Ontology highlight
ABSTRACT:
PROVIDER: PRJNA873207 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21281731_1.fastq.gz | Fastqsanger.gz | |||
| SRR21281731_2.fastq.gz | Fastqsanger.gz | |||
| SRR21281732_1.fastq.gz | Fastqsanger.gz | |||
| SRR21281732_2.fastq.gz | Fastqsanger.gz | |||
| SRR21281733_1.fastq.gz | Fastqsanger.gz |
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Project description:High sugar character is one of the important assessment indexes for selecting and breeding excellent sugarcane varieties. In order to screen important proteins that may be involved in sugar synthesis and accumulation during the ripening process of different sugarcane varieties, and to provide theoretical basis for future breeding of sugarcane varieties with high sugar maturity, the early-maturing sugarcane variety GL05-136 and late-maturing sugarcane variety GR2 were used as experimental materials. iTRAQ technique was used to identify the intraspecific and interspecific proteomic differences between the two sugarcane varieties at different sampling periods.
2024-12-12 | PXD058835 |
Project description:Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected. Keywords: Expression profiling by array
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Project description:Transcriptome comparsions and integrated systems analysis were used to identify candidate genes associated with fruit acidity control and gene coexpression subnetworks involved in fruit acid accumulation. mRNA profiles of fruit tissues at two stages (45 days postanthesis (DPA); and 142 DPA) from four varieties with differing fruit acidity.
2016-04-13 | E-GEOD-78046 | biostudies-arrayexpress
Project description:The diazotrophic CBAmC strain of Nitrospirillum amazonense has been reported to promote growth of sugarcane variety RB867515 when inoculated under field conditions in a consortium with four other nitrogen-fixing bacteria. The present work had the objective of accessing the influence of the sugarcane apoplast fluid from variety RB867515 on the global transcriptomic and proteomic profiles of CBAmC strain cultured in vitro. The comparative analysis between the transcriptome and proteome profiles showed strong consistency between the results of the two approaches. Data analysis revealed that expression levels of transcripts and proteins related to cell motility and signal transduction, among other functions, were strongly downregulated in the presence of the apoplast fluid. In contrast, transcripts and proteins were upregulated for functional categories including chaperones, iron homeostasis and multidrug efflux transporters. In conclusion, the results showed that the metabolic state of N. amazonense during cultivation in the presence of the apoplast fluid is directed to functions capable of supporting adaptation to the complex environment of the sugarcane apoplast.
2019-07-12 | PXD013518 | Pride
Project description:Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem. Keywords: stem development profile
2006-11-19 | GSE5021 | GEO
Project description:Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected. Keywords: Expression profiling by array Total RNA from internodes pool from high brix plants and low brix plants was hybridized to dual channel arrays. Internodes from the same stage of development and from the same progeny were compared. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).
2009-02-11 | E-GEOD-14730 | biostudies-arrayexpress
Project description:To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including one F1 population derived from cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.
2019-12-17 | GSE128450 | GEO
Project description:The expression profile of mature internodes (In9) and immature (In1) internodes of high brix and low brix plants was compared. Internodes were collected from plants with high brix content and from plants with low brix content from Progeny 2. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected 7 and 11 months after planting. Keywords: Expression profiling by array
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Project description:Sucrose is the major product of photosynthesis in many higher plants. It is transported from the source tissue through the phloem to various sink tissues to support plant growth, development and reproduction. Knowledge of the signal transduction pathways involved in carbohydrate metabolism is limited. Genes involved in the regulation of sucrose synthesis and accumulation could be used as tools in the development of genetically manipulated plants with higher sucrose content or aid in breeding programs as molecular markers. Using the SUCEST (Sugarcane EST) database information and a microarray approach, the expression profiles of 1920 sugarcane (Saccharum spp.) genes encoding signal transduction elements, transcription factors and stress-related proteins were analyzed. In order to assess their involvement in sucrose metabolism, the expression profiles of individuals from a sugarcane population segregated for sugar content were compared. From a population of 500 F1 individuals, the seven with the highest and the seven with the lowest sugar contents were selected, pooled and profiled using cDNA microarrays. Twenty-four genes were identified as differentially expressed. Five of them were more expressed in the plants with the highest sugar contents and 19 in the plants with the lowest sugar contents. RNA-blot hybridization was used to validate the expression profiles obtained for individuals in each group. These genes were shown to have differential expression throughout the growing season and in the different tissues. Our data supports the view that sugar levels modulate a complex signal transduction network that seems to involve responses related to stress. Keywords: Segregated population
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