Much of phenotypic variation is the result of alteration in gene expression patterns. Maize exhibits extremely high levels of diversity in DNA sequences, gene expression and phenotypes. Transcript profiling studies were conducted to explore the relationship between genotype and gene expression patterns. Consistent with prior reports these studies demonstrated that gene expression can be controlled not only by genetic but also epigenetic determinants. Importantly, the identified widespread natural antisense transcripts (NATs) and hundreds of the NAT-eQTL regulating the expression of NATs further increase the complexity of gene expression. These observations and conclusions enhance our understanding of various fundamental biology questions. For example, heterosis is the phenomenon that the progeny of particular inbred lines exhibit superior performance as compared to both parents. We have hypothesized that such extreme phenotypic variations between inbred and hybrid are explained by multiple factors, including epigenetic factors such as those studied here.