The conservation of allelic DNA methylation and its relationship with imprinting in maize.

Genomic imprinting refers to allele-specific expression of genes depending on parental origin, which is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected. However, the intraspecific genome-wide allelic epigenetic variation of maize and its correlation with imprinting variants remain elusive. Here, three reciprocal hybrids were generated by crossing inbred lines CAU5, B73 and Mo17 to analyze the intraspecific conservation of the imprinted genes in maize kernel. In our study, majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum and Arabidopsis) and enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation exists as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes by CRISPR/Cas9 method resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and imprinted genes play an important role in kernel development.