Multiple gene clusters responsive to Plasmopara viticola infection in grapevines

Abstract

Plasmopara viticola is a plant pathogenic oomycete that causes downy mildew in grapevines. Shine Muscat, a hybrid grapevine cultivar of Vitis vinifera and V. labrascana produced in Japan, exhibits resistance to P. viticola. Transcriptome analyses were performed to elucidate the mechanism of defense against P. viticola infection in Shine Muscat. Using two sets of RNA seq data and V. vinifera genome information, transcriptome analyses reproducibly identified 269 and 55 grapevine genes that were upregulated and downregulated, respectively, in response to P. viticola infection. Gene ontology analysis of the differentially expressed genes suggested that Shine Muscat recognizes P. viticola invasion at the cell membrane, with subsequent transmission of signals into the cells to initiate a response. Furthermore, P. viticola–responsive paralogous genes were distributed among 8 clusters located on chromosomes 2, 5, 6, 9, 12, and 16 in the V. vinifera genome. These gene clusters encode PR5, PR10, dirigent protein, pleiotropic drug resistance protein, an uncharacterized protein, phenylalanine ammonia-lyase, ethylene-responsive transcription factor, and stilbene synthase, respectively. The gene cluster encoding ethylene-responsive transcription factor was downregulated by P. viticola infection, whereas the other 7 gene clusters were upregulated. With the exception of the gene cluster encoding the uncharacterized protein, the genes were associated with plant defense mechanisms, suggesting that synchronized transcription of these gene clusters plays an important role in the grapevine defense mechanism against P. viticola. This is the first study to identify multiple infection-responsive gene clusters in the grapevine genome.