Examinando por Autor "Rothkegel, Karin"
Mostrando 1 - 7 de 7
Resultados por página
Opciones de ordenación
Ítem De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development(BMC Genomics, 2019-02-06) Vergara-Pulgar, Cristian; Rothkegel, Karin; González-Agüero, Mauricio; Pedreschi, Romina; Campos-Vargas, Reinaldo; Defilippi, Bruno G.; Meneses, ClaudioBackground: Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar 'Hass' especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of 'Hass' fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest). Results: The 'Hass' de novo transcriptome contains 62,203 contigs (x=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate ≤ 0.01) found 8672 genes considering all developmental stages. From this analysis, genes were clustered according to their expression pattern and 1209 genes show correlation with the four developmental stages. Conclusions: Candidate genes are proposed as possible biomarkers for monitoring the development of the 'Hass' avocado fruit associated with lipid metabolism, ethylene signaling pathway, auxin signaling pathway, and components of the cell wall.Ítem DNA methylation and small interference RNAs participate in the regulation of MADS-box genes involved in dormancy in sweet cherry (Prunus avium L.)(Oxford University Press, 2017-12) Rothkegel, Karin; Sánchez, Evelyn; Montes, Christian; Greve, Macarena; Tapia, Sebastián; Bravo, Soraya; Prieto, Humberto; Almeida, Andréa MiyasakaEpigenetic modifications can yield information about connections between genotype, phenotype variation and environmental conditions. Bud dormancy release in temperate perennial fruit trees depends on internal and environmental signals such as cold accumulation and photoperiod. Previous investigations have noted the participation of epigenetic mechanisms in the control of this physiological process. We examined whether epigenetic modifications were modulated in MADS-box genes, potential candidates for the regulation of bud dormancy and flowering in sweet cherry (Prunus avium L.). We identified and cloned two MADS-box genes homologous to the already-characterized dormancy regulators DORMANCY-ASSOCIATED MADS-box (DAM3 and DAM5) from Prunus persica (L.) Batsch. Bisulfite sequencing of the identified genes (PavMADS1 and PavMADS2), Methylated DNA Immunoprecipitation and small RNA deep sequencing were performed to analyze the presence of DNA methylations that could be guided by non-coding RNAs in the floral buds exposed to differential chilling hours. The results obtained reveal an increase in the level of DNA methylation and abundance of matching small interference RNAs (siRNAs) in the promoter of PavMADS1 when the chilling requirement is complete. For the first intron and 5′ UTR of PavMADS1, de novo DNA methylation could be associated with the increase in the abundance of 24-nt siRNA matching the promoter area. Also, in the second large intron of PavMADS1, maintenance DNA methylation in all cytosine contexts is associated with the presence of homologous siRNAs in that zone. For PavMADS2, only maintenance methylation was present in the CG context, and no matching siRNAs were detected. Silencing of PavMADS1 and PavMADS2 coincided with an increase in Flowering Locus T expression during dormancy. In conclusion, DNA methylations and siRNAs appear to be involved in the silencing of PavMADS1 during cold accumulation and dormancy release in sweet cherry. © The Author 2017. Published by Oxford University Press. All rights reserved.Ítem Global Methylation Analysis Using MSAP Reveals Differences in Chilling-Associated DNA Methylation Changes during Dormancy Release in Contrasting Sweet Cherry Varieties(MDPI, 2022-10) Narváez, Gabriela; Muñoz Espinoza, Claudia; Soto, Esteban; Rothkegel, Karin; Bastías, Macarena; Gutiérrez, José; Bravo, Soraya; Hasbún, Rodrigo; Meneses, Claudio; Almeida, Andrea MiyasakaDormancy 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. © 2022 by the authors.Ítem Identificación de genes asociados a la detección de frío y tolerancia a bajas temperaturas durante la acumulación de horas frío en Prunus avium var ‘Kordia’ a partir de datos de RNA-seq y MethyIC-seq(Universidad Andrés Bello, 2021) Sandoval Belmar, Paula Andrea; Meneses, Claudio; Rothkegel, Karin; Facultad de Ciencias de la VidaEl cerezo (Prunus avium L.), es una especie frutal de clima templado que pasa por un proceso llamado dormancia durante otoño e invierno, para enfrentar factores ambientales adversos. Durante este proceso el tejido dormante (yemas) debe acumular una cierta cantidad de horas frío (“Chilling hours” = CH; horas <7,2 ºC), el requerimiento de frío depende del genotipo y/ o cultivar y completarlo es crítico para que ocurra la salida de dormancia y posteriormente la floración. Estudios anteriores determinaron que la acumulación de frío está asociada a cambios en el nivel de metilación y expresión de los genes. La metilación del ADN consta de la adición de un grupo metilo al carbono 5’ de la citosina y en plantas ocurre en tres contextos: CG: CHG y CHH (donde H = A, T o C). La metilación del ADN puede en regiones codificantes y no codificantes regulando la transcripción de genes cercanos. A partir del perfil de metilación de un locus de interés se pueden identificar Regiones Diferencialmente Metiladas (RDMs), las que pueden tener un efecto en expresión de un gen. En este sentido, genes asociados a la detección y tolerancia a bajas temperaturas son diferencialmente regulados mediante metilaciones del ADN durante endodormancia en Prunus avium var. ‘Kordia’ Se identificaron genes diferencialmente expresados y diferencialmente metilados durante la acumulación de horas frío a partir de datos generados en el metiloma y transcriptoma (Rothkegel