Characterization of MdMYB68, a suberin master regulator in russeted apples.
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana benthamiana
PROVIDER: GSE220694 | GEO | 2023/01/23
REPOSITORIES: GEO
Similar Datasets
Project description:⢠A comparison of the transcriptomes of russeted vs. waxy apple exocarps previously highlighted a tight relationship between a gene encoding a MYB-type transcription factor, MdMYB93, and some key suberin biosynthetic genes. The present work assesses the role of this transcription factor in the suberization process. ⢠A phylogenetic analysis of MdMYB93 and Arabidopsis thaliana MYBs was performed and the function of MdMYB93 was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight the MdMYB93-regulated genes. UPLC-TripleTOF and GC-MS were used to investigate alterations in phenylpropanoid, soluble free lipid, and lipid polyester contents. ⢠A massive accumulation of suberin and its biosynthetic precursors in MdMYB93 agro-infiltrated leaves was accompanied by a remobilization of phenylpropanoids and an increased amount of lignin precursors. Gene expression profiling displayed a concomitant alteration of lipid and phenylpropanoid metabolism, cell wall development, and extracellular transport, with a large number of induced transcripts predicted to be involved in suberin deposition. ⢠The present work supports a major role of MdMYB93 in the regulation of suberin deposition in russeted apple skins, from the synthesis of monomeric precursors, their transport, polymerization, and final deposition as suberin in primary cell wall. In order to draw a consistent picture of a gene expression profile of the MYB93 induced was performed comparing of 4 biological replicates of Nicotiana benthamiana leaves infiltrated with Pearleygate103 35S::MdMYB93 and 4 biological replicates of control plants infiltrated with P19 only.
2016-07-15 | E-GEOD-83618 | biostudies-arrayexpress
Project description:• A comparison of the transcriptomes of russeted vs. waxy apple exocarps previously highlighted a tight relationship between a gene encoding a MYB-type transcription factor, MdMYB93, and some key suberin biosynthetic genes. The present work assesses the role of this transcription factor in the suberization process. • A phylogenetic analysis of MdMYB93 and Arabidopsis thaliana MYBs was performed and the function of MdMYB93 was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight the MdMYB93-regulated genes. UPLC-TripleTOF and GC-MS were used to investigate alterations in phenylpropanoid, soluble free lipid, and lipid polyester contents. • A massive accumulation of suberin and its biosynthetic precursors in MdMYB93 agro-infiltrated leaves was accompanied by a remobilization of phenylpropanoids and an increased amount of lignin precursors. Gene expression profiling displayed a concomitant alteration of lipid and phenylpropanoid metabolism, cell wall development, and extracellular transport, with a large number of induced transcripts predicted to be involved in suberin deposition. • The present work supports a major role of MdMYB93 in the regulation of suberin deposition in russeted apple skins, from the synthesis of monomeric precursors, their transport, polymerization, and final deposition as suberin in primary cell wall.
2016-07-15 | GSE83618 | GEO
Project description:Apple russeting is characterized by the deposition of suberin in the inner part of the epidermal cell walls. It develops at the fruit surface when the integrity of the cuticle has been lost. Cutin and wax composition (including triterpene profile) is also affected in russeted skin. In the present work, the fruit growth kinetic of two closely related apple varieties, ‘Canada Gris’ and ‘Canada Blanc’, which display russeted and waxy skin phenotypes, respectively, was investigated. We used a combination of transcriptomic, proteomic, and metabolomic approaches to better understand the molecular events associated with cuticle failure and suberization. A particular interest was also given to the triterpene specifically found in russeted skins and their synthesis. Our results indicate that the decreased synthesis of cutin and wax, observed in russeted skin throughout fruit development, is a determining factor for russeting. We identified a lipid transfer protein (LTP-3) as a potential key player in cuticle formation. Metabolomics highlighted a large diversity of triterpene-hydroxycinnamates in russeted tissues whose accumulation was highly correlated with suberin-related genes, including some enzymes belonging to the BAHD (HXXXD-motif) acyltransferase family. This study shed light for the first time on the crosstalk between triterpene and suberin pathways.
2022-02-22 | PXD022712 | Pride
Project description:Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations. In order to draw a consistent picture of the gene expression profiles specific to both russeted and waxy apples and at the same time to highlight and interpret the mechanism leading to the russeted phenotype, a bulk RNA-sequencing was performed on the exocarp of a group of three distinct fully-russeted apple varieties ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and a second one including 3 fully waxy varieties ('Gala', 'CRAW/Ma/AF42', and 'CRAW/Ma/AG94').
2015-02-01 | E-GEOD-61040 | biostudies-arrayexpress
Project description:Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations.
2015-02-01 | GSE61040 | GEO
Project description:Our previous studies, comparing russeted vs. waxy apple skin, highlighted a MYeloBlastosys (Myb) transcription factor (MdMYB52-like), which displayed a correlation with genes associated to the suberization process. The present article aims to assess its role and function in the suberization process. Phylogenetic analyses and research against Arabidopsis thaliana MYBs database were first performed and the tissue specific expression of MdMYB52-like was investigated using RT-qPCR. The function of MdMYB52-like was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight differentially regulated genes in response MdMYB52-like. Transcriptomic data were supported by analytical chemistry and microscopy. A massive decreased expression of photosynthetic and primary metabolism pathways was observed with a concomitant increased expression of genes associated with phenylpropanoid and lignin biosynthesis, cell wall modification and senescence. Interestingly key genes involved in the synthesis of suberin phenolic components were observed. The analytical chemistry displayed a strong increase in the lignin content in the cell walls during MdMYB52 expression. More specifically, an enrichment in G-Unit lignin residues was observed, supporting transcriptomic data as well as previous work describing the suberin phenolic domain as a G-unit enriched lignin-like polymer. The time-course qPCR analysis revealed that the observed stress response, might be explain by this lignin biosynthesis and by a possible programmed senescence triggered by MdMYB52-like. The present work supports a crucial regulatory role for MdMYB52 in the biosynthesis of the suberin phenolic domain and possibly in the fate of suberized cells in russeted apple skins.
2022-09-26 | GSE212828 | GEO
Project description:Russeting of apple fruit is a non-invasive physiological disorder. It occurs mainly in 'Golden Delicious' apple and its hybrids, while understanding of its molecular mechanism is still limited. In this study, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative (iTRAQ) proteomic analysis to detect changes in the expression levels of genes and proteins during russeting formation in russeted and non-russeted skin of 'Golden Delicious' apple. We set up three comparison groups representing the three developmental stages in the russeting formation process. With the formation of fruit russeting, there were 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups as detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptome and proteome data revealed related-genes involved in lignin biosynthesis are significant changes at different developmental stages during apple russeting formation. Some other transcription factors, such as MYBs, NACs and LIMs were also involved in apple russeting formation. In this study, one LIM transcription factor was preliminarily determined to be involved in lignin biosynthesis by combining to PAL-box element. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling apple russeting formation.
2019-09-26 | PXD014960 | Pride
Project description:Apple skin russeting naturally occurs in many varieties, particularly in 'Golden Delicious' and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted and non-russeted skin of 'Golden Delicious' apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400 and MD17G1225100) involved in lignin biosynthesis are significant changes during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.
2019-11-04 | GSE136842 | GEO
Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes.
2010-11-05 | GSE24523 | GEO
Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes. Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.
2010-11-05 | E-GEOD-24523 | biostudies-arrayexpress