Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner

Abstract

Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilience against water scarcity; particularly the molecular mechanisms in response to drought stress have become an underlying issue for its improvement. To better understand water stress and the molecular mechanisms we performed a de novo transcriptomic assembly of sugarcane (var. Mex 69–290). A total of 16 libraries were sequenced in a 2x100 bp configuration on a HiSeq-Illumina platform. A total of 536 and 750 genes were differentially up-regulated along with the stress treatments for leave and root tissues respectively, while 1093 and 531 genes were differentially down-regulated in leaves and roots respectively. Gene Ontology functional analysis showed that genes related to response of water deprivation, heat, abscisic acid, and flavonoid biosynthesis were enriched during stress treatment in our study. The reliability of the observed expression patterns was confirmed by RT-qPCR. Additionally, several physiological parameters of sugarcane were significantly affected due to stress imposition. The results of this study may help identify useful target genes and provide tissue-specific data set of genes that are differentially expressed in response to osmotic stress, as well as a complete analysis of the main groups is significantly enriched under this condition. This study provides a useful benchmark for improving drought tolerance in sugarcane and other economically important grass species.

Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113

“…Introduction Sugarcane crop of the family Poaceae globally fulfills the need for sugar, bioethanol, animal feed, and molasses [1][2][3]. Sugarcane cultivation requires a large amount of nitrogen (N) fertilizers that varies nearly 120 to 320 kg ha -1 or more.…”

Transcriptome, Genetic Transformation and Micropropagation: Some Biotechnology Strategies to Diminish Water Stress Caused by Climate Change in Sugarcane

“…More recently (2017), in our laboratory Pereira-Santana and cols. [52] analyzed the transcriptomic profile of the 2nd most important sugarcane cultivar in Mexico, 'Mex 69-290', in response to osmotic stress. In such study, authors employed the High-throughput sequencing system HiSeq-Illumina (2x100bp) to analyze 16 cDNA libraries representing leaves and roots of in vitro-grown plantlets exposed to PEG-8000 during 0, 24, 48, and 72 hours.…”

“…Even when some of these TF families seemed underrepresented (like NAC and MYC), they still provide a useful benchmark to conduct phylogenetic, expression, and functional analysis. [52]. The heat map was generated with the ComplexHeatmappackage v1.14.0 [52] in R v3.4.1 [53].…”

“…[52]. The heat map was generated with the ComplexHeatmappackage v1.14.0 [52] in R v3.4.1 [53]. (B) Abundance of major stress-related TF families and Dirigent protein family in arabidopsis, rice, sorghum, and sugarcane.…”

“…For this analysis the complete predicted proteomes (primary transcripts only) of arabidopsis, rice, and sorghum were obtained from Phytozome v. 12 [55]. Sugarcane predicted protein dataset was obtained from the transcriptome assembly of Pereira-Santana and cols [52] HMM searches were performed using HMMER3 v3.1b2 (http://hmmer.org/) and set to a cut-off e-value of 1e-05 and a score above the inclusion threshold of each HMM profile.…”