Examinando por Autor "Pedreschi, Romina"

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    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, Claudio
    Background: 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.
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    Ítem
    Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
    (2019-12) Carrasco-Valenzuela, , Tomás; Muñoz-Espinoza, Claudia; Riveros, Aníbal; Pedreschi, Romina; Arús, Pere; Campos-Vargas, Reinaldo; Meneses, Claudio
    Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. ‘Venus’ selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed ‘Response to auxin’ as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers. © Copyright © 2019 Carrasco-Valenzuela, Muñoz-Espinoza, Riveros, Pedreschi, Arús, Campos-Vargas and Meneses.
  • Miniatura
    Ítem
    Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
    (Frontiers Media S.A., 2019-12) Carrasco-Valenzuela, Tomás; Muñoz-Espinoza, Claudia; Riveros, Aníbal; Pedreschi, Romina; Arús, Pere; Campos-Vargas, Reinaldo; Meneses, Claudio
    Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. ‘Venus’ selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed ‘Response to auxin’ as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers. © Copyright © 2019 Carrasco-Valenzuela, Muñoz-Espinoza, Riveros, Pedreschi, Arús, Campos-Vargas and Meneses.
  • Miniatura
    Ítem
    Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
    (Frontiers Media S.A., 2019-12) Carrasco-Valenzuela, Tomás; Muñoz-Espinoza, Claudia; Riveros, Aníbal; Pedreschi, Romina; Arús, Pere; Campos-Vargas, Reinaldo; Meneses, Claudio
    Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. ‘Venus’ selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed ‘Response to auxin’ as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers. © Copyright © 2019 Carrasco-Valenzuela, Muñoz-Espinoza, Riveros, Pedreschi, Arús, Campos-Vargas and Meneses.
  • Miniatura
    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, Claudio
    The 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.
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    Ítem
    Metabolite Profiling Reveals the Effect of Cold Storage on Primary Metabolism in Nectarine Varieties with Contrasting Mealiness
    (MDPI, 2023-02) Olmedo, Patricio; Zepeda, Baltasar; Delgado-Rioseco, Joaquín; Leiva, Carol; Moreno, Adrián A.; Sagredo, Karen; Blanco-Herrera, Francisca; Pedreschi, Romina; Infante, Rodrigo; Meneses, Claudio; Campos-Vargas, Reinaldo
    Chilling injury is a physiological disorder caused by cold storage in peaches and nectarines. The main symptom of chilling injury is mealiness/wooliness, described as a lack of juice in fruit flesh. In this work, we studied two nectarine varieties (Andes Nec-2 and Andes Nec-3) with contrasting susceptibility to mealiness after cold storage. A non-targeted metabolomic analysis was conducted by GC-MS to understand if changes in metabolite abundance are associated with nectarine mealiness induced by cold storage. Multivariate analyses indicated that in unripe nectarines, cold storage promoted a higher accumulation of amino acids in both varieties. Interestingly, for ripe nectarines, cold storage induced an accumulation of fewer amino acids in both varieties and showed an increased abundance of sugars and organic acids. A pathway reconstruction of primary metabolism revealed that in ripe nectarines, cold storage disrupted metabolite abundance in sugar metabolism and the TCA cycle, leading to a differential accumulation of amino acids, organic acids, and sugars in mealy and juicy nectarines. © 2023 by the authors
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    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, 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. © 2022 by the authors.