Potato Tuber Dormancy Release and Sprout Elongation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46000 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6176130_1.fastq.gz | Fastqsanger.gz | |||
| ERR6176130_2.fastq.gz | Fastqsanger.gz | |||
| ERR6177892_1.fastq.gz | Fastqsanger.gz | |||
| ERR6177892_2.fastq.gz | Fastqsanger.gz | |||
| ERR6177046_1.fastq.gz | Fastqsanger.gz |
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Project description:An in vivo and in vitro potato tuber development gene expression study. For in vitro tuber development expression analysis, RNA was isolated from in vitro microtubers at 2, 5, 10, 20 and 30 days following observed tuber induction. Two microtuber populations were used as biological replicates for the developmental stages. The RNA from all developmental stages was pooled to generate the reference samples. Ten microarray hybridizations were performed. For in vivo tuber development expression analysis, RNA was isolated from tubers growing in growth chamber conditions. Tissues were divided into six group, according to developmental size: stolon (no tuber formation), 1-5 mm tubers, 6-10 mm tubers, 11-15 mm tubers, 16-25 mm tubers, and 26-35 mm tubers. Two biological replicates of ten plants each were grown sequentially in the same growth chamber. The RNA from all developmental stages was pooled to generate the reference samples. Twelve microarray hybridizations were performed. For all experiments, the RNA was labeled using the indirect labeling method with random hexamer primers. Amplified cRNA was used as labeling template for stolons. Total RNA was used as labeling template in all other labeling reactions.
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Project description:The aim of this study is to analize the genes that are up or down-regulated in response to sprouting promoting effectors such as GAs and light, in order to elucidate the signalling cascades triggered during this process. Half sections of certified pathogen tested Spunta tubers were put into sterile MS-agar (0.7%) containing flasks at 16„aC and subjected to different treatments: Dark controls: Tuber sections were incubated for 10 or 35 days in complete darkness. Light control: Tuber sections were incubated for 10 days under continuous light conditions. Treatments performed in complete darkness during 35 days: a) GA treatment: 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma) b) Sucrose treatment: 1% sucrose c) GA & sucrose treatment: 5 uM GA3 (Sigma) + 1% sucrose Treatments performed in light (10 days)d) GA treatment : 5 uM GA3 (Sigma). Three independent biological replicates of each condition (3 controls and 4 treatments) wereperformed. At the moment of harvest (10 or 35 days) sprout length was measured and photographs of the different samples were taken. Sprouts were excised and frozen in liquid Nitrogen. Total RNA was obtained using the Trizol reagent (Invitrogen) according to the manufacturer¡¦s instructions. RNAs were quantified by OD: 260/280 and checked in agarose gels. Keywords: Loop design
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Project description:Potato (Solanum tuberosum L) is a natural host of Potato spindle tuber viroid (PSTVd) which can cause characteristic symptoms on developing plants including stunting phenotype and distortion of leaves and tubers. PSTVd is the type species of the family Pospiviroidae, it can replicate in the nucleus and the viroid RNA moves systemically in infected plants. Its KF440-2 strain can cause severe symptoms in potato. It is not well understood how the viroid can affect host genes for successful invasion and which genes show altered expression levels upon infection. In this study, we used a high-scale method to identify differentially expressed genes in potato. We have identified defence, stress and sugar metabolism related genes having altered expression levels upon infection. Additionally, hormone pathways connected genes showed up- or down-regulation. Our primary focus is on the identification of genes which can affect tuber formation as the viroid infection can strongly influence tuber development, especially tuber shape is affected. DWARF1/DIMINUTO, Gibberellin 7-oxidase and BEL5 protein were identified and validated which showed differential expression in viroid infected tissues suggesting that gibberellin and brassinosteroid pathways have a possible role in tuber development upon PSTVd infection.
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