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Document Type

Dissertation - University Access Only

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Mathematics and Statistics

First Advisor

Anne Fennell


Grapevines are the most widely cultivated fruit crop in the world. Drought has become an increasingly important constraint on their survivability and productivity due to global climate change. However, there is limited molecular information available for rootstock responses in water stressed conditions. In this study, RNA-seq data were generated from Vitis riparia root and shoot tissues under water deficit (WD) and control (C) physiological conditions to develop an understanding of grapevine rootstock responses to water stress. A total of 1,385 and 6,925 Vitis genes were differentially expressed, and 20 and 33 molecular pathways were significantly enriched in WD relative to C treatments in root and shoot tissues, respectively. Blast comparison of de novo assembled V. riparia root and shoot transcriptomes revealed a high similarity with the V. vinifera V1 gene models. A total of 21,974 EST-SSR, 266,284 SNP, and 14,904 indel predicted molecular markers were identified from the assembled transcripts. Root vascular cylinder (RVC) datasets introduced complexities to the statistical analysis as they differed in size and sequencing depth relative to the whole root datasets. Several parametric and non-parametric bioinformatics tools using different normalization and statistical analysis algorithms were investigated to address the complexity associated with RNA-seq data analysis. In RVC, a total of 2,001 genes were differential expressed (q-value < 0.05 in WD relative to C treatment, among which 789 were up-regulated and 1,212 were down-regulated. This study provides extensive information on V. riparia's response to water stress at the molecular level and provides some of the first whole genome analysis of water stress in grapevine roots. Specifically, it is noted that the grapevine roots and shoots differ in their response to WD. ROS responsive genes, and several dehydration responsive transcription factors (ABA-dependent and independent) were more prevalent in shoot, while ABA biosynthesis and aquaporin genes were significantly enriched in root under WD conditions. These differential tissue responses highlight candidate genes that can be further functionally characterized for a role in WD tolerance and susceptibility. The root and shoot WD transcriptomes and predicted molecular markers provide valuable resources for functional gene analysis and for marker assisted breeding.

Library of Congress Subject Headings

Grapes -- Water requirements
Grapes -- Drought tolerance
Grapes -- Effect of stress on
Grapes -- Genetics


Includes bibliographical references (pages 117-129)



Number of Pages



South Dakota State University


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