Document Type

Dissertation - Open Access

Award Date

2022

Degree Name

Doctor of Philosophy (PhD)

Department / School

Agronomy, Horticulture, and Plant Science

First Advisor

Anne Fennell

Keywords

Endodormancy, Genome Assembly, Grapevine, RNA-seq, Vitis Riparia

Abstract

Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in woody perennial plants is bud endodormancy, a state of hibernation that is activated in response to decreasing temperatures and photoperiod. The current understanding of this process is limited, but it is believed that induction into endodormancy is controlled by a combination of hormones and transcriptional regulators internal to the cell. Grapevines have variable resistance to cold depending on species. Of the approximately 80 identified grapevine species, North American and Asian grapevines have more enhanced winter survival. Vitis riparia, the riverbank grapevine, is one of the most resistant of the genus and has been identified to enter endodormancy at longer day lengths. Investigating why V. riparia responds differently may reveal key genes and molecular mechanisms needed for photoperiod induced endodormancy induction. To investigate this speciesspecific response, we first sought to establish a genome assembly for this nonmodel species. Sequencing and assembly of DNA from V. riparia resulted in 69,616 scaffolds at an N50 of 518,740. Reference, mapping, and nonhomologous estimates of misassembly suggest that this draft assembly is of a high quality. cDNA sequence prediction from multiple RNA-seq studies resulted in 40,019 genes. Variations in gene families demonstrated that there were genetic differences between V. riparia and V. vinifera which could explain the difference in response to photoperiod and winter survival. One of the best indicators in plants of the physiological response to external regulators is changes in gene expression. We measured changes in expression during endodormancy transition in two F2 genotypes at multiple time periods of exposure to short day (SD, 13h) and long day (LD, 15h) photoperiods. Expression of genes associated with cell cycle control and phenylpropanoid biosynthesis were downregulated in response to SD treatment. The F2-110 genotype which more closely resembled V. riparia had greater natural expression of auxin signaling genes than the F2-040. This was further confirmed by coexpression networks that were highly correlated with short day induced endodormancy transition and F2-110 genotypes. Regulation of endodormancy induction is a primary concern for this study. We performed small-RNA seq to find miRNA that were differentially regulated during dormancy transition. A machine learning based prediction of miRNA identified 216 regulatory sequences in the non-model V. riparia genome. We found that miRNA families 166 and 167 were predominantly upregulated during dormancy transition. This coincided with downregulation of cell cycle control genes and suppression of cyclins and expansins by the MYB3R1 transcription factor. Motif enrichment of gene co-expression clusters identified PLETHORA 1 as a major regulator of the stem cell state during dormant conditions. These results suggest that auxin is a major regulator of endodormancy through control of cell differentiation in the bud apical meristem. Auxin signaling may therefore also be a contributor to the enhanced dormancy response in V. riparia due to an increased sensitivity to auxin in the buds. Further research is needed to determine auxin’s role in regulation of the process of endodormancy and what effect it has in crop winter survival.

Number of Pages

139

Publisher

South Dakota State University

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Rights Statement

In Copyright