Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato

Abstract

Potato (Solanum tubersosum L.) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms to such stress in potato are largely unknown. To gain insight into the transcriptome dynamics that are associated with drought stress, genome-wide gene expression profile was conducted by Solexa sequencing to generate a large dataset and a comprehensive transcriptome profile for potato. Here, we report a reference for the potato transcriptome using leaf tissues under drought-stressed condition from a local potato cultivar 'Longshu 3'. Analysis of 86,965,482 RNA-Seq reads permitted the detection and quantification of expression levels of 7,284 genes at transcriptional levels, among them, 6,754 genes were enriched in draught-treated leaves while 6,419 in control. We identified 842 drought-responsive up-regulated and 494 down-regulated candidate genes with significantly differentially expression under continued drought stress treatments. Those differently expressed genes were mostly enriched in 89 gene categories and 21 KEGG pathways. Drought-stressed leaves had increased expression of genes involved in stress response compared with control leaves. A subset of differentially expressed genes associated with drought response was examined using quantitative real-time PCR. These results provide a broad spectrum of candidate genes that are essential for understanding the molecular regulation of potato in response to abiotic stresses.

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

“…However, as I. nil might have a high degree of heterozygosity, it is not feasible to consider whole genome sequencing of I. nil because of the high costs and time consumption. Fortunately, RNA sequencing provides a more powerful approach for mapping and quantifying the transcriptomes (Zhang et al 2014). Compared with traditional large-scale EST sequencing, RNA sequencing provides more abundant information for biological studies and offers more fundamental insights into biological processes, etc.…”

“…Fortunately, with the advent of next-generation sequencing (NGS) technology in recent years, genomic information in previously uncharacterized systems can be generated (Grabherr et al 2011). Currently, high-throughput RNA sequencing (RNA-Seq) has emerged as a powerful and cost-efficient tool for transcriptome analysis, and it has also been used for transcript profiling in various nonmodel plant species, including potato (Solanum tuberosum L.) (Zhang et al 2014), pennycress (Thlaspi arvense) (Dorn et al 2013), sweet potato (Ipomoea batatas) (Firon et al 2013) and radish (Raphanus sativus L.) (Wang et al 2012a).…”

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

“…Transcriptome profi les under drought response have been analyzed in horticultural plants that are vulnerable to drought such as potato ( Solanum tubersosum ) (Massa et al 2013 ;Zhang et al 2014 ), rice ( Oriza sativa ) (Zong et al 2013 ), and common beans ( Phaseolus vulgaris ) (Müller et al 2013 ). Similarly, several drought-tolerant species such as Agave deserti and Agave tequilana have been studied based on RNA-seq experiments (Gross et al 2013 ).…”

Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

“…Therefore, studying of transcriptome will provide important insights into the critical transcription factors and regulatory enzymes, their expression patterns, and the regulation of transcribed regions in drought stress conditions. Compared with the former methods, RNA-seq technologies are much simpler and more cost-effective, and wildly used in many plant species (Zhang et al, 2014;Robertson et al, 2010) for discovering novel transcripts and comparing gene expression, for instance, Ipomoea batatas (Tao et al, 2012), Ipomoea nil (Wei et al, 2015), Brassica napus (Trick et al, 2009), Zea mays , and Picrorhiza kurrooa (Gahlan et al, 2012).…”

“…Drought tolerance has been observed in many plants, including wild Arachis (Brasileiro et al, 2015), Ammopiptanthus (Zhou et al, 2012), Lolium arundinaceum (Saha et al, 2015), and potato (Zhang et al, 2014). To elucidate the mechanism underlying drought stress, it is important to determine the change of gene expression level in response to this biological process.…”