Transcriptome Analysis of Potato TubersEffects of Different Agricultural Practices
Open accessAbstract
The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments.
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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”
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”
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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Cites
Cheng, K. C., Beaulieu, J., Iquira, E., Belzile, F. J., Fortin, M. G., & Strömvik, M. V. (2008) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf073505i · Cited by 76 · see citing works
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Barański, M., Średnicka-Tober, D., Volakakis, N., Seal, C., Sanderson, R., Stewart, G. B., Benbrook, C., Biavati, B., Markellou, E., Giotis, C., et al. (2014) · British Journal of Nutrition · doi:10.1017/s0007114514001366 · Cited by 684 · see citing works
Self-citationvan 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., et al. (2012) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf204696w · Cited by 26 · see citing works
Self-citationGene expression profiling for food safety assessment: Examples in potato and maize
Dijk, J. P. V., Leifert, C., Barros, E., & Kok, E. J. (2010) · Regulatory Toxicology and Pharmacology · doi:10.1016/j.yrtph.2010.06.012 · Cited by 23 · see citing works
Self-citationTétard-Jones, C., Edwards, M., Rempelos, L., Gatehouse, A., Eyre, M., Wilcockson, S., & Leifert, C. (2013) · Agronomy · doi:10.3390/agronomy3010059 · Cited by 14 · see citing works
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- Authors
- van Dijk, J. P., Cankar, K., Scheffer, S. J., Beenen, H. G., Shepherd, L. V. T., Stewart, D., Davies, H. V., Wilkockson, S. J., Leifert, C., Gruden, K., & Kok, E. J.
- Affiliations
- National Institute of Biology (SI)
- ORCID
- Venue
- Journal of Agricultural and Food Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-02-25
- Volume
- 57
- Issue
- 4
- Pages
- 1612-1623
- ISSN
- 0021-8561 (ISSN-L)
- 1520-5118
- OpenAlex
- W1544157226
- Cited by
- 47
- References
- 1
- Citations by year
- 2023: 1 · 2022: 3 · 2021: 1 · 2020: 3 · 2019: 3 · 2018: 2 · 2017: 4 · 2016: 2 · 2015: 2 · 2014: 6 · 2013: 2 · 2012: 4
- FWCI
- 9.50
- Type
- journal article
- Language
- en
- Open access
- green
- research.wur.nl
- Locations
- Journal of Agricultural and Food Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Potato Plant Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetics and Plant Breeding
- Keywords
- potato tubers, transcriptome, gene expression, food safety, cDNA microarray, potato varieties, environmental factors, Sante, genetic variation, toxicity prediction, plant breeding
- MeSH terms
- Agriculture, Breeding, Environment, Solanum tuberosum, Species Specificity, Gene Expression, Polymerase Chain Reaction, DNA, Plant, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Plant Tubers
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