Internode elongation is an important trait in sugarcane as it affects the sugarcane yield. Gibberellin (GA) is a key modulator of internode elongation in sugarcane. Understanding the gene expression features of GA-mediated internode elongation has both scientific and practical significance. This study aimed to examine the transcriptomic changes in the internode elongation of sugarcane following GA treatment. Eighteen cDNA libraries from the internode tissues on days of 0, 3, and 6 in control and GA treatment groups were sequenced and their gene expression were studied. RNA-seq analysis revealed 1,338,723,248 reads and 70,821 unigenes from elongating internodes of sugarcane. Comparative studies discovered a large number of transcripts that were differentially expressed in GA-treated samples compared to the control. Further analysis revealed that the differentially expressed genes were enriched in the metabolic process, one-carbon compound transport, and single-organism process. Kyoto Encyclopedia of Genes and Genomes pathway annotation showed significant enrichment in photosynthesis and plant hormone signal transduction, indicating its involvement in internode elongation. The function analysis suggested that metabolic pathways and biosynthesis of secondary metabolites, plant hormones, and cell wall components were enriched in the internodes of the GA-treated plants. The hub genes were identified, with the function of cellulose synthesis. The results of this study provide a global view of mRNA changes during sugarcane internode elongation and extend our knowledge of the GA-mediated cellular processes involved in sugarcane stem growth.

Background: Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results: Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions: Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Background: Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results: In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. Conclusion: Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

Sugarcane (Saccharum officinarum L.) is a sugar crop capable of ratoon cultivation, and its ratooning ability directly relates to sugarcane production costs and planting benefits. Sugarcane ridges with missing seedlings and gaps are an important reason for the reduction in the number of effective stalks and the years of ratooning of ratoon sugarcane. Therefore, analyzing the differences and correlations in important agronomic traits during yield formation within ratoon sugarcane populations after replanting treatment is of paramount importance for guiding ratoon cultivation. In this study, the 3rd-year ratoon sugarcane of the main varieties Guiliu 2 (GL2), Guitang 44 (GT44), and Yuetang 00236 (YT236), which are widely cultivated, served as the target population for replenishment. Using stem cuttings of Guifu 98-296 (GF296) as the replanting material, replanting treatment was applied to sugarcane ridges with missing seedlings and gaps in the planting plots of the after mentioned three varieties. Unreplanted populations served as their respective controls (CK). At harvest in the 3rd, 4th, and 5th ratoon years, data on important agronomic traits and sucrose content of the sugarcane populations under the replanting and non-replanting treatments were investigated. An analysis was conducted to ascertain the differences and correlations among agronomic trait indicators. The economic benefits of the replanting treatment and CK were calculated. The findings of the study demonstrated that the number of effective stalks in the replanted populations of GL2, GT44, and YT236 was significantly higher than in the non-replanted control groups (CK), with an increase ranging from 10.72 to 45.26%. The yield of both the replanted and CK groups for GL2, GT44, and YT236 decreased by 9.56–54.14% with prolonged the years of ratooning. Conversely, the yield of the replanted populations increased by 28.19–158.61% over extended ratooning years. Significant variations were observed in plant height, stem diameter, and single-stalk weight among the original ratoon sugarcane varieties (GL2, GT44, YT236) and their respective CK groups across different ratooning years. In the non-replanted groups, the number of effective stalks exhibited a highly significant negative correlation with the years of ratooning (correlation coefficients: GL2: − 0.907, GT44: − 0.931, YT236: − 0.756), and yield also showed a highly significant negative correlation with the years of ratooning (GL2: − 0.915, GT44: − 0.905, YT236: − 0.930). Notably, after replanting, the negative correlation between the years of ratooning and both yield and effective stalk number was eliminated, indicating improved population structure. Furthermore, the replanted GL2, GT44, and YT236 populations exhibited increased economic benefits, with cumulative net income gains over three ratooning seasons of 48,120.80 CNY ha⁻¹, 46,765.80 CNY ha⁻¹, and 42,398.60 CNY ha⁻¹, respectively. In conclusion, GF296 replanting effectively extended the years of ratooning by three years, substantially enhanced economic returns, and is suitable for large-scale implementation. The present study provides a theoretical basis for constructing high-yield populations, maximising ratoon potential, and achieving high-efficiency cultivation.