New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage

Abstract

In the scope of the present work, four SuperSAGE libraries have been generated, using bulked root tissues from four drought-tolerant accessions as compared with four bulked sensitive genotypes, aiming to generate a panel of differentially expressed stress-responsive genes. Both groups were submitted to 24 hours of water deficit stress. The SuperSAGE libraries produced 8,787,315 tags (26 bp) that, after exclusion of singlets, allowed the identification of 205,975 unitags. Most relevant BlastN matches comprised 567,420 tags, regarding 75,404 unitags with 164,860 different ESTs. To optimize the annotation efficiency, the Gene Ontology (GO) categorization was carried out for 186,191 ESTs (BlastN against Uniprot-SwissProt), permitting the categorization of 118,208 ESTs (63.5%). In an attempt to elect a group of the best tags to be validated by RTqPCR, the GO categorization of the tag-related ESTs allowed the in silico identification of 213 upregulated unitags responding basically to abiotic stresses, from which 145 presented no hits after BlastN analysis, probably concerning new genes still uncovered in previous studies. The present report analyzes the sugarcane transcriptome under drought stress, using a combination of high-throughput transcriptome profiling by SuperSAGE with the Solexa sequencing technology, allowing the identification of potential target genes during the stress response.

Differential gene expression in drought-tolerant sugarcane roots

“…Boaretto et al (2014) found that improved performance of tolerant cultivar IACSP 94-2094 under 2 levels of soil water restriction (70 and 30% Soil Available Water Content) was associated with a more efficient antioxidant system response, particularly under conditions of mild stress, compared the susceptible cultivar IACSP 95-5000. Kido et al (2012) subjected 20 commercial sugarcane cultivars to water stress for 3, 10, and 20 days and observed increased expression in the glutathione peroxidase-encoding gene in tolerant cultivars. According to Dedemo et al (2013), plants activate enzymes that promote the removal of reactive oxygen species to protect themselves from abiotic stress.…”

“…In addition, genes related to the mechanisms of drought tolerance may increase the understanding of the basic mechanisms in the evolutionary adaptation to this type of stress. These genes can be used in studies of plant transformation to develop drought-tolerant varieties and tested to improve field productivity in agricultural production (Nepomuceno et al, 2001;Lenka et al, 2011;Kido et al, 2012). A thorough understanding of the plant response to abiotic stress at the molecular level is a prerequisite for its effective management (Deshmukh et al, 2014).…”

“…Several techniques have been used to identify drought-responsive genes (Kido et al, 2012), and the cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique widely used to identify genes that are differentially expressed in tolerant plants in response to biotic or abiotic stresses. This technique is rapid, inexpensive, reproducible, sensitive, and has been successfully used previously for this purpose in sugarcane (Que et al, 2011).…”

De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress

“…Several transcriptome studies have tried to clarify the mechanisms used by sugarcane to overcome the difficulties encountered in water-deficit regions (Sugiharto et al, 2002;Rocha et al, 2007;Rodrigues et al, 2009;Iskandar et al, 2011;Kido et al, 2012;Andrade et al, 2015;Vantini, et al, 2015;Li et al, 2016). RNA sequencing (RNA-Seq) is one of the latest techniques used for the study of transcriptomes.…”

“…However, most transcriptome studies (e.g., microarrays, SAGE, cDNA-AFLP) in sugarcane (Rodrigues et al, 2009;Kido et al, 2012;Vantini et al, 2015), as well as the study of Vargas et al (2014) using the RNA-Seq technology, have evaluated the effect of short-term water stress (usually the complete absence of irrigation) and of water stress in young plants. These designs can lead to poorly acceptable results regarding the drought sensitivity or tolerance of plants under real field conditions where water restriction usually lasts for several months.…”