The present invention provides systems and methods for generating clonal root lines, clonal root cell lines, clonal plant cell lines, and clonal plants and for expressing gene products in such cell lines and plants. According to certain of the inventive methods, a viral vector containing a polynucleotide of interest operably linked to a promoter is introduced into a plant or portion thereof. Plant material (e.g., leaf portions) containing the viral vector are used to generate clonal root lines, e.g., by contacting them with A. rhizogenes so as to form hairy roots. The hairy roots are derived from single ancestral cells and are therefore clonal. These clonal root lines contain the viral vector and express the polynucleotide of interest. Clonal root cell lines, clonal plant cell lines, and clonal plants are obtained from the clonal roots. According to certain other inventive methods, a viral vector containing a polynucleotide of interest operably linked to a promoter is introduced into cells of a plant cell line (e.g., pre-existing or newly derived) that is maintained in culture. Clonal plant cell lines that express the polynucleotide of interest are obtained, e.g., by successive rounds of enrichment until a population of cells exhibiting stable expression is obtained. Clonal plants whose cells contain the viral vector are obtained from the clonal plant cell lines using standard methods. The invention provides clonal root lines, clonal root cell lines, clonal plant cell lines, and clonal plants generated using the inventive methods.