High‐throughput sequence analysis of small RNA s in grapevine ( V itis vinifera L .) affected by grapevine leafroll disease

Summary Grapevine leafroll disease ( GLRD ) is one of the most economically important virus diseases of grapevine ( V itis spp.) worldwide. In this study, we used high‐throughput sequencing of c DNA libraries made from small RNA s (s RNA s) to compare profiles of s RNA populations recovered from own‐rooted Merlot grapevines with and without GLRD symptoms. The data revealed the presence of s RNA s specific to G rapevine leafroll‐associated virus 3 , H op stunt viroid ( H p SV d), G rapevine yellow speckle viroid 1 ( GYSV d‐1) and G rapevine yellow speckle viroid 2 ( GYSV d‐2) in symptomatic grapevines and s RNA s specific only to H p SV d, GYSV d‐1 and GYSV d‐2 in nonsymptomatic grapevines. In addition to 135 previously identified conserved micro RNA s in grapevine ( V vi‐mi R s), we identified 10 novel and several candidate V vi‐mi R s in both symptomatic and nonsymptomatic grapevine leaves based on the cloning of mi RNA star sequences. Quantitative real‐time reverse transcriptase‐polymerase chain reaction ( RT‐PCR ) of selected conserved V vi‐mi R s indicated that individual members of an mi RNA family are differentially expressed in symptomatic and nonsymptomatic leaves. The high‐resolution mapping of s RNA s specific to an ampelovirus and three viroids in mixed infections, the identification of novel V vi‐mi R s and the modulation of certain conserved V vi‐mi R s offers resources for the further elucidation of compatible host–pathogen interactions and for the provision of ecologically relevant information to better understand host–pathogen–environment interactions in a perennial fruit crop.