Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening

<p>Abstract</p> <p>Background</p> <p>Since its discovery more than 100 years ago, potato (<it>Solanum tuberosum</it>) tuber cold-induced sweetening (CIS) has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in the process. However, many uncertainties still exist, as the relative contribution of each gene to the process is often unclear, possibly as the consequence of the heterogeneity of experimental systems. Some enzymes associated with CIS, such as β-amylases and invertases, have still to be identified at a sequence level. In addition, little is known about the early events that trigger CIS and on the involvement/association with CIS of genes different from carbohydrate-associated genes. Many of these uncertainties could be resolved by profiling experiments, but no GeneChip is available for the potato, and the production of the potato cDNA spotted array (TIGR) has recently been discontinued. In order to obtain an overall picture of early transcriptional events associated with CIS, we investigated whether the commercially-available tomato Affymetrix GeneChip could be used to identify which potato cold-responsive gene family members should be further studied in detail by Real-Time (RT)-PCR (qPCR).</p> <p>Results</p> <p>A tomato-potato Global Match File was generated for the interpretation of various aspects of the heterologous dataset, including the retrieval of best matching potato counterparts and annotation, and the establishment of a core set of highly homologous genes. Several cold-responsive genes were identified, and their expression pattern was studied in detail by qPCR over 26 days. We detected biphasic behaviour of mRNA accumulation for carbohydrate-associated genes and our combined GeneChip-qPCR data identified, at a sequence level, enzymatic activities such as β-amylases and invertases previously reported as being involved in CIS. The GeneChip data also unveiled important processes accompanying CIS, such as the induction of redox- and ethylene-associated genes.</p> <p>Conclusion</p> <p>Our Global Match File strategy proved critical for accurately interpretating heterologous datasets, and suggests that similar approaches may be fruitful for other species. Transcript profiling of early events associated with CIS revealed a complex network of events involving sugars, redox and hormone signalling which may be either linked serially or act in parallel. The identification, at a sequence level, of various enzymes long known as having a role in CIS provides molecular tools for further understanding the phenomenon.</p

amda 2 13 a major update for automated cross platform microarray data analysis

Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3′ IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix..

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening-3

N (4°C; 26 days). For each time point, three independent tubers were analyzed and data are plotted as means ± SD.<p><b>Copyright information:</b></p><p>Taken from "Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening"</p><p>http://www.biomedcentral.com/1471-2164/9/176</p><p>BMC Genomics 2008;9():176-176.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2358903.</p><p></p

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening-6

Se pyrophosphorylase (UGPase; TA24502_4113) upon tuber incubation at 4°C was monitored over 26 days. The Relative Expression Level (REL) is reported (REL of the control, 17°C tubers equals 1).<p><b>Copyright information:</b></p><p>Taken from "Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening"</p><p>http://www.biomedcentral.com/1471-2164/9/176</p><p>BMC Genomics 2008;9():176-176.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2358903.</p><p></p

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening-8

Plicates for each condition as indicated) and the intersection between these probesets and those over the 70% perfect alignment (%_PERF_ALIGN) threshold. The length of each branch of the dendrogram indicates (1 – Pearson) correlation coefficients as a measure of similarity. The column between the dendrogram and the heatmap represents the probesets either differentially expressed and selected with the 70% perfect alignment threshold (yellow) and the probesets differentially expressed but not selected by the perfect alignment threshold (black).<p><b>Copyright information:</b></p><p>Taken from "Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening"</p><p>http://www.biomedcentral.com/1471-2164/9/176</p><p>BMC Genomics 2008;9():176-176.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2358903.</p><p></p

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening-4

113; potato chloroplast-targeted β-amylase PCT-BMYI); glucan phosphorylase (TA24089_4113) and glucan-water dikinase (TA25853_4113) upon tuber incubation at 4°C was monitored over 26 days. The Relative Expression Level (REL) is reported (REL of the control, 17°C tubers equals 1).<p><b>Copyright information:</b></p><p>Taken from "Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening"</p><p>http://www.biomedcentral.com/1471-2164/9/176</p><p>BMC Genomics 2008;9():176-176.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2358903.</p><p></p

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening-1

522.1.S1_at; potato counterpart TA26174_4113; 2.96 fold induction) is shown as an example. The figure was generated as follows: based on the Global Match File, potato SPS (Transcript Assembly TA26174_4113) best aligns to the target sequence of probeset Les.3522.1.S1_at. Thus, the 11 probes (perfect match probes, PM) associated with this probeset (on the left, upper sequences) were aligned to TA26174_4113. The 25 nt-long potato subsequences that align to tomato probes are reported below the tomato probe sequences, numbered from 1 to 11. Mismatches are highlighted in red. Red and blue bars represent signal intensities associated with perfect match and mismatch probes, respectively. Similar intensities were obtained for the two biological replicates of control and cold conditions, but for the sake of clarity only one of the two GeneChip replicates is shown.<p><b>Copyright information:</b></p><p>Taken from "Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening"</p><p>http://www.biomedcentral.com/1471-2164/9/176</p><p>BMC Genomics 2008;9():176-176.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2358903.</p><p></p