Abstract: The present invention relates to the field of plant molecular breeding, and provides methods for estimating additive and dominant genetic effects of single methylation polymorphisms (SMPs) on quantitative traits. The method comprises the following steps: 1) collecting samples and measuring phenotype in a natural population, and extracting genomic DNA from the samples; 2) constructing MethylC-seq libraries using the sample genomic DNA, and sequencing; 3) identifying the SMPs from the DNA methylation sequencing reads, and performing genotyping; and 4) performing epigenome-wide association study on the SMPs and the phenotypic data using a Mixed Linear Model (MLM), identifying SMPs that are significantly associated with the phenotype, and estimating the additive and dominant genetic effects. The method can provide a new technical guidance for gene marker-assisted breeding, and has important theoretical and breeding values.