Abstract：To accurately identify exogenous chromosome fragments or genes plays an important role in crop genetic improvement. Although the molecular markers have been widely used in detection of exogenous chromosome fragments or genes, the efficiency of identificating a few positive plants in large group is very low. In this study, DNA samples of 147 plants in BC2F1 population which was established by Gossypium hirsutum Xinluzao 48 and G. barbadense chromosome segment substitution lines CSSL-122 through hybridization and backcross were used as materials, which were arrayed by constructing 2 dimensional matrix. The test samples were mixed according to the row and column, respectively, to get m rows of mixed samples and n columns of mixed samples, taking m=n=8 matrices as example: The m×n=64 mixed samples were obtained to test. The positive samples containing exogenous chromosome fragments in the matrix could be identified accordingly to the detection results. Results showed that exogenous Gossypium barbadense chromosome fragments in G. hirsutum could be detected quickly by using the test method of establishing a matrix mixing bank based on PCR-SSR. In addition, the accuracy of the method was verified by means of sample detection one by one furtherly. Statistical analysis showed that frequency of positive sample detection was less than 7.81%, cost saving ratio of detecting the samples could be maintained at more than 50%. Detection method of constructing the matrix mixed pool based on PCR-SSR will provide a new method for the rapid identification of exogenous Gossypium barbadense chromosome fragment in Gossypium hirsutum.
