Browsing by Author "Rothkegel, Karin"

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    Global Methylation Analysis Using MSAP Reveals Differences in Chilling-Associated DNA Methylation Changes during Dormancy Release in Contrasting Sweet Cherry Varieties
    (2022) Narvaez, Gabriela; Munoz-Espinoza, Claudia; Soto, Esteban; Rothkegel, Karin; Bastias, Macarena; Gutierrez, Jose; Bravo, Soraya; Hasbun, Rodrigo; Meneses, Claudio; Miyasaka Almeida, Andrea
    Dormancy is an adaptive strategy developed by temperate perennial crops to protect overwinter tissues from unfavorable environmental conditions. Sweet cherry (Prunus avium L.), a member of the Rosaceae family, requires chilling to overcome dormancy. The time of harvest is directly correlated with chilling requirements in sweet cherries. Consequently, early and late season varieties have low and high chilling requirements, respectively. There is evidence that the expression of dormancy-related genes is regulated by DNA methylation. In this work, methylation-sensitive amplified polymorphism (MSAP) was applied to study genome-wide DNA methylation changes associated with dormancy in two low-chill varieties, 'Royal Dawn' and 'Glen Red', and one high-chill variety, 'Kordia'. Our primary results suggest that the occurrence of progressive DNA demethylation is associated with chilling accumulation during dormancy in the three varieties, independent of their chilling requirements. Genes were identified with different methylation status changes, detected by MSAP, related to cell wall remodeling and energy metabolism. Several MSAP profiles among the varieties were observed, suggesting that fine epigenetic control is required to coordinate hormonal and environmental signals that induce dormancy and its release.
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    Nitrogen sensing and regulatory networks: It’s about time and space
    (2024) Shanks, Carly M.; Rothkegel, Karin; Brooks, Matthew D.; Cheng, Chia-Yi; Álvarez, José M.; Ruffel, Sandrine; Krouk, Gabriel; Gutiérrez Ilabaca, Rodrigo Antonio; Coruzzi, Gloria M.
    A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its “hit-and-run” mode of target gene regulation, and temporal transcriptional cascade identified by “network walking.” Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
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    Transcriptome and Gene Regulatory Network Analyses Reveal New Transcription Factors in Mature Fruit Associated with Harvest Date in Prunus persica
    (2022) Nunez-Lillo, Gerardo; Perez-Reyes, Wellasmin; Riveros, Anibal; Lillo-Carmona, Victoria; Rothkegel, Karin; Miguel Alvarez, Jose; Blanco-Herrera, Francisca; Pedreschi, Romina; Campos-Vargas, Reinaldo; Meneses, Claudio
    Harvest date is a critical parameter for producers and consumers regarding agro-industrial performance. It involves a pleiotropic effect controlling the development of other fruit quality traits through finely controlling regulatory mechanisms. Fruit ripening is a process in which various signals and biological events co-occur and are regulated by hormone signaling that produces the accumulation/degradation of multiple compounds. However, the regulatory mechanisms that control the hormone signaling involved in fruit development and ripening are still unclear. To investigate the issue, we used individuals with early, middle and late harvest dates from a peach segregating population to identify regulatory candidate genes controlling fruit quality traits at the harvest stage and validate them in contrasting peach varieties for this trait. We identified 467 and 654 differentially expressed genes for early and late harvest through a transcriptomic approach. In addition, using the Arabidopsis DAP-seq database and network analysis, six transcription factors were selected. Our results suggest significant hormonal balance and cell wall composition/structure differences between early and late harvest samples. Thus, we propose that higher expression levels of the transcription factors HB7, ERF017 and WRKY70 in early harvest individuals would induce the expression of genes associated with the jasmonic acid pathway, photosynthesis and gibberellins inhibition. While on the other hand, the high expression levels of LHY, CDF3 and NAC083 in late harvest individuals would promote the induction of genes associated with abscisic acid biosynthesis, auxins and cell wall remodeling.