Methods and compositions are provided that employ microRNA (miRNA) that, when expressed in a plant cell, is capable of reducing the level of mRNA of a target sequence (i.e. endogenous sequence) without reducing the level of mRNA of one or more closely related sequences. While miRNAs can be designed with specificity for a particular target sequence, the instant application demonstrates that a miRNA can specifically silence a target sequence without silencing a closely related sequence having high sequence identity to the target sequence. In certain embodiments, an endogenous target sequence can be suppressed with a recombinant miRNA expression construct without silencing a recombinant polynucleotide of interest having a sequence closely related to the target sequence. Such methods and compositions employ recombinant miRNA expression constructs which produce a 21-nt miRNA. Transgenic plant cells, plants and seeds incorporating miRNA expression constructs and recombinant polynucleotide constructs comprising polynucleotides of interest are also provided.
