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Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage

ABSTRACT: Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2 - 4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE138254 | GEO | 2019/11/14

REPOSITORIES: GEO

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Project description:A transcriptome analysis was applied on two peach (Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify cold-responsive genes that might be involved in tolerance to long low temperature storage. Peach fruit from ‘Morettini No2’ and ‘Royal Glory’, a sensitive and a tolerant, to chilling injury cultivars, respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (25°C) or subjected to 4 and 6-weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. Microarray experiments, employing the peach microarray platform (μ PEACH 1.0), were carried out by comparing harvested fruit against 4- and 6-week cold-stored fruit. The analysis identified 173 and 313 genes that were differentially expressed in ‘Morettini No2’ and ‘Royal Glory’ fruit after 4 weeks, respectively. However, the 6 weeks cold storage provoked a decrease in the total number of genes differentially expressed in both cultivars. RNA blot analysis validated the differential expression of certain genes showed in microarray data. Among these genes, two heat shock proteins (hsps), a putative β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related protein PR-4B precursor were induced during cold storage in both cultivars. The induction of hsps and the putative β-D-xylosidase appeared to be independent on the duration of postharvest treatment. On the other hand, transcript levels of lipoxygenase were quite constant during postharvest ripening, while a strong reduction or disappearance was observed after cold storage. A dehydration-induced RD22-like protein showed a reduction in the accumulation of transcripts during postharvest ripening independently on the temperature conditions. Overall, the current study shed some light on the molecular aspects of cold stress in peach fruit quality and identified some ripening and/or cold-induced genes which function need further elucidation.

Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design

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Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage

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