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.

Abstract: A method for identifying plant lncRNA and gene interaction includes obtaining population SNP genotype data of the lncRNA and the gene; obtaining population expression abundance data of the gene in the studied tissue; and obtaining target trait population phenotypic data. When three restrictive conditions defined by the method are satisfied at the same time, it is indicated that the lncRNA and the gene are interacted with each other and together affect the phenotypic variation of the target trait of the plant. The method is used to accurately detect the interaction relationship between P. tomentosa lncRNA LNC-0052611 and gene Pto-COMT25, and the interaction relationship affects the phenotypic variation of a diameter at breast height of P. tomentosa.