High‐throughput sequence analysis of small RNAs in grapevine ( Vitis vinifera L.) affected by grapevine leafroll disease

Summary

Grapevine leafroll disease ( GLRD) is one of the most economically important virus diseases of grapevine ( Vitis spp.) worldwide. In this study, we used high‐throughput sequencing of c DNA libraries made from small RNAs (s RNAs) 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 RNAs specific to Grapevine leafroll‐associated virus 3 , Hop stunt viroid ( Hp SVd), Grapevine yellow speckle viroid 1 ( GYSVd‐1) and Grapevine yellow speckle viroid 2 ( GYSVd‐2) in symptomatic grapevines and s RNAs specific only to Hp SVd, GYSVd‐1 and GYSVd‐2 in nonsymptomatic grapevines. In addition to 135 previously identified conserved micro RNAs in grapevine ( Vvi‐mi Rs), we identified 10 novel and several candidate Vvi‐mi Rs 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 Vvi‐mi Rs indicated that individual members of an mi RNA family are differentially expressed in symptomatic and nonsymptomatic leaves. The high‐resolution mapping of s RNAs specific to an ampelovirus and three viroids in mixed infections, the identification of novel Vvi‐mi Rs and the modulation of certain conserved Vvi‐mi Rs 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.