Differential gene expression in drought-tolerant sugarcane roots

Abstract

ABSTRACT. Drought is one of the most frequent abiotic stresses limiting the productivity and geographical distribution of sugarcane culture. The use of drought-tolerant genotypes is one approach for overcoming the effects of water stress. We conducted a comparative study to identify gene expression profiles under water stress in tolerant sugarcane roots. Two different cultivars, 1 drought tolerant (RB867515) and 1 drought susceptible (SP86-155), were evaluated at 4 sampling time points (1, 3, 5, and 10 days) using the cDNA-amplified fragment length polymorphism technique. A total of 173 fragments were found to be differentially expressed in response to water stress in the tolerant cultivar. Seventy of these were cloned, sequenced, and categorized. Similarity analysis using Candidate genes to drought tolerance in sugarcane BLAST revealed that 64% of the fragments differentially expressed code proteins classified as no hits (23%), hypothetical (21%), or involved in stress response (20%), with others were involved in communication pathways and signal transduction, bioenergetics, secondary metabolism, and growth and development. Four genes were analyzed and validated using real-time quantitative polymerase chain reaction to determine their expression and showed consistency with the cDNA-amplified fragment length polymorphism analyses. Our results contribute insight into the molecular responses to water stress in sugarcane and possibility to the development of cultivars with improved tolerance to drought.

Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific

“…However, the association between genotype and phenotype remains a challenge, despite many attempts 36,37 . Several studies have identified drought-induced genes in order to identify targets for molecular breeding 25,[38][39][40] . However, as most of these studies only harvest at one timepoint, it is possible that important rhythmic drought-induced genes are missed 41 .…”

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

“…Vantini et al (2015) observed differentially expressed genes between tolerant and sensitive sugarcane varieties along time (1, 3, 5, and 10 days after withholding water) in root tissues. At the beginning of the stress (1 and 3 days), genes encoding proteins with protection function (chaperones, heat shock proteins, antioxidant enzymes and protease inhibitor proteins) were induced in the tolerant variety.…”

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

“…Little is known about the bHLH family in plants. Vantini et al (2015), investigating the effects of water deficit in sugarcane, observed the expression of bHLH after 3 days of water stress (complete absence of irrigation). Studying A. thaliana, Hao et al (2012) concluded that bHLH, together with factors that interact with phytochromes, regulates cell elongation and plant development in response to light and hormones.…”

“…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.…”

“…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.…”