Epigenetic variations in plant hybrids and their potential roles in heterosis.

Heterosis, one of the most important biological phenomena, refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass, growth rate and yield. Despite its successful application in breeding and agronomic production of many crop and animal varieties, the molecular basis of heterosis remains elusive. The classic genetic explanations for heterosis centered on three hypotheses: dominance (Davenport, 1908; Bruce, 1910; Keeble and Pellew, 1910; Jones, 1917), overdominance (East, 1908; Shull, 1908) and epistasis (Powers, 1944; Yu et al., 1997). However, these hypotheses are largely conceptual and not connected to molecular principles, and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al., 2003). Recently, many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level. These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g., Swanson-Wagner et al., 2006; Zhang et al., 2008; Wei et al., 2009; Song et al., 2010). Research suggests that genetic components, including cis-acting elements and trans-acting factors, are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker, 2007; Springer and Stupar, 2007; Zhang et al., 2008). However, other research indicates that epigenetic components, the regulators of chromatin states and genome activity, also have the potential to impact heterosis (e.g., Ha et al., 2009; He et al., 2010;