The plants transformed by either Agrobacterium-mediated or directly delivered DNA transformation possess complex transgenic loci. The transgenes tend to be integrated into gene-rich regions on chromosomes due to selection of transgenic cells during tissue culture rather than integrated elsewhere randomly. Fragments of transferred DNA are interspersed with genomic DNA and filler DNA at most of transgenic loci except a few which contain complete single-copy of transgene. Analysis of transgenic loci flanking sequences indicated that deletion, duplication and chromosomal rearrangement often occurred for transgene and genomic DNA. The complete transgenic structure is important for its expression in transformed plants.
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