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

Abstract

ABSTRACT. Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 8459 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (4): 8458-8468 (2014) DNA methylation variations in maize hybrids and parents fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.

Soil Selenium (Se) Biofortification Changes the Physiological, Biochemical and Epigenetic Responses to Water Stress in Zea mays L. by Inducing a Higher Drought Tolerance

“…In this paper, the MSAP technique was used in order to determine the level of DNA methylation in Z. mays under either water deficiency or Se treatment. The average of total relative cytosine methylation was 60.85% and was higher than that 26.15 and 32.15%, previously reported for maize leaves by Zhao et al (2007) and Yang et al (2011) , respectively, but it was lower than 68.55% reported in the same species by Sun et al (2015) .…”

Heterotic patterns of primary and secondary metabolites in the oilseed crop Brassica juncea

“…On the other hand, if both parental alleles contribute equally to gene expression in a hybrid, they are said to exhibit additive behavior and the expression level of genes or proteins is equal to the average of both the parents referred to as the mid-parent value (MPV). High throughput methods have enabled the re-examination of the proportion of additive and non-additive expressions in heterosis, including analysis of quantitative trait loci (QTL; Li et al 2008;Meyer et al 2010;Shi et al 2011;Andorf et al 2012;Giraud et al 2014;Liu et al 2014a), gene expression (Song et al 2007;Stupar et al 2008;Ma et al 2011;Shen et al 2012;Qin et al 2013), genome-wide transcriptomics (Paschold et al 2012;Zhai et al 2013;Ding et al 2014;Paschold et al 2014;Zhiguo et al 2014;Groszmann et al 2015, Wang et al 2015, DNA methylation pattern analysis (Shen et al 2012;Liu et al 2014b), comparative proteomics (Dahal et al 2012;Wang et al 2014) and small and micro RNA transcriptomics (Ding et al 2012;Shen et al 2012;Li et al 2014;Zhang et al 2014;Xin et al 2015). However, none of the current genetic models sufficiently explain heterosis in polyploid plants, which is compounded by genomic dosage, complex allelic and genic interactions, and epigenetic regulation.…”

Transcriptome variations in hybrids of wild emmer wheat (Triticum turgidum ssp. dicoccoides)

“…A reduction in methylation can also take place following a ‘genomic shock’, as seen in events like hybridization or allopolyploidization [ 28 ]. As an illustration, in maize, hybrids derived from two inbred lines exhibited decreased methylation levels in comparison to their corresponding inbred counterparts, with the highest degree of demethylation observed in the hybrids [ 29 ]. Similarly, in this study, the methylation levels in the F4 hybrids were found to be lower compared to the parental lines.…”