice-Zizania introgressants was confined to these two elements or other TEs experienced reactivation
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