Evaluation of the relationship between DNA methylation status and heterosis in soybean with MethylRAD technique

Heterosis plays an important role in the breeding of commercial crops, but the molecular mechanism behind this phenomenon is still unclear. To better understand the molecular basis of heterosis in soybean, the correlation between DNA methylation status and heterosis in soybean was tested. From three soybean varieties used as parents, six hybrid combinations were generated. Twelve traits of the nine materials were investigated to study the relationship between DNA methylation level differences and heterosis. In this study, MethylRAD technique was used to evaluate the genomic methylation status among the six reciprocal soybean F1 hybrids and their parents in the immature grains. Results showed that the total site number of methylation and methylation levels of the F1 hybrids with strong heterosis were in a status between the two parents and the ones with weak heterosis were generally below that of two parents. Thus, it was beneficial to promote heterosis when the numbers of methylation sites and methylation levels were between two parents. Among three types of methylation variations, the type that parental demethylated and the progeny methylated (type A) may be relative to improve heterosis of some traits. The type A of methylation variations was significantly positively correlated with the mid-parent heterosis (MPH) of the fat content (r = 0.98**), the branch number per plant (r = 0.84), and also was significantly positively correlated with the BPH of the branch number per plant (r = 0.82*) and the stems thick (r = 0.81*). These results implied that both the methylation and demethylation in hybrids relative to their parents may control the expression of the genes that were associated with partial phenotypic variation in hybrids.