Allele-specifc expression refers to the preferential expression of one of the two alleles in a diploid genome,which has been thought largely attributable to the associated cis-element variation and allele-specifc epigenetic modifcation patterns.Allele-specifc expression may contribute to the heterosis(or hybrid vigor) effect in hybrid plants that are produced from crosses of closely-related species,subspecies and/or inbred lines.In this study,using Illumina high-throughput sequencing of maize transcriptomics,chromatic H3K27me3 histone modifcation and DNA methylation data,we developed a new computational framework to identify allele-specifcally expressed genes by simultaneously tracking allele-specifc gene expression patterns and the epigenetic modifcation landscape in the seedling tissues of hybrid maize.This approach relies on detecting nucleotide polymorphisms and any genomic structural variation between two parental genomes in order to distinguish paternally or maternally derived sequencing reads.This computational pipeline also incorporates a modifed Chi-square test to statistically identify allele-specifc gene expression and epigenetic modifcation based on the Poisson distribution.
