In order to provide theoretical basis for the screening and identification of excellent materials and the preliminary study of resistance mechanisms in flowering Chinese cabbage(Brassica rapa var. parachinensis) cultivars, the SCoT polymorphism was used to analyze by native polyacrylamide gel electrophoresis with Caixin65, Caixin69 and F2 segregating lines. The detection efficiency, genetic diversity and differential cloning bands of native polyacrylamide gel electrophoresis were analyzed. The results showed that the native polyacrylamide gel could detect the SCoT polymorphism and genetic diversity between parents and offspring, and SCoT bands were more and clearer on native polyacrylamide gel than agarose gel, which elevated the detection efficiency of SCoT. Ten native polyacrylamide gel differential fragments were selected for cloning and sequencing, and four insect-susceptible sequences and six insect-resistant sequences were obtained. GENSCAN predicted that 8 of 10 SCoT sequences had promoter, terminal and open reading frame of genes. Homology search showed that function from 4 SCoT sequences obtained from Caixin69 included Brassica napus ubiquitin carboxyl-terminal hydrolase MINDY-1-like (LOC106367017) mRNA, B. rapa subsp. pekinensis clone KBrB026J02 complete sequence, B. rapa mitochondrial pyruvate carrier 2 (LOC103839865) mRNA, B. oleracea HDEM genome scaffold C3. Function from 6 SCoT sequences obtained from Caixin65 included B. rapa RNA pseudouridine synthase 4 mitochondrial (LOC103869454) mRNA, Trichodermaharzianum CBS 226.95 hypothetical protein (M431DRAFT_397944) mRNA, B. rapa subsp. nipposinica mitochondrial DNA complete sequence cultivar: Oushou hakusai, B. napus uncharacterized LOC106451263 (LOC106451263) mRNA, B. rapa subsp. pekinensis clone KBrB017P15 complete sequence. The analysis based on native polyacrylamide gel electrophoresis elevated the clarity and resolution SCoT marker, the detection level of genetic diversity level and accuracy of clone sequences. SCoT analysis based on native polyacrylamide gel electrophoresis was not only an efficiency method to detect genetic level, but also a simple and efficiency method to clone genes which could be used in genomics. The study improved the screening and identification efficiency of excellent strains, speeded up the breeding process, and provided a theoretical basis for further research on the mechanism of the insect-resistant breeding of flowering Chinese cabbage.
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