Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

Abstract

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.

Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

“…These are two chemicals that regulate plant growth in sugar farming with different effects. GA stimulates sugarcane internode elongation by regulating the genes associated with zeatin biosynthesis, nitrogen metabolism, and plant hormone signal transduction pathway [ 41 ], while DPC suppresses sugarcane growth. However, compared to the clear mechanism of GA-stimulated growth, the molecular mechanisms of DPC are unclear.…”

Enhanced Activity of Genes Associated With Photosynthesis, Phytohormone Metabolism and Cell Wall Synthesis Is Involved in Gibberellin-Mediated Sugarcane Internode Growth

“…Our earlier studies indicated that miRNA-mRNA pairs are involved in zeatin biosynthesis, nitrogen metabolism, and plant hormone signal transduction pathways, and are strongly associated with internode elongation and development in sugarcane (Qiu et al, 2019a). Moreover, GA content in leaves significantly increased after GA spraying (Qiu et al, 2019b).…”

Global Transcriptome Changes of Elongating Internode of Sugarcane in Response to Mepiquat Chloride

“…GA and DPC are two pairs of chemicals that regulate plant growth in sugar farming with different effects. GA stimulates sugarcane internode elongation by regulating genes associated to zeatin biosynthesis, nitrogen metabolism and plant hormone signal transduction pathway [43] while the DPC depressed sugarcane growth. However, compared to the clear mechanism of GA stimulated growth, the molecular mechanisms of DPC is blur.…”