Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

Abstract

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.

Genome-Wide Identification, Characterization, and Expression Analysis of Glutamate Receptor-like Gene (GLR) Family in Sugarcane

“…The transcriptome data of different sugarcane tissues, including bud, leaf, epidermis, stem pith, and root from ten-month-old sugarcane cultivar ROC22, were derived from the transcriptome of our group (unpublished). The transcriptome data of different sugarcane cultivars under the stress of S. scitamineum were obtained from Que et al [71], and the materials were selected from ROC22 (susceptible cultivar) and Yacheng 05-159 (YC05-159, resistant cultivar) with the bud samples infected by S. scitamineum for 0, 1, 2, and 5 d. The cold stress transcriptome data (PRJNA636260) were obtained from Huang et al [72], and the selected material was GX87-16 cultivar, which was treated at low temperature two weeks after pot planting, and the leaf samples of 0, 0.5, 1, and 6 h after treatment were taken. The drought stress transcriptome data (PRJNA590595) of Co 06022 (susceptible cultivar) and Co 8021 (resistant cultivar) were obtained from Selvi et al [73].…”

Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress

“…In addition, cold stress leads to increased peroxidation of the leaf membrane, and increased soluble sugar, proline, and MDA content, but decreased chlorophyll content in sugarcane [ 28 , 29 ]. At a molecular level, studies revealed that cold stress influenced the expression of several genes in sugarcane, including those identified by bioinformatic analyses to be involved in calcium metabolism [ 30 , 31 ]. Similar results were reported in other plant species [ 32 , 33 , 34 ].…”

Transcriptional Regulation of Cold Stress Tolerance in Plants. Present Status and Future Prospects

“…Overexpressed OsmiR528 cell lines improve lowtemperature tolerance and stress response transcription factors. A distinct group of miRNAs, including miR444, miR169, and miR396, increases lignin metabolism, transcription, and signal transduction in sugarcane via regulating cold stress [147]. The structural characteristics of miRNA and TF revealed that the interaction of miRNA and transcription factors governs multiple gene expression, which aids in cellular protection against various abiotic stresses[148].…”