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DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in  Brassica , a set of intraspecific hybrids in  Brassica rapa  and  B. napus  and interspecific hybrids between  B. rapa  and  B. napus , together with parental lines, were used to monitor alterations in cytosine methylation at  5′-CCGG  sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of  Brassica , although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at  5′-CCGG  sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from  B. rapa  and  B. napus .

DNA Methylation Alterations at 5′-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus