The invention belongs to the technical field of rape 
molecular breeding, in particular relates to a preparation method of a codominant SNP (
Single Nucleotide Polymorphism) 
molecular marker closely linked with the 
linolenic acid content of a cabbage type rape and application thereof as the marker in the auxiliary selection of the low 
linolenic acid cabbage type rape. The low 
linolenic acid cabbage type rape strain A254 and high linolenic acid cabbage type rape strain A177 genomes 
DNA are amplified by using primers to respectively obtain two 
DNA amplified fragments, then 
cloning, sequencing and 
nucleotide sequences comparison are carried out on the four 
DNA amplified fragments; according to the difference of the sequences, the second bases at 3'-end of a 
forward primer and a 
reverse primer are mispaired, primer pairs of YQ-fad31-1, YQ-fad31-2, YQ-fad32-1 and YQ-fad32-2 are designed, the PCR (
Polymerase Chain Reaction) amplification is carried out on the primer pairs of YQ-fad31-1, YQ-fad31-2, YQ-fad32-1 and YQ-fad32-2, and the PCR amplification and 
group detection effects are analyzed to obtain the codominant SNP 
molecular marker linked with low linolenic acid genes of the cabbage type rape. The invention provides a new marker for the rape 
molecular breeding. In the invention, a mispairing strategy of the 3'-end of the primer is firstly applied to the development and the detection of the SNP polymorphic marker of the cabbage type rape, and a means of synchronously mispairing the 
forward primer and the 
reverse primer is firstly adopted to develop the SNP marker based on the PCR amplification and an 
agarose gel electrophoresis in the cabbage type rape of an allopolyploid 
crop. The invention synchronously discloses a method for preparing the 
molecular marker and the application thereof.