Saccharum hybrid cultivar
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ABSTRACT:
PROVIDER: PRJNA573559 | ENA |
REPOSITORIES: ENA
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Project description:Background: Sugarcane is an important sugar and energy crop largely used for bioethanol production in the world. The development of sugarcane cultivars with high sucrose content and yield is one of the biggest challenges of breeding programs nowadays. To identify genes networks that underlie sucrose content and yield, we used a custom designed oligonucleotide array with 21,901 different probes to study the transcriptome from breeding populations of sugarcane contrasting to sucrose content and genotypes contrasting to photosynthesis rate. Results: Physiological and biochemical data reveals that the transcriptome profiles described here showed a close relationship between sucrose content and stem development. A total of 2135 genes were differentially expressed in at least one experimental hybridization. We identified genes related to carbohydrate metabolism, cell wall metabolism and signal transduction. The same oligoarrays was used to detect transcription in both sense and antisense orientation. The enriched functional category from antisense expressed genes reveals light harvesting and circadian clock as the two top categories that can be related to photosynthesis and yield in sugarcane. Conclusions: Knowledge on the mechanisms underlying carbon partitioning and its relationship with sucrose accumulation in sugarcane stems would help defines routes to increase yield. Our findings showed for instance that sucrose accumulation and yield in sugarcane may be regulated by hormone signaling pathways, light harvesting and circadian clock genes. Analysis of the expression data and gene category enrichment provided an insight into signaling pathways and transcriptional control contrasting in high brix and low brix plants as well as differing photosynthesis rates and yield.
2016-12-31 | GSE44389 | GEO
Project description:Sugarcane established industrial crop providing sugar, ethanol and biomass-derived electricity around the world. Cane sugar content is an important, breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at crop level, mainly due to the limited understanding of its regulation. MiRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remains unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis etc. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed.752 targets of 368 miRNAs (609 targets for 260 known miRNAs and 168 targets for 108 novel miRNAs) were identified by degradom sequencing.Several known and novel miRNAs and their target genes associated with sugar metabolism, sugar transport and sucrose storage were identified in this study.This new insight into the complex network of sucrose accumulation in sugarcane will help identify candidate targets for sucrose improvement in sugarcane through molecular means.
2021-12-30 | GSE188303 | GEO
Project description:Sugarcane (Saccharum spp. hybrid) is an economically important crop that is widely grown for its sucrose content, and somatic embryogenesis is a promising approach for efficient micropropagation and genetic transformation in this context. The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Comprehensive proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Our study advances the understanding of the molecular mechanisms of somatic embryogenesis in sugarcane, highlighting the regulation of key proteins during this process. Proteins involved in photosynthesis and starch accumulation were not detected during callus induction. In contrast, proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1 proteins) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation (GDM) showed only a slight, non-significant increase, suggesting that additional regulatory layers are involved in embryogenic competence. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.
2026-01-15 | PXD068502 | Pride
Project description:In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues. There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane. During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively. Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively. Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h). A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed. Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed. Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves.
2008-07-01 | GSE11934 | GEO
Project description:We performed cell wall proteins (CWPs) extraction and analysis from sugarcane 7-month-old young and mature leaves and basal and apical internodes in order to point the differences regarding the cell wall proteome composition in these specific organs and diverse developmental stages. We used two different extraction methods for leaves CWPs: destructive and non-destructive. For internodes, only the non-destructive technique was used. The collection of CWPs was identified through LC-MS/MS analyses. Altogether, 110 sugarcane CWPs were identified and classified into eight functional categories. Sugarcane has one of the highest coverage of CWPs identified by mass spectrometry, reaching 283.
2019-04-24 | PXD012761 | Pride
Project description:sugarcane Genome sequencing and assembly and sugarcane population resequencing data
| PRJNA1509098 | ENA