Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

Abstract

Allopolyploidy, or the combination of two or more distinct genomes in one nucleus, is usually accompanied by radical genomic changes involving transposable elements (TEs). The dynamics of TEs after an allopolyploidization event are poorly understood. In this study, we analyzed the methylation state and genetic rearrangements of a high copied, newly amplified terminal-repeat retrotransposon in miniature (TRIM) family in wheat termed Veju. We found that Veju insertion sites underwent massive methylation changes in the first four generations of a newly formed wheat allohexaploid. Hypomethylation or hypermethylation occurred in $43% of the tested insertion sites; while hypomethylation was significantly predominant in the first three generations of the newly formed allohexaploid, hypermethylation became predominant in the subsequent generation. In addition, we determined that the methylation state of Veju long terminal repeats (LTRs) might be correlated with the deletion and/or insertion of the TE. While most of the methylation changes and deletions of Veju occurred in the first generation of the newly formed allohexaploid, most Veju insertions were seen in the second generation. Finally, using quantitative PCR, we quantitatively assessed the genome composition of Veju in the newly formed allohexaploid and found that up to 50% of Veju LTRs were deleted in the first generation. Retrotransposition bursts in subsequent generations, however, led to increases in Veju elements. In light of these findings, the underlying mechanisms of TRIM rearrangements are discussed.

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

“…Totally beyond our expectation and in a sharp contrast with the recent report showing strikingly high levels of genetic dynamics including rampant element loss and retrotranspostional burst of the Veju retrotransposon family over the first five generations (S1-S5) in a newly formed allohexaploid wheat line (Kraitshtein et al 2010), we detected near complete genetic stasis in all the plant individuals (n ¼ 11) collected over 3-5 selfed generations of three independently synthesized allohexaploid wheat lines with different genotypic combinations ( Figure 1A). Specifically, out of the 595, 622, and 632 bands scored for the three sets of allohexaploid wheat lines (Table S3), we detected from zero to three loss or gain events for the 11 individual plants; moreover, most of the losses were also detected in the corresponding parental DNA mixtures, indicating they were not "real" genetic changes associated with allohexaploidization, but resulting from PCR competition between the divergent parental species DNA (data not shown), consistent with the findings by a recent study monitoring microsatellite loci .…”

“…A recent study by Kraitshtein et al (2010) demonstrated that extraordinarily high frequencies of both genetic and DNA methylation changes occurred at genomic loci flanking a high copy-number retroelement Veju (Sanmiguel et al 2002) across the initial generations (S1-S5) in wheat. In particular, the genetic changes were found to include rampant loss of .50% of the original element copies in the first three generations, and followed by element reinsertion, underscoring the stunning dynamics of the elements per se and/or their flanking sequences (Kraitshtein et al 2010).…”

“…The protocols for transposon display (TD) and methylationsensitive transposon display (MSTD) were essentially as reported (Kraitshtein et al 2010). Nested primers respectively specific to one terminus of each of the two retrotransposon families, Veju (Sanmiguel et al 2002) and BARE-1 (Manninen and Schulman 1993), together with a primer matching the MseI adapter sequence, were used (supporting information, Table S1).…”

“…They found strikingly high frequencies (.50%) of both genetic change (including massive element loss followed by retrotranspositional burst) and methylation alteration in the studied line over the first five successive generations (Kraitshtein et al 2010). Because only one line was used plus only euploidy was verified at the cytological level by conventional chromosome counting, it remained unclear whether the documented changes bear relevance to speciation of T. aestivum.…”

“…More recently, Kraitshtein et al (2010) have conducted a genome-wide analysis on genetic and DNA methylation changes at genomic loci flanking a high-copy number retrotransposon family called Veju (Sanmiguel et al 2002) in a single newly synthesized allohexaploid wheat line. They found strikingly high frequencies (.50%) of both genetic change (including massive element loss followed by retrotranspositional burst) and methylation alteration in the studied line over the first five successive generations (Kraitshtein et al 2010).…”