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 dsRNA as template and the Life Sciences 454 high-throughput sequencing. In phase 1 (year 1) of this project we selected FPS Syrah clone 6 which was showing sever pitting, grooving and wood necrosis on the woody cylinder including die back and declining. For control a healthy looking Syrah clone 8 was selected. The data revealed that the Syrah clone 6 supported a mixed infection that included seven different RNA genomes including 4 viruses and 3 viroids. In the second phase (year 2) of the project, 5 more syrah clones were selected. These clones included three which are reported to produce high incidence of Syrah decline syndrome (clons B0 and B1 obtained from France and clone 99) and 2 with moderate incidence (clones 525 and 877). Total of 76.6 megabases of sequence information, from 371,906 fragment reads (each approximately 200 bases long) were initially produced from these five source vines in which 354,441 were high quality reads. The assembly and sequence analysis of the quality reads showed that Grapevine rupestris stem pitting associated virus (GRSPaV) was present in all of these vines with the highest concentration (based on the number of reads) compared to any other viruses found in these vines. Grapevine rupestris vein feathering virus (GRVFV) and Grapevine redglobe virus (GRGV) were found in clones 99 and 877 and Grapevine syrah virus 1 (GSyV-1) was found only in clone 877 in a very low titer. In a different experiment detailed information was obtained in regards to the population of the strains of the viruses found in these plants. In this study, for example, the sequences of GRSPaV found in each Syrah clone were compared with the sequences of different strains of the virus found in the GenBank. All 7 Syrah clones used in our investigation were carrying all 9 different strains of the virus (reported up to date) except for clon 525 which lacked strains Hail and Char (both reported from Japan). However, large amount of GRSPaV sequences still available from each Syrah clone that did not match the sequences of any existing strain and they may belong to new strains of the virus.