Plant viral vectors are valuable tools for host gene analysis, thus possessing important applications as reverse genetics tools for gene function studies. Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA virus of Secoviridae. Insertion of relatively short cDNA fragments (96nts) corresponding to different regions of soybean (Glycine max) phytoene desaturase1 (GmPDS1) into the 3' UTR of BPMV RNA2 initiated weak photobleaching manifested by white spots along the veins of soybean leaves. MFold algorithm was used to predict the RNA secondary structure of a 66 nucleotide region (nt #400-466) within the 5' UTR of BPMV RNA2. This region could potentially fold into a stem-loop (SL) designated as SLC. The functional analysis indicated the importance of the bottom section of the stem because disrupting this portion of structure completely abolished the BPMV infectivity. A 47 nt region, SLA, spanning from nt #263-309 of the 5' UTR of BPMV RNA2 was deleted. Nonviral inserts (GmPDS1 or GmPDS1/GmDCL4) of up to 325 and 625 nt, respectively, were tolerated by the same region and successfully down regulated the expression of their corresponding genes. Furthermore, one insertion mutant, V5UE-GmPDS1/GmDCL2, underwent recombination in the infected plants, leading to the truncation of 112nts (nt #250-361).