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Drought and cold stresses are the main environmental factors that affect the yield of sugarcane, and DREB genes play very important roles in tolerance to drought, cold, and other environmental stresses. In this study, bioinformatics analysis was performed to characterize Saccharum spontaneum SsDREB genes. RNA sequencing (RNA-seq) was used to detect the expression profiles of SsDREBs induced by cold and drought stresses. According to our results, there are 110 SsDREB subfamily proteins in S. spontaneum, which can be classified into six groups; 106 of these genes are distributed among 29 chromosomes. Inter-and intraspecies synteny analyses suggested that all DREB groups have undergone gene duplication, highlighting the polyploid events that played an important role in the expansion of the DREB subfamily. Furthermore, RNA-seq results showed that 45 SsDREBs were up-or downregulated under cold stress; 35 of them were found to be involved in responding to drought stress. According to protein-protein interaction analysis, SsDREB100, SsDREB102, and SsDREB105 play key roles during the response to cold stress. These results reveal that functional divergence exists between collinear homologous genes or among common origin genes in the DREB subfamily of S. spontaneum. This study presents a comprehensive analysis and systematic understanding of the precise mechanism of SsDREBs in response to abiotic stress and will lead to improvements in sugarcane.

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BackgroundInternode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied.ResultsBased on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane.ConclusionsThe results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.