Transcriptome analysis of potato tubers - effects of different agricultural practices

Jeroen P van Dijk; Katarina Cankar; Stanley J Scheffer; Henriek G Beenen; Louise V  T	 Shepherd; Derek Stewart; Howard V Davies; Steve J Wilcockson; Carlo  Leifert; Kristina  Gruden; Esther J Kok

doi:10.1021/jf802815d

Transcriptome analysis of potato tubers - effects of different agricultural practices

Jeroen P van Dijk, Katarina Cankar, Stanley J Scheffer, Henriek G Beenen, Louise V T Shepherd, Derek Stewart, Howard V Davies, Steve J Wilcockson, Carlo Leifert, Kristina Gruden, Esther J Kok

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Abstract

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.
Copyright © 2009 American Chemical Society

Original language	English
Pages (from-to)	1612-1623
Number of pages	12
Journal	Journal of Agricultural and Food Chemistry
Volume	57
Issue number	4
DOIs	https://doi.org/10.1021/jf802815d
Publication status	Published - 2009

Keywords

solanum tuberosum
cDNA microarray
gene expression
food safety
organic input systems

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1021/jf802815d

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title = "Transcriptome analysis of potato tubers - effects of different agricultural practices",

abstract = "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.Copyright {\textcopyright} 2009 American Chemical Society",

keywords = "solanum tuberosum, cDNA microarray, gene expression, food safety, organic input systems",

author = "{van Dijk}, {Jeroen P} and Katarina Cankar and Scheffer, {Stanley J} and Beenen, {Henriek G} and Shepherd, {Louise V T} and Derek Stewart and Davies, {Howard V} and Wilcockson, {Steve J} and Carlo Leifert and Kristina Gruden and Kok, {Esther J}",

year = "2009",

doi = "10.1021/jf802815d",

language = "English",

volume = "57",

pages = "1612--1623",

journal = "Journal of Agricultural and Food Chemistry",

issn = "1520-5118",

publisher = "American Chemical Society",

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TY - JOUR

T1 - Transcriptome analysis of potato tubers - effects of different agricultural practices

AU - van Dijk, Jeroen P

AU - Cankar, Katarina

AU - Scheffer, Stanley J

AU - Beenen, Henriek G

AU - Shepherd, Louise V T

AU - Stewart, Derek

AU - Davies, Howard V

AU - Wilcockson, Steve J

AU - Leifert, Carlo

AU - Gruden, Kristina

AU - Kok, Esther J

PY - 2009

Y1 - 2009

N2 - 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.Copyright © 2009 American Chemical Society

AB - 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.Copyright © 2009 American Chemical Society

KW - solanum tuberosum

KW - cDNA microarray

KW - gene expression

KW - food safety

KW - organic input systems

U2 - 10.1021/jf802815d

DO - 10.1021/jf802815d

M3 - Article

C2 - 19173602

SN - 1520-5118

VL - 57

SP - 1612

EP - 1623

JO - Journal of Agricultural and Food Chemistry

JF - Journal of Agricultural and Food Chemistry

IS - 4

ER -

Transcriptome analysis of potato tubers - effects of different agricultural practices

Abstract

Keywords

UN SDGs

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