Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses

Abstract

A plant virus cDNA chip was developed by using viral cDNA clones and microarray technology. The cDNA chip was designed for detection and differentiation of the four species of selected cucurbit-infecting tobamoviruses [target viruses: Cucumber green mottle mosaic virus (CGMMV); Cucumber fruit mottle mosaic virus (CFMMV); Kyuri green mottle mosaic virus (KGMMV); and Zucchini green mottle mosaic virus (ZGMMV)]. The chip consisted of cDNA clones of the four cucurbit-infecting tobamoviruses, two target-related tobamoviruses, and another three unrelated plant viruses. Polymerase chain reaction products were amplified from the selected cDNA clones and arrayed onto slide glass. The cDNA chip, which was called cucurbit-virus chip, detected successfully specific target viruses. When applied to probes made from ZGMMV-infected samples, ZGMMV reacted strongly with its homologous cDNA and moderately reacted with KGMMV and CFMMV, while it did not react with CGMMV on the same chip. CGMMV probe gave strong signal intensity to its homologous cDNA spot and weakly reacted with ZGMMV, KGMMV, and CFMMV. The signal intensity of all combinations of probe and target was correlated significantly with nucleotide sequence identities between the probes and target viruses based on scatter diagrams. The signals could be made as image files for specific virus detection, and this could be useful for virus identification and differentiation. This is the first report of plant virus detection by using cDNA chip technology.