There are at least 2 ways we can narrow down the random insertion of transgenes in the genomes when doing plant genetic transformation.
1. Site-specific recombination (SSR) system- mediated gene integration. Most SSR systems derive from microbes or lower eukaryotes such as yeast. A transgene can be directed to a pre-determined 'landing-pad' (at a locus) through the site-specific recombination between a specific sequence on the landing pad and a specific sequence on a plasmid carrying your gene-of-interest. Please visit my profile for this topic.
2. Designer nuclease (such as ZFN, TALEN etc)- mediated gene integration at a specific locus through homologous recombination. Designer nucleases cause DNA double-stranded breaks (DSBs) at a specific locus. The cellular DSB repair systems will kick in to fix the break, including a homologous recombination (HR) mechanism. By providing a donor plasmid with your gene-of-interest, this gene can be integrated into the specific locus through HR.