Author ORCID Identifier

https://orcid.org/0009-0009-9043-9968

Date Available

7-26-2024

Year of Publication

2023

Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation

College

Agriculture, Food and Environment

Department/School/Program

Plant and Soil Sciences

First Advisor

Dr. Carlos M. Rodríguez López

Abstract

Epigenetic memory of the growing environment is a process capable of increasing plants’ resilience to abiotic stimuli. The cultivated grapevine is a long-living perennial species with a large corpus of research suggesting that plant adaptation to the environment has implications for the selection of genetic material in a changing climate. Moreover, vine age has been traditionally correlated with enhanced fruit quality. Recent studies have shown that environment/age-acquired traits in grapevine (e.g., adaptation to the growing environment and fruit/wine quality, respectively) are associated with epigenetic mechanisms. These studies also indicate that of propagation type affects the maintenance/erasure of the acquired traits (i.e., callus-cutting propagation erases epigenetic memory, while plants propagated using layering maintain the acquired traits). This is important since commercial vineyards are almost exclusively propagated using callused cuttings. The main goal of this thesis is to characterize the molecular processes occurring during callused cutting propagation in grapevines to determine the mechanisms erasing epigenetic memory. We hypothesize that the observed phenotypic differences between ortets and their ramets are the result of a molecular rejuvenation induced by the vegetative propagation process and that the callus tissue generated during vegetative propagation is the source of a mobile signal responsible for the rejuvenation of the propagules. To test these hypotheses, I used 1) a multi-omic approach to compare epigenetic and gene expression profiles in grapevine leaves produced before (old) and after (rejuvenated) propagation to the first leaf produced by seed-derived plantlets (juvenile), to determine if callused cutting production induces a molecular rejuvenation that explains the phenotypic differences observed in commercial vineyards; 2) analyzed the molecular changes associated with callus formation and progression to determine the possibility of the generation of mobile signals causing rejuvenation; and 3) used a bioinformatic approach to compare the sequential appearance of RNA molecules in callus tissues prior to apical meristems as an indication of their mobility. Briefly, my results show that the global DNA methylation and gene expression profiles of rejuvenated and juvenile vines are more similar to each other than to old ones. Detailed analysis showed that the DNA methylation and expression of genes (protein-coding and microRNA) of two pathways regulating the juvenile to adult-phase transition show a reversion to the juvenile state in vegetatively propagated plants. Additionally, functional analysis of differentially expressed genes during callus production identified an increased expression of RNA methylation and RNA transport pathways, indicating the possibility of RNA mobility. Finally, a number of potential mobile RNAs acting as rejuvenation signals were identified bioinformatically. These results support our hypothesis that callused cutting propagation in grapevine induces a transient/partial molecular rejuvenation of the propagule, and we propose a multi-omic gene model explaining this process. The findings of this study provide a characterization of rejuvenation, callus formation/dedifferentiation, and how epigenetic memory works in the case of vegetative propagation of perennials. Insights obtained from this study can be used further to improve grapevine tolerance to abiotic and biotic stress.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2023.320

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Supplementary Files TR.zip (3281 kB)
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