et al, 2020). El análisis de enriquecimiento de las tres condiciones de frío reveló que a las 443 CH y a las 1295 CH, la categoría de “Proceso metabólico” es la más sobrerrepresentada, mientras que a las 1637 CH se destaca la presencia de “Respuesta a estímulo”. Adicionalmente, se identificaron factores de transcripción asociados a RDMs tales como PavYY1, PavNFCY3 y PavERF13, los que a su vez están involucrados en la respuesta de hormonas como ABA, giberelinas y etileno durante la acumulación de frío. El análisis continuó con un segundo set de datos , conformado por subclusters de co-expresión y subcluster de RDMs generados a partir de los GDEs y RDMs identificadas en la secuenciación del metiloma y transcriptoma (Rothkegel et al., 2020). Se observó que la categoría de “Respuesta a estímulo” fue la más sobrerrepresentada en los subclusters 8 y 6 de RDMs. Las regiones estan relacionadas a genes de respuesta a estrés y respuesta a estímulo abiótico. Se observó que esta categoría también está sobrerrepresentada en el subcluster 10 de co-expresión, compuesto por genes que incrementan su expresión. A partir de la categoría de “Respuesta a estímulo” se identificaron cuatro genes asociados a la tolerancia a bajas temperaturas candidatos a ser regulados por cambios en el nivel de metilación durante la acumulación de frío. Los genes (PavHSP70, PavWER, PavRPM1 y PavCRRSP38) tienen RDMs regiones río arriba y río abajo de la región codificante, que presentan una correlación negativa entre su nivel de metilación y expresión. Estos resultados contribuyen al estado del arte en nuestra área, aportando evidencia in silico de rol de genes asociados a la tolerancia a bajas temperaturas y regulados por metilación del ADN durante la acumulación de frío en dormancia de yemas florales.Ítem Identification of Metabolite and Lipid Profiles in a Segregating Peach Population Associated with Mealiness in Prunus persica (L.) Batsch(2020-04) Lillo-Carmona, Victoria; Espinoza, Alonso; Rothkegel, Karin; Rubilar, Miguel; Nilo-Poyanco, Ricardo; Pedreschi, Romina; Campos-Vargas, Reinaldo; Meneses, ClaudioThe peach is the third most important temperate fruit crop considering fruit production and harvested area in the world. Exporting peaches represents a challenge due to the long-distance nature of export markets. This requires fruit to be placed in cold storage for a long time, which can induce a physiological disorder known as chilling injury (CI). The main symptom of CI is mealiness, which is perceived as non-juicy fruit by consumers. The purpose of this work was to identify and compare the metabolite and lipid profiles between two siblings from contrasting populations for juice content, at harvest and after 30 days at 0 °C. A total of 119 metabolites and 189 lipids were identified, which showed significant differences in abundance, mainly in amino acids, sugars and lipids. Metabolites displaying significant changes from the E1 to E3 stages corresponded to lipids such as phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG) and lysophosphatidylcholines (LPC), and sugars such as fructose 1 and 1-fructose-6 phosphate. These metabolites might be used as early stage biomarkers associated with mealiness at harvest and after cold storage.Ítem Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds(MDPI, 2022-09) Soto, Esteban; Sanchez, Evelyn; Nuñez, Carlos; Montes, Christian; Rothkegel, Karin; Andrade, Paola; Prieto, Humberto; Miyasaka Almeida, AndreaIn sweet cherry (Prunus avium), as in other temperate woody perennials, bud dormancy allows for survival in adverse environmental conditions during winter. During this process, environmental signals such as short days and/or low temperatures trigger internal signals that enable buds to become tolerant to the cold. The process involves tracking chilling units up to chilling the requirement fulfillment to resume growth, a transition involving transcriptional regulation, metabolic signaling, and epigenetic-related regulatory events. Massive sequencing of small RNAs was performed to identify miRNAs involved in sweet cherry dormancy by comparing their expression in field (regular seasonal) and controlled non-stop (continuous) chilling conditions. miRNAs highlighted by sequencing were validated using specific stem-loop PCR quantification, confirming expression patterns for known miRNAs such as miR156e, miR166c, miR172d, miR391, miR482c, and miR535b, as well as for newly proposed miRNAs. In silico prediction of the target genes was used to construct miRNA/target gene nodes. In particular, the involvement of the sweet cherry version for the miR156/SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN genes whose expression was opposite in the two conditions suggests their involvement on dormancy regulation in sweet cherry. miRNA levels indicate that the regulation of stress-related genes and hormone synthesis modulates the expression of calcium metabolism and cell development-associated genes. Understanding the regulatory networks involved in sweet cherry dormancy, particularly in the context of miRNA involvement, represents the first step in the development of new agricultural strategies that may help overcome the increasing challenges presented by global climate change. © 2022 by the authors.Ítem Transcriptome and Gene Regulatory Network Analyses Reveal New Transcription Factors in Mature Fruit Associated with Harvest Date in Prunus persica(MDPI, 2022-12) Núñez Lillo, Gerardo; Pérez Reyes, Wellasminb; Riveros, Anibal; Lillo Carmona, Victoria; Rothkegel, Karin; Álvarez, José Miguel; Blanco Herrera, Francisca; Pedreschi, Romina; Campos Vargas, Reinaldo; Meneses, ClaudioHarvest 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. © 2022 by the authors.