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We have developed a new transformation method called MATVS (Multi-Auto-Transformation Vector System). The oncogenes (ipt or rol genes) of Agrobacterium are used as selectable markers to regenerate transgenic cells and to select marker-free transgenic plants in the MATVS. The chimeric ipt gene or the rol genes are combined withthe site-specific recombination R/RS system to remove the oncogenes from the transgenic cells after transformation. We report here the application of MATVS to transformation of tobacco, aspen, rice and snapdragon. (I) The GST-MAT vector pMAT8 has the native ipt gene and the R gene with a chemical inducible promoter (GST-II-27). Use of the GST-MAT vector generated marker-free transgenic tobacco plants cotaining a single copy transgene at high frequency. (2) Use of the GST-MAT vector pRBI11 containing the rbcS 3B-ipt gene produced transgenic marker-free hybrid aspen plants without crossing. (3) Use of the ipt-type MAT vector, pNPI30GFP, containing the 35S-ipt and 35S-R, genes, resulted in the regeneration of marker-free transgenic reice plants directly from infected scutellum tisues at high frequency within 1 mo. (4) Use of the rol-type MAT vector pNPI702, containing the rol genes and the 35S-R gene, produced transgenic marker-free plants of tobacco and snapdragon at high frequency without crossing. Our results show that the promoter of the ipt gene, the preculture periods of plant tissues and the culture medium are important factors to improve the generation efficiency of marker-free transgenic plants. We can rapidly produce marker-free transgenic plants without the production of ipt-shooty intermediates. Therefore, it is a most promising method to save time and work for the generation of marker-free transgenic plants in crops.