Alterations in inheritance pattern and level of cytosine DNA methylation, and their relationship with heterosis in rice

Abstract

Novel hybrid-specific/heterotic gene expression patterns observed from expression studies suggest the need to characterize the underlying regulatory mechanism(s) to reveal the biological basis of heterosis in crop plants. To gain an insight into the molecular basis of heterosis in rice, we investigated the inheritance pattern and level of cytosine methylation, a major epigenetic regulatory mechanism, in the leaf tissue of an elite Indian rice hybrid KRH2 and its parents at three stages (15 day-old, 35 day-old seedling and flag leaf) and their correlation with heterosis using methylation-sensitive amplification polymorphism (MSAP) technique. In contrast to parents, the level of methylation was high during initial growth stages and reduced as the hybrid grew. Even though, a majority of cytosine methylation profiles were transmitted to hybrid at all stages, a considerable level (25.4%) of cytosine methylation pattern was observed to be novel in hybrid and some of these altered loci were identified to code for known/hypothetical proteins. It was also observed that demethylation events occurred more predominantly during early stages than hypermethylation while the frequency of demethylation events decreased in flag leaf with a remarkable increase in hypermethylation in the hybrid. These bi-directional events in methylation in KRH2 were validated in six hybrids with different levels of grain yield heterosis and the level of cytosine methylation in the hybrid was observed to be significantly correlated with heterosis.

Effect of DNA methylation on molecular diversity of watermelon heirlooms and stability of methylation specific polymorphisms across the genealogies

“…Systematic analyses involving transmission genetics and QTL location will provide direct evidence on how these methylation specific polymorphisms impact phenotypic diversity. There are comparable studies from other plants such as in Arabidopsis (Cervera et al 2002;Riddle and Richards 2002), rice (Ashikawa 2001;Wang et al 2004;Sakthivel et al 2010), Pisum (Knox and Ellis 2001) and cotton (Keyte et al 2006) suggesting that the MPs are widespread among plants and can serve as epigenetic markers for use in plant breeding. Data on the influence of DNA methylation on QTLs and the potential use of epigenetic markers for QTL analysis is on hand for humans (Gibbs et al 2010).…”

Analysis of DNA methylation patterns and levels in maize hybrids and their parents

“…The methylation fragments were divided into 4 major groups (Zhao et al, 2008;Sakthivel et al, 2010) (Figure 1, Table 2, and Table S2). The same bands that were detected in both hybrids and their parents were called monomorphic bands, which were grouped into class A bands (196 roots, 395 leaves, 501 embryos, and 364 endosperms were included in this group); class B bands included the decreased levels of methylation or demethylation pattern in hybrids relative to its parents; class C bands included the increased levels of methylation or hypermethylation pattern in hybrids compared to its parents; and class D bands included the different methylated sites between 2 parents and different methylation patterns of hybrids from 1 parent.…”

Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

“…Most of the studies in plants using methylation-sensitive amplification fragment length (MS-AFLP) indicate prominent additive effects in cytosine methylation patterns, with typical Mendelian inheritance (35,36,54,55) with few examples of non-additive effects in hybrids, potentially related to phenotypic plasticity and adaptation (56,57).…”