Thesis
Small RNA Profiling in a Red-Fruited Wine Grape Cultivar Infected with Grapevine Red Blotch Virus
Washington State University
Master of Science (MS), Washington State University
2023
DOI:
https://doi.org/10.7273/000005324
Abstract
Viral diseases are a significant threat to the sustainability of the grape and wine industry in Washington State. Red blotch disease, caused by Grapevine red blotch virus (GRBV, genus Grablovirus, family Geminiviridae), negatively impacts vine health, fruit yield, and quality, leading to substantial economic losses to growers. While recent studies have enhanced our understanding of the epidemiology of GRBV and its effects, little is known about the molecular basis of virus-host interactions. Since small RNAs (sRNAs) are known to play a central role in host-virus interactions, this study was undertaken to investigate sRNA dynamics in two tissue types at two phenological stages (asymptomatic pre- and symptomatic post-veraison) of GRBV-infected grapevines (Vitis vinifera cv. Merlot). High-throughput sequencing (HTS) was employed to analyze total RNA isolated from leaf and berry samples collected from healthy and virus-infected Merlot vines at both phenological stages. Host-specific microRNAs (miRNAs) and virus- and viroid-derived siRNAs (vsiRNAs and vdsiRNAs) were identified from high-quality reads from HTS. Among the 140 miRNAs detected, 41 belonging to 18 miRNA families exhibited significant differential expression in response to GRBV infection. Notably, miR159, miR166, miR395, miR396, and vvi-miR2950 were differentially expressed in both berries and leaves. Furthermore, 50 miRNAs showed differential expression in samples from pre- and post-veraison stages. A total of 58 conserved and 41 novel targets for known V. vinifera miRNAs were predicted and validated using degradome sequencing data from leaf samples from pre- and post-veraison stages. Additionally, vdsiRNAs specific to Grapevine yellow-speckle viroid-1 and Hop stunt viroid were found in all samples, while vsiRNAs specific to GRBV were present only in GRBV-positive samples. Out of the 83 most abundant vsiRNAs, putative targets within the grapevine transcriptome were identified for eight vsiRNAs. The vsiRNAs predominantly ranged from 19 to 24 nucleotides (nt), with the 21nt size being the most abundant. Mapping vsiRNAs across the GRBV genome revealed an uneven distribution, with vsiRNA-generating hotspots predominantly located in the V3 ORF. Interestingly, significantly higher levels of HSVd RNAs were observed in GRBV-positive samples compared to GRBV-negative samples, suggesting a potential synergistic interaction between the two pathogens.
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Details
- Title
- Small RNA Profiling in a Red-Fruited Wine Grape Cultivar Infected with Grapevine Red Blotch Virus
- Creators
- Noah Patrick Nilson Ault
- Contributors
- Naidu Rayapati (Advisor)Ramanjulu Sunkar (Committee Member)Roy Navarre (Committee Member)Gary Grove (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Department of Plant Pathology
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University
- Number of pages
- 140
- Identifiers
- 99901031037901842
- Language
- English
- Resource Type
- Thesis