The present invention provides a method for selecting genomic DNA fragments which are useful for providing a plant with an agriculturally advantageous improvement. The method of the present invention comprises the steps of: 1) preparing genomic DNA from a plant, which is then cloned into a cloning vector to form a genomic DNA library; 2) introducing a genomic fragment from each of the genomic clones constituting the genomic DNA library separately into a plant to produce transgenic plants; 3) cultivating the transgenic plants or progeny thereof to select a plant exhibiting an agriculturally advantageous phenotypic variation; and 4) selecting the genomic DNA fragment, which was introduced in step (2) into the plant selected in step (3), as a purposed genomic DNA fragment.