Etiology and Detection of the Cause of Syrah Decline in Syrah grapevine

Syrah decline disease is a well documented problem in California and France. It is characterized by swelling and cracking of the graft union, stem pitting and grooving, and premature leaf reddening. French scientist have been studying this problem since 1999 and have failed to find any correlation with genetic incompatibility, known pathogens (viruses, bacteria, fungi, viroids), or environmental conditions. The potential of the Syrah decline disease to be associated with a virus is suspicious and the symptoms observed support the hypothesis.

In a search for viruses associated with decline symptoms of Syrah grapevines, we have undertaken an analysis of total plant RNA sequences using Life Sciences 454 high-throughput sequencing. 67.5 megabases of quality sequence data were derived from reverse-transcribed cDNA fragments, and screened for sequences of viral or viroid origin. The data revealed that a Syrah vine, FPS clone 6, showing decline symptoms supported a mixed infection that included seven different RNA genomes. Four viruses and three viroids were identified. Three viruses were found to be the predominant agents in a declining Syrah plant. Two of these were known viruses, each of which has been observed to cause a mild or asymptomatic infection when present singly. Grapevine rupestris stem-pitting associated virus (GRSPaV, a foviavirus) was the most prevalent virus in the census, as represented by fragment count. Another predominant virus found was a marafivirus, Grapevine rupestris vein-feathering virus (GRVFV) and The third one

was a new virus tentatively named Grapevine Syrah virus 1 (GSyV-1) and was most closely homologous to GRVFV. GSyV-1 differed from other marafivirus species by 40% or more and had not been identified in multiple analyses done using previously available technologies but the high number of fragments generated by the 454 analysis allowed for its identification against the background of the related and more prevalent GRVFV. The fourth virus found was a known virus, Grapevine leafroll associated virus 9, with low reads indicating to be present in the plant at low titer. Diagnostic primers were designed from unique sequence regions on the genome of GSyV-1. A field survey was conducted on samples collected from Napa, Sonoma and Yolo Co. using the specific detection primers for the virus. A preliminary analysis of 154 plants in vineyards where decline was evident showed only thirty vines (19%) positive for the virus. Further surveys are underway.

In the second experiment, samples were prepared from five Syrah clones and submitted to 454 sequencing facilities on November 2008 and the sequences were ready in early December. Total reads of 371,906 reads with approximately 200 nucleotides per read were produced and the sequence analysis is in progress. The Syrah clones included in this experiment were, clones 99 (high incidence of decline according to French scientists), 877 and 525 (both with moderate incidence of decline). Two other clones are designated as B0 and B1 which were obtained from France for this research project. B0 clone showed cracks at the union with no red leaf canopy and B1 showed cracks with red leaf canopy.