Abstract：Marker-assisted selection (MAS) is one of main techniques, which can greatly accelerate the process and improve the efficiency of plant breeding, but it depends on the data of molecular genetic diversity, especially on the research on target genes and the development of linked marker to target genes. Sucrose content is one of the most important characters, which closely related to the sucrose metabolism genes. In cultivation, cold stress is an important factor that affects the growth of sugarcane. For above, TRAP marker was occupied to study on the genetic diversity of thirty-three important sugarcane clones, including some main cultivars, recent released varieties and some germplasms introduced abroad recently. The total of five genes related to sucrose metabolism plus one related to cold stress were selected as target genes and were used to design the anchored primers for pairing with nine arbitrary primers. In total, there were 90 primer combinations and thirty-four combinations of primers were screened to produce clear banding patterns and polymorphisms. The result showed that a total of 579 bands were scored with the 34 pairs of primed screened, of which 288 taking 49.74% in total were polymorphisms. Thus, the polymorphism results from combinations of forward fixed and arbitrary primers reflected that the exonic regions outside the open reading frames (ORFs) of sugarcane genes have a very high mutation rate and diversity. The cluster analyses using UPGMA revealed a narrow genetic diversity among the entries with genetic distance (GD) ranging from 0.26 to 0.63. At the GD level of 0.52, 33 sugarcane , the cluster analysis based on TRAP analysis with six target-genes, while can’t contribute completely to parentage grouping of the 33 clones, can really reflect the variation degree of these 33 sugarcane clones based on TRAP polymorphism of these key genes. At the same time, some special germplasms were found. Therefore, the data from the TRAP analysis can enhance the accumulation of basic data of parent selection and combination configuration and help in high-sucrose and cold-tolerance breeding practice. Furthermore, it can also be concluded from this study that TRAP marker technique have many other merits, such as good repeatability, high efficiency, and easy operation, which suggests its great potential applicability in sugarcane classification, important trait marker etc. In a word, the results of this study have an important theoretical and practical
