Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties.

Grapevine Rupestris stem pitting-associated virus (GRSPaV) is a member of the genus Foveavirus within the family Flexiviridae. GRSPaV is closely associated with the disease Rupestris stem pitting and is frequently detected in grapevines worldwide. Previous research in several laboratories suggests that GRSPaV consists of a family of sequence variants. However, the genetic composition of GRSPaV variants in viral isolates from scion and rootstock varieties has not been studied extensively. In this report, the genetic diversity and population structure of GRSPaV isolates from scion and rootstock varieties were analysed using two pairs of primers targeting two different genomic regions encoding the helicase domain of the replicase and the capsid protein. In total, 190 cDNA clones derived from 24 isolates were sequenced and analysed. At least four major groups of GRSPaV variants were found to exist in grapevines. Interestingly, the majority of the scion varieties (9/10) that were analysed, regardless of their genetic background and geographical origin, harboured complex viral populations composed of two to four distinct viral variants. In contrast, the viral populations in isolates from rootstock varieties were homogeneous and comprised a single variant. The practice of grafting between scion and rootstock varieties commonly used in modern viticulture, coupled with the frequent regional and international exchange of propagating materials, may have played a major role in the ubiquitous distribution and mixed infections of distinct GRSPaV variants among scion varieties. The possible origin and evolution of GRSPaV are also discussed.