Methods and compositions using a site-specific integration system are combined with methods and compositions which deliver compositions via microinjection directly to the embryo sac of a plant. The methods allow for various components of the site-specific recombination system to be introduced into the cellular environment of the embryo sac a composition comprising at least one component of the site-specific recombination system is injected into an embryo sac, providing improved efficiency of expression, recombination, integration, exchange, excision and/or inversion of a polynucleotide of interest. The polynucleotide of interest may be stably integrated into the genome of the egg cell, zygote, embryo, or endosperm, and tissues, plant parts, and/or plants produced therefrom. Cells, egg cells, zygotes, embryos, endosperm, tissues, seeds, and/or plants produced by the methods and comprising the polynucleotide(s) of interest are also provided.