Construction method and use of corps methylation differential DNA marker linkage map

The invention relates to a construction method of a crop methylation difference DNA marker linkage map, and the application thereof, aiming at obtaining the advantages of being more directly relevant to gene expression and being applied to the assistant breeding of crops. The invention firstly obtains methylation specificity DNA segments, then determines the linkage strength among the segments and among target character and the separation segments according to the similarity and difference of the methylation difference segments among hybridization parents and the separation condition of the segments in descendant groups such as hybridization and backcross, etc.; methylation difference DNA molecule markers closely linked with the target character is searched so as to construct a methylation sensitive molecule marker linkage map in the period; and the method can be used for assisting selection of good character in breeding.