Alterations in cytosine methylation and species-specific transcription induced by interspecific hybridization between Oryza sativa and O. officinalis

Abstract

Interspecific hybridization and polyploidization may involve programmed genetic and epigenetic changes. In this study, we used the methylation-sensitive amplified polymorphism (MSAP) method to survey cytosine methylation alterations that occurred in F(1) hybrid and BC(1) progeny following interspecific hybridization between Oryza sativa and O. officinalis. Across all 316 parental methylated sites, 25 (7.9%) cytosine methylation alterations were detected in the F(1) and/or BC(1) progeny. Thirty additional cytosine methylation alterations were detected at parental non-methylated or novel sites. In total, 55 cytosine methylation alterations (90.9% of all alterations) were detected in the F(1) hybrid, which were maintained in the BC(1) progeny. The alterations in cytosine methylation were biased toward the O. officinalis parent and were in some cases repeatable in independent hybridizations between O. sativa and O. officinalis. Twelve fragments showing cytosine methylation alterations were isolated, sequenced and subsequently validated by methylation-sensitive Southern blot analysis. Where possible, we designed species-specific primers to amplify the polymorphic transcripts from either the O. sativa or the O. officinalis parent using reverse transcription (RT)-PCR in combination with single-strand conformation polymorphism (SSCP) analysis. In four of five cases, modified gene expression could be correlated with the altered cytosine methylation pattern. Our results demonstrated cytosine methylation alterations induced by interspecific hybridization between a rice cultivar and its wild relative, and indicated a direct relationship between cytosine methylation alteration and gene expression variation.

Trans Chromosomal Methylation in Arabidopsis hybrids

“…However, crosses between genetically similar parents such as Arabidopsis accessions or subspecies of rice can produce hybrids displaying significant heterosis, apparently breaking down the relationship between genetic distance and extent of hybrid vigor (6, 7). It has been reported that the epigenome evolves at a significantly faster rate than the genetic sequence (8-10), consistent with genetically similar parents having markedly different epigenomes (11)(12)(13)(14)(15)(16)(17)(18)(19)(20). These epigenomic systems, such as DNA methylation and small RNAs, play a vital role in genomic stability, development, and the regulation of genes within a plant.…”

Genetic and epigenetic status of triple exotic consanguinity cotton introgression lines

“…Further sequencing results of the methylation polymorphism fragments confirmed that most of the DNA methylation alteration happened at the repetitive sequences or non-coding sequences. However, the movement of transposable elements induced by DNA methylation alteration played an important role in the regulation of gene expression (Jin et al, 2008;Xu et al, 2009). The potential impacts, especially methylation alternation of transposable elements should be investigated on PD0111 and PD0113.…”

Flexible shift on gene body methylation and transcription of LpCYP72A161 exposed to temperature stress in perennial ryegrass

“…The important role of cytosine methylation in epigenetic regulation of gene expression has been well documented (Jin et al, 2008). DNA methylation is closely related to gene expression, and it appears that different methylated regions in genes have different effects on gene expression (Lou et al, 2014).…”