The Identification and Interpretation of Differences in the Transcriptomes of Organically and Conventionally Grown Potato Tubers
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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 fertilizer, and each combined with either organic or conventional crop protection, giving four different treatments. Samples were derived from the European project QualityLowInputFood (QLIF). Microarray data were analyzed using different statistical tools (multivariate, principal components analysis (PCA); univariate, analysis of variance (ANOVA)) and with pathway analysis (hypergeometric distribution (HGD) and gene set enrichment analysis (GSEA)). Several biological processes were implicated as a result of the different treatments of the plants. Most obvious were the lipoxygenase pathway, with higher expression in organic fertilizer and lower expression in organic crop protection; the starch synthase pathway, with higher expression in both organic crop protection and fertilizer; and the biotic stress pathway, with higher expression in organic fertilizer. This study confirmed that gene expression profiling in combination with pathway analysis can identify and characterize differences between plants grown under different environmental conditions.
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There are statistically significant interactions between fertilisation and crop protection protocols with respect to gene and protein expression patterns.
“there were some statistically significant interactions between fertilisation and crop protection protocols with respect to gene and protein expression pattern”
A switch from pesticide-based conventional to organic crop protection protocols has a significant but more limited effect than fertilisation regimens on gene and protein expression patterns.
“Also, a switch from pesticide-based conventional to organic crop protection protocols has been shown to have a significant, but more limited effect than fertilisation regimens”
The switch from mineral to organic fertilisers results in significant differences in gene and protein expression patterns and, as a result, in secondary metabolite profiles; approximately 10% of proteins have been found to be either up- or down-regulated in response to contrasting fertiliser inputs in potato and wheat.
“Recent studies have shown that the switch from mineral to organic fertilisers results in significant differences in gene and protein expression patterns and, as a result, in secondary metabolite profiles; for example, approximately 10 % of proteins have been found to be either up- or down-regulated in response to contrasting fertiliser inputs in potato and wheat( 10 – 15 ).”
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- Authors
- van Dijk, J. P., Cankar, K., Hendriksen, P. J. M., Beenen, H. G., Zhu, M., Scheffer, S., Shepherd, L. V. T., Stewart, D., Davies, H. V., Leifert, C., Wilkockson, S. J., Gruden, K., & Kok, E. J.
- Affiliations
- RIKILT—Institute of Food Safety (Wageningen UR), Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
- Wageningen University & Research (NL)
- James Hutton Institute (GB)
- Newcastle University (GB)
- National Institute of Biology (SI)
- ORCID
- Venue
- Journal of Agricultural and Food Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-02-22
- Volume
- 60
- Issue
- 9
- Pages
- 2090-2101
- ISSN
- 0021-8561 (ISSN-L)
- 1520-5118
- OpenAlex
- W2035805209
- Cited by
- 26
- References
- 59
- Citations by year
- 2024: 1 · 2023: 2 · 2021: 2 · 2020: 3 · 2018: 1 · 2017: 4 · 2016: 1 · 2015: 1 · 2014: 4 · 2013: 3 · 2012: 4
- FWCI
- 4.35
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- Locations
- Journal of Agricultural and Food Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Repository of the University of Ljubljana (University of Ljubljana) (publishedVersion, other-oa)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Javna Agencija za Raziskovalno Dejavnost RS
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Organic Food and Agriculture
- Life Sciences › Agricultural and Biological Sciences › Food Science › Potato Plant Research
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Plant Growth and Agriculture Techniques
- Keywords
- potato tubers, organic farming, conventional farming, organic fertilizer, gene expression profiling, transcriptome, lipoxygenase pathway, biotic stress response, pathway analysis
- MeSH terms
- Analysis of Variance, Fertilizers, Solanum tuberosum, RNA, Plant, Gene Expression Profiling, Plant Tubers, Microarray Analysis, Food, Organic, Organic Agriculture, Transcriptome
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