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

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.

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

Background: Mepiquat chloride (DPC) is an extensively used chemical to control internode growth and compact canopies in cultured plants. Previous studies suggested that DPC could 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 the high-quality long transcripts from internode of sugarcane by PacBio Sequel System. A total of 72,671 isoforms with N50 as 3,073 were generated. These long isoforms were used for the following RNA-seq as reference. Subsequently, short reads generated from Illumina Hiseq 4000 platform were used for comparing the differentially expressed genes in DPC and control groups. The transcriptome profiling showed the 6 days post DPC treatment had the most significant changed genes. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating DPC affected multiple pathways beside depressed gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the constructed 36 modules, the top positive correlated module with stage of 6 day post spraying DPC was sienna3. Stf0 sulphotransferase, cyclin-like F-box and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. The qPCR demonstrated the high accuracy of RNA-seq result. Conclusion: Taken together, we demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

Multi-analysis of sheath senescence provides new insights into bamboo shoot development at the fast growth stage

Sheath senescence is an important part of bamboo shoot development during the fast growth stage. However, no information has been reported about this distinctive process until now. Using multiple approaches, we found that sheath senescence is a complex process that occurs sequentially with chloroplast corruption, chlorophyll degradation, and water loss. Reactive oxygen species (ROS), salicylic acid, and abscisic acid also accumulate in the senescing sheath. Transcriptome analysis showed that NAC and WRKY transcription factors, such as NAC2 and WRKY75, as well as their possible downstream target genes, such as those involved in ROS production, proteolysis, and nutrition recycling, constitute the gene network of the bamboo sheath senescence process. Furthermore, the initiation of sheath senescence might be triggered by hexokinase genes, such as HXK6, which is localized to the mitochondrion and could promote leaf senescence when overexpressed in Arabidopsis. Sheath senescence occurs after the growth decrease of the internodes, which provides assimilates. The slowing of internode growth possibly results in sugar accumulation, such as glucose, in the sheath, which finally upregulates hexokinase genes and initiates sheath senescence. These findings reveal that sheath senescence is a multilevel regulation process and has a close link to the corresponding internode growth, which provides new insights into the shoot development of bamboo during the fast growth stage.

Multi-analysis of sheath senescence provides new insights into bamboo shoot development at the fast growth stage

Sheath senescence is an important part of bamboo shoot development during the fast growth stage. However, no information has been reported about this distinctive process until now. Using multiple approaches, we found that sheath senescence is a complex process that occurs sequentially with chloroplast corruption, chlorophyll degradation and water loss. Reactive oxygen species (ROS), salicylic acid and abscisic acid also accumulate in the senescing sheath. Transcriptome analysis showed that NAC and WRKY transcription factors, such as NAC2 and WRKY75, as well as their possible downstream target genes, such as those involved in ROS production, proteolysis and nutrition recycling, constitute the gene network of the bamboo sheath senescence process. Furthermore, the initiation of sheath senescence might be triggered by hexokinase genes, such as HXK6, which is localized to the mitochondrion and could promote leaf senescence when overexpressed in Arabidopsis. Sheath senescence occurs after the growth decrease of the internodes, which provides assimilates. The slowing of internode growth possibly results in sugar accumulation, such as glucose, in the sheath, which finally upregulates hexokinase genes and initiates sheath senescence. These findings reveal that sheath senescence is a multilevel regulation process and has a close link to the corresponding internode growth, which provides new insights into the shoot development of bamboo during the fast growth stage.

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

Background: Mepiquat chloride (DPC) is an extensively used chemical to control internode growth and compact canopies in cultured plants. Previous studies suggested that DPC could 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 the high-quality long transcripts from internode of sugarcane by PacBio Sequel System. A total of 72,671 isoforms with N50 as 3,073 were generated. These long isoforms were used for the following RNA-seq as reference. Subsequently, short reads generated from Illumina Hiseq 4000 platform were used for comparing the differentially expressed genes in DPC and control groups. The transcriptome profiling showed the 6 days post DPC treatment had the most significant changed genes. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating DPC affected multiple pathways beside depressed gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the constructed 36 modules, the top positive correlated module with stage of 6 day post spraying DPC was sienna3. Stf0 sulphotransferase, cyclin-like F-box and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. The qPCR demonstrated the high accuracy of RNA-seq result. Conclusion: Taken together, we demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage

Previous studies on the fast growth of bamboo shoots mainly focused on the entire culm. No work about the fast elongation of a single internode, which is the basic unit for the fast growth of bamboo shoots, has been reported so far according to our knowledge. In this study, we have systematically investigated the regulating mechanisms underlying the fast growth of a single bamboo internode of Bambusa multiplex (Lour.) Raeusch. ex Schult. We discovered that the growth of the internode displays a logistic pattern, and the two sections located in the bottom of the internode, one for cell division and, another for cell elongation, each with an ~1-cm length, comprise the effective zones for the internode growth. RNA-Seq analysis identified a number of genes potentially involved in regulating the fast growth of bamboo internode such as those that have positive roles in promoting cell growth or division, which were dramatically down-regulated in the internode at fast growth decreasing stage. Further analysis revealed that sugar plays an important role in promoting the fast growth of bamboo internodes through inhibition of BmSnf1. Mechanical stress is found to be involved in the triggering of the internode growth decrease through activation of the generation of reactive oxygen species by upregulating Calmodulins. These results provide systematic insight into the biological mechanisms underlying the fast growth of bamboo shoots based on the behavior of a single internode.

Growth of Xanthium (Compositae) internodes at different positions on the stem

Internode growth of vegetative <em>Xanthium</em> plants was studied at various levels on the stem with application of the plastochron index. The bottom internodes were of small size and they displayed small rates of growth. Both, the size of the internodes and their growth rates increased proceeding in the acropetal direction. Rates of cortical cell elongation followed a bell shaped curve, starting with a rate of 7 µm per day, reaching a peak of 15 µm per day and stopping after leaf plastochron index 14. Young internodes, smaller than 25 mm, grew at a constant relative elemental rate of 0.2 day^-1 throughout. Internodes larger than 30 mm displayed an acropetal pattern of elongation.