Grain-yield heterosis in Zea mays L. shows positive correlation with parental difference in CHG methylation

Heterosis has been extensively exploited in maize (Zea mays L.), but the underlying molecular basis remains poorly understood. Identification of molecular markers in the inbred parental lines, which is reliably associated with heterosis, is of apparent breeding interest. We report here that a specific type of cytosine-methylation-based epigenetic difference, that is, CHG methylation (H is A, C, or T) at the 5'-CCGG sites of randomly sampled genomic loci, is positively correlated with grain yield (GY) heterosis in maize (P < 0.01). This conclusion was reached based on an analysis of cytosine methylation differences for 12 maize parental inbred lines by methylation-sensitive amplification polymorphism analysis and on field trials for GY of the inbred parental lines together with 132 [F.sub.1] hybrids produced by complete diallel crossing. Multiple regression analysis showed that the parental difference in CHG methylation level (relative amount) was positively correlated with both midparent heterosis and better-parent heterosis in GY. In contrast, no correlation with GY heterosis was detected for parental differences in CG or total (CG+CHG) methylation levels. Also, no significant correlation was obtained between the amplified fragment length polymorphism-based genetic difference and heterosis in GY for the same set of inbred lines and hybrids. We conclude that parental difference in CHG methylation is a promising molecular marker for grouping germplasms into heterotic groups in maize. doi: 10.2135/cropsci2010.01.0023