Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Differences in the transcriptomes of organically and conventionally grown potatoes.

ABSTRACT: Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis.

ORGANISM(S): Solanum tuberosum

SUBMITTER: Jeroen van Dijk

PROVIDER: E-MTAB-605 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The identification and interpretation of differences in the transcriptomes of organically and conventionally grown potato tubers.

van Dijk Jeroen P JP Cankar Katarina K Hendriksen Peter J M PJ Beenen Henriek G HG Zhu Ming M Scheffer Stanley S Shepherd Louise V T LV Stewart Derek D Davies Howard V HV Leifert Carlo C Wilkockson Steve J SJ Gruden Kristina K Kok Esther J EJ

Journal of agricultural and food chemistry 20120222 9

In the European integrated research project SAFEFOODS, one of the aims was to further establish the potential of transcriptomics for the assessment of differences between plant varieties grown under different environmental conditions. Making use of the knowledge of cellular processes and interactions is one of the ways to obtain a better understanding of the differences found with transcriptomics. For the present study the potato genotype Santé was grown under both organic and conventional ferti ...[more]

PMID: 22300527

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Project description:This study was designed to identify changes in gene expression that occur when corn was grown on different landscape features. Specifically on the backslope or summit/shoulder of a hill. In rolling landscapes, plant available water varies drastically by location and soil type. Almost simultaneously, plants may be flooded out in footslope locations whereas plants in summit locations may be suffering from severe drought. The objective of this study was to determine the influence of landscape position on corn (Zea mays) productivity and gene regulation. Corn was sampled at V12 for plant growth characteristics and transcriptome analysis at summit/shoulder and lower backslope positions. Plants at the summit had 16% less leaf area and biomass compared with plants at the toeslope. Gene expression analysis using microarray chips, transcriptome analysis, and qPCR indicated that plants at the summit had 708 genes down-regulated and 399 genes up-regulated compared to control plants at the lower back slope. GSEA (Gene Set Enrichment Analysis) indicated tolerance to cold, salt, and drying were increased in summit/should plants compared to control toeslope plants. However, nutrient uptake, recovery from wounding, pest and fungal disease resistance, along with photosynthetic capacity were all down-regulated in moderate water stresses plants. These responses suggest that corn preferentially responses to water stress as the expense of its ability to respond to other stresses. Three biological replicates for the control (backslope) and six biological replicate of summit/shoulder-grown plants were collected. The resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had three to six biological replicates for each growth condition and two technical replicates for each biological sample.

Dataset Information

Differences in the transcriptomes of organically and conventionally grown potatoes.

Publications

The identification and interpretation of differences in the transcriptomes of organically and conventionally grown potato tubers.

Similar Datasets

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