Identification of differentially expressed genes in potato associated with tuber dormancy release

Abstract

Potato (Solanum tuberosum L.) tuber dormancy and sprouting is very important to potato cultivation and processing. In the present experiment, suppression subtractive hybridization was employed to identify differentially expressed genes in potato associated with tuber dormancy release. 576 random clones were selected from subtractive library and successfully sequenced. A total of 304 effective expressed sequence tags (ESTs) were obtained ultimately. The ESTs have been deposited in the EMBL\GenBank\DDBJ nucleotide sequence data libraries under accession numbers from JK483901 to JK484204. GO annotation showed that 45, 34 and 3 % ESTs were associated with binding, catalytic activity and signaling respectively, some of which were confirmed to be involved in plant dormancy breaking, however, 14 % of the ESTs did not show significant homology to any database proteins. A real-time quantitative PCR (RT-qPCR) analysis of the expression patterns of 14 selectable transcripts showed that 13 selected candidate genes were significantly up-regulated in the development process of tuber from dormancy to sprouting. A full length cDNA of ADP-ribosylation factor (ARF) gene was cloned and found it belonged to potato ARF1 gene. Tissue specific expression analysis showed ARF1 expression level was the highest in tuber. RT-qPCR analysis of the expression profile of ARF1 gene from potato tuber dormancy to sprouting revealed that the ARF1 gene expression was significantly increased after tuber dormancy breaking, which suggested that it probably associated with tuber dormancy and sprouting.

Regulation of potato tuber sprouting

“…A more recently performed SSH strategy led to the identification of approx. 300 differentially expressed ESTs and the authors described an ADP-ribosylation factor to be co-regulated with tuber dormancy break; however, they did not compare their data with the previously published results (Liu et al 2012).…”

“…Alternatively, differential display or suppression subtractive hybridisation (SSH) approaches using dormant and sprouting tubers (FaivreRampant et al 2004;Liu et al 2012) were applied to produce cDNA libraries enriched in genes up-regulated during dormancy release. Agrimonti et al (2000) identified two genes, referred to as G1-1 and A2-1, whose expression was induced or strongly repressed during transition from dormancy to sprouting.…”

Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato

“…The genetic mechanisms and any key genes associated with the state of dormancy or dormancy release were not found (Suttle, 2007), large scale ESTs library sequencing (Crookshanks et al, 2001;Ronning et al, 2003;Kloosterman et al, 2008), suppressive subtractive hybridization cDNA (Faivre-Rampant et al, 2004;Liu et al, 2012) and microarray hybridizations (Campbell et al, 2008;Hartmann et al, 2011) have traditionally been applied to deduce and quantify the transcript profiles of different potato tissues or developmental stages related to tuber dormancy and sprouting, which partially demonstrated that tuber dormancy release was associated with marked changes of gene expression related to transcription and translation, phytohormone and protein metabolism, but it was limited and incomplete resource for gene discovery and analysis in tuber dormancy release. The transcriptome study could present a comprehensive set of transcribed regions throughout the genome.…”

Expression of the Pluripotency Transcription Factor OCT4 in the Normal and Aberrant Mammary Gland

“…OCT4 is a self-renewal transcription factor (TF) that is found silenced in the vast majority of somatic cells. It has been established that the normal resting breast (from non-pregnant, non-lactating women) as well as cell lines derived from it have very little expression of OCT4 and associated embryonic TFs (Tai et al, 2005; Beltran et al, 2011; Lengerke et al, 2011; Hassiotou et al, 2012; Liu et al, 2012). However, we have recently demonstrated high expression of OCT4 and its associated TFs in the normal lactating breast and in cells isolated from breastmilk (Hassiotou et al, 2012).…”