Kloosterman, Bjorn, De Koeyer, David, Griffiths, Rebecca, Flinn, Barry, Steuernagel, Burkhard, Scholz, Uwe, Sonnewald, Sophia, Sonnewald, Uwe, Bryan, Glenn J., Prat, Salome, Banfalvi, Zsofia, Hammond, John P., Geigenberger, Peter, Nielsen, Kare L., Visser, Richard G. F. and Bachem, Christian W. B.. (2008) Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Functional & Integrative Genomics, Vol.8 (No.4). pp. 329-340. ISSN 1438-793X

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Abstract

The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci).

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)
Journal or Publication Title:	Functional & Integrative Genomics
Publisher:	Springer
ISSN:	1438-793X
Date:	November 2008
Volume:	Vol.8
Number:	No.4
Number of Pages:	12
Page Range:	pp. 329-340
Identification Number:	10.1007/s10142-008-0083-x
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Martin Lague (AAFC), Genome Canada, Atlantic Canada Opportunities Agency, New Brunswick Department of Agriculture, Fisheries and Aquaculture, Scottish Government Rural and Environment Research and Analysis Directorate, EU-SOL, Centre of BioSystems Genomics (CBSG), The Netherlands Genomics Initiative/Netherlands Organization for Scientific Research
Grant number:	1004889-1, AFA03/04-096, PL 016214-2 EU-SOL
URI:	http://wrap.warwick.ac.uk/id/eprint/29377

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