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opencc-zeroJul 2020View details →

Data from: Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

Naturally occurring autopolyploid species such as the autotetraploid potato Solanum tuberosum face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid S. tuberosum using fluorescence in situ hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7-48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of S. tuberosum as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.

opencc-zeroDec 2013View details →

Data from: Invasion of Solanum tuberosum L. by Aspergillus terreus: a microscopic and proteomics insight on pathogenicity

Background: Aspergillus terreus is one of the most harmful filamentous fungal pathogen of humans, animals and plants. Recently, researchers have discovered that A. terreus can cause foliar blight disease in potato (Solanum tuberosum L.). We used light and scanning electron microscopy, and performed proteomics analysis in an attempt to dissect the invasion process of A. terreus in this important crop. Results: Microscopic study revealed that invasion of leaf tissue is marked by rapid germination of A. terreus phialidic conidia (PC) by 4 h after inoculation. By 8 h after inoculation, primary germ tubes from PC differentiated into irregular protuberance, often displayed stomata atropism, and failed to penetrate via the epidermal cells. Colonization of leaf tissues was associated with high rate of production of accessory conidia (AC). These analyses showed the occurrence of a unique opposing pattern of AC, tissue-specific and produced on melanized colonizing hyphae during the infection of leaf tissue. A significant proteome change hallmarked by differential expression of class I patatin, lipoxygenase, catalase-peroxidase complex, and cysteine proteinase inhibitor were observed during tuber colonization. These proteins are often involved in signal transduction pathways and crosstalk in pathogenic responses. Conclusion: A. terreus abundantly produced AC and multipolar germinating PC to invade potato leaf tissue. Additionally, A. terreus differentially induced enzymes in potato tuber during colonization which facilitates rapid disease development.

Fig. 2 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties

Fig. 2. Biplot of Principal Component Analysis based on VOCs and Amino acids from leaves of Solanum allotetraploids (a), autotetraploids (b) and cultivated varieties (c). Components were calculated using Euclidean distances. Amino acids are depicted in the three-letter code. a) Allotetraploids (4xAL2 and 4xAL4) and diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH). b) Autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3) and diploid S. kurtzianum parental line (2xPL). c) S. tuberosum cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).

Fig. 3 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties

Fig. 3. Hierarchical cluster analysis (represented by a heat-map) of amino acids content in leaves of potato allo- and autotetraploids and cultivated varieties. Dendrograms were constructed by UPGMA clustering method for 18 amino acids and 10 lines: diploid S. kurtzianum parental line (2xPL), diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH), three autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3), two allotetraploids (4xAL2 and 4xAL4) and three cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).

Fig. 1 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties

Fig. 1. Fold change of compounds content in allotetraploids (a) and autotetraploids (b) relative to their respective diploid parental line. Fold change is expressed as log10(Tetraploid/Diploid). Horizontal lines are the average of the absolute logFC for each evaluated line, letters denote differences by Duncan's multiple range test (P <0.05).

opencc-by-4.0Nov 2023View details →

Effects of Fertigation Treatment Using a Subsurface Drip System on Spring Potato (Solanum Tuberosum L.) Growth and Yield

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Fig. 4 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 4. Transcript accumulation of genes associated with wound induced suberization. Transcript accumulation of known and putative genes encoding steps in suberin biosynthesis, from starch degradation to final assembly, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point. Numbered pathway steps correspond to numbers in the suberin roadmap (Supplemental Fig. S4). Fumarase (step 63) is included as a step in the TCA pathway, but is shown in grey because its sequence did not have a corresponding PGSC gene identification number, and therefore transcript abundance could not be estimated in this study.

Fig. 6 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 6. Transcript accumulation of wound-induced CASP and GDSL genes. Transcript accumulation of known and putative CASP and GDSL genes, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point.

Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 wound-induced and suberin-associated genes encompassing primary carbohydrate metabolism and the formation of suberin phenolic and aliphatic monomers were subjected to WGCNA. Genes belonging to carbohydrate (C), tricarboxylic acid cycle (TCA), shikimate pathway (S), phenolic metabolism (P), phenolic assembly (PA), fatty acid biosynthesis (FAB), fatty acid modification (FAM) and aliphatic assembly (AA) are colour-coded (see legend). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 2. Gene set enrichment analysis (GSEA) of biological processes across differentially expressed genes (DEGs). Time point comparison panels represent a union parametric analysis of gene set enrichment (PAGE) of biological process (BP) categorized gene ontology (GO) terms. Nodes represent gene sets and their size represents a range from 5 to 464 genes, and edges show overlapping genes between sets, with width representing ranges from 5 to 149 genes. Blue sets are downregulated, red are up-regulated, and grey nodes denote terms that were not detected as significantly differentially regulated (i.e. enriched) at that time point comparison. Labels denote assigned node numbers that correspond to Table 1 with associated GO ID, GO term and regulation overview. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 1. Global overview of the wound-healing transcriptome. A. Principle component analysis (PCA) of RNA-seq libraries. Colours represent biological replicate libraries generated from the same time point (gene log2FPKM space with scaling). B. Differentially expressed genes (DEGs) across time point comparisons. Genes were considered significantly up- or down-regulated if they met p ≤ 0.01 and |log2 (fold change)| (| LFC|) ≥ 2 significance cut-offs. Lists of significantly DEGs were generated using voom by applying these parameters with the Benjamini-Hochberg procedure to TMM-normalized HT-Seq count data. C. Venn diagram of DEGs significantly up- (red) or down-regulated (blue) over the wound-healing time course. Genes were considered significantly up- or down-regulated if they met p ≤ 0.01 and |LFC| ≥ 2 significance cut-offs. Lists of significantly DEGs were generated using voom by applying these parameters with the Benjamini-Hochberg procedure to TMM-normalized HT-Seq count data. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 5. Transcript accumulation of genes associated with wound induced ABA biosynthesis and degradation. Transcript accumulation of known and putative genes encoding steps in ABA biosynthesis and degradation, over the wound-healing time course were retrieved from RNA-seq data. Heatmaps depict log2FPKM means for n = 3 biological replicates for each time point. Numbered pathway steps correspond to numbers in the ABA metabolism pathway (Supplemental Fig. 6).

Fig. 7 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes

Fig. 7. RT-qPCR validation of select wound-induced genes. Gene expression values for 14 genes from RT-qPCR (ΔΔCq) and RNA-seq (CPM) analyses were normalized to 0 dpw values, then log2-transformed to generate log2 (foldchange) values. Pearson's correlation coefficients were calculated for log2 (foldchange) values from the two experimental procedures, with α = 0.05 (Supplemental Table 9). The 95% confidence interval was calculated and plotted as 95% confidence bands.

opencc-by-4.0Apr 2022View details →

Enhanced Weathering Using Basalt Rock Powder: Carbon Sequestration, Co-benefits and Risks in a Mesocosm Study With Solanum tuberosum data

Dataset used in the work: Enhanced Weathering Using Basalt Rock Powder: Carbon Sequestration,Co-benefits and Risks in a Mesocosm Study With Solanum tuberosum authors:  Arthur Vienne, Silvia Poblador , Miguel Portillo-Estrada, Jens Hartmann, Samuel Ijiehon, Peter Wadeand Sara Vicca

Fig. 3 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties

Fig. 1 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties

publicAug 2016View details →

Data from: Identification of four novel stu-miR169s and their target genes in Solanum tuberosum and expression profiles response to drought stress

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