Study : The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

Identification

Name

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

Identifier

dXJuOkVWQS9zdHVkeS9QUkpOQTMwNTcyOA==

Source

Data link

Link to this study on EBI European Nucleotide Archive

Description

Nitrogen (N) fertilization is an important abiotic factor for the growth of potato (S. tuberosum) because of its potential effects on yield. Because excess N in the soil runs off into water systems and negatively impacts the environment, studies on N use by the plant are key to decrease N-fertilizer use. Three commercial potato cultivars (Shepody, Russet-Burbank and Atlantic) were grown under two different rates of applied N-fertilizer (0 kg N ha-1 and 180 kg N ha-1) to obtain more information on the underlying gene regulation mechanisms associated with N. Plants with no added N had significantly lower concentrations of petiole nitrates, chlorophyll level indices, biomass and yield per hectare. Total mRNA samples were taken at two different time-points during the growth season and used for sequencing. The results for each cultivar and time-point were analysed separately to find differentially expressed genes. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed in plants from all potato cultivars when they were grown with added N-fertilizer. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed to find overrepresented motifs using three motif discovery algorithms (Seeder, Weeder and MEME). Nine different motifs were found, indicating potential gene regulatory mechanisms for potato under N-deficiency. Overall design: Differential gene expression in leaf tissue of S. tuberosum from three different cultivars (Shepody, Russet-Burbank and Atlantic), at two different time points, with four repetitions per treatment, using an Illumina HiSeq 2000.

Data files

Genotype

Accession number	Name	Taxon