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ABSTRACT:
PROVIDER: PRJNA471743 | ENA |
REPOSITORIES: ENA
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Project description:According to the key words, the gene set, including oxidation-reduction, RNA silence, disease resistance, phytohormone, phosphorylation, dephosphorylation, transcription factor, receptor, kinase, ubiquitination and RNA binding,etc. from sugarcane and the whole CDS sequence from smut genome, was achieved and used as targets in the present microarray assay. Based on smut infection samples from smut-susceptible sugarcane genotype YC71-374 and smut-resistant sugarcane genotype NCo376, the hybridization was conducted and validated by real-time fluorescent quantitative PCR. It would provide a basic data for the study on sugarcane-smut interaction mechanism, which referred to sugarcane smut resistance and smut pathogