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

Abstract

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha−1 was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.

Nitrogen Deficiency Induced Alterations in the Root Proteome of a Pair of Potato (Solanum tuberosum L.) Varieties Contrasting for their Response to Low N

“…Over the years many transcriptomic studies have been conducted to understand plant response to high and low concentration of N. They showed that various biological processes, such as amino and nucleic acid synthesis, protein folding, RNA processing, and hormone biosynthesis are rapidly affected when nitrate is depleted or resupplied . Recently, the role of genes taking part in amino acid metabolism was emphasized by transcriptomic study in potato . However, as yet, few equivalent studies at the proteomic level have been reported.…”

Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding

“…ncbi.nlm.nih.gov/geo/) -это база данных, в которой собра ны результаты высокопроизводительного секвенирования транскриптомов (RNAseq) и анализа экспрессии генов с использованием микрочипов, в том числе для S. tuberosum (Rensink et al, 2005;Carvallo et al, 2011;Evers et al, 2012;Zhang et al, 2013;Stare et al, 2015;Gálvez et al, 2016). База данных GEO включает несколько разделов, в том числе DataSets, который содержит описание эксперимен тов по секвенированию транскриптомов.…”

“…В этом разделе суммированы данные 1 583 экспериментов, посвященных анализу транскриптома картофеля. Результаты транс криптомных экспериментов в БД GEO представлены в 30 публикациях, в число которых входят исследования по изменению транскриптома картофеля в ответ на за ражение вирусами Petek et al, 2014;Stare et al, 2015), на воздействие факторами абиотического стресса (Gálvez et al, 2016), различия в уровне экспрессии генов miRNA в зависимости от стадии развития (Lakhotia et al, 2014). Первичные данные секвенирования транс криптомов в экспериментах RNAseq представлены в базе данных NCBI SRA (Sequence Read Archive), основном мировом архиве результатов высокопроизводительного секвенирования нуклеотидных последовательностей.…”

Transcriptome analysis of tobacco root response to different concentrations of nitrate

“…Recently, Gálvez et al. (Gálvez, Tai, Lagüe, Zebarth, & Strömvik, 2016) identified 30 over‐expressed genes and 9 under‐expressed genes in potato ( Solanum tuberosum L.) with supplemented NO 3 − . These findings highlight the case to further investigate the potential regulatory mechanisms of gene in flue‐cured tobacco in response to NO 3 − supply.…”