Parental epigenetic difference in DNA methylation-level may play contrasting roles for different agronomic traits related to yield heterosis in maize

Although, maize is the crop wherein heterosis or hybrid vigor has been exploited to nearly the fullest extent, the molecular and genetic basis underlying this remarkable biological phenomenon remains largely an enigma. To further explore the issue from an epigenetic perspective, we sought to probe for possible relationships between the parental epigenetic difference in the form of DNA methylation revealed by the epigenetic marker MSAP, among a set of 11 maize inbred lines and heterosis in four agronomic traits manifested by a set of 30 F1 hybrids resulting from a half-diallel crossing among the inbred lines. We found that a specific type of DNA methylation-level difference, that is, relative CHG (H denotes A, C or T) methylation levels at the 5'-CCGG-3' sites exhibits a statistically significant negative correlation with heterosis in the number of rows per ear (NRE) and a positive correlation with the number of kernels per row (NKR), whereas, no correlation was detected between any of the DNA methylation-level differences and the rest two studied traits, 100-kernel weight (HKW) and kernel weight per ear (KWE). In a sharp contrast, parental genetic distance revealed by the genetic marker AFLP did not show any correlation with heterosis for any of the four studied agronomic traits. Our results suggest that parental epigenetic difference in particular types of DNA methylation-level difference plays some significant roles in the manifestation of heterosis of specific traits in maize, but the effects can be in opposite directions, and hence, offsetting each other and cumulating to cryptic effects on yield, itself.