A rice microRNA, miR164 gene, that controls plant root system development and fertility, is obtained through gene isolation, cloning and function verification. Uses of a nucleic acid fragment comprising miR164, which fragment may confer a transformed plant with the ability to increase root number and to alter fertility, wherein the said nucleic acid fragment is selected from one of the following nucleotide sequences: 1) a DNA sequence as shown in SEQ ID NO: 1; 2) a RNA sequence as shown in SEQ ID NO:2; or 3) the conserved sequence of miR164 having the same function as 1) or 2). The nucleotide sequence containing the precursor of miR164 is ligated with an exogenous promoter and introduced into rice to obtain transgenic rice plants which has large root systems but became infertile. The fertility can be restored by external application of phytohormones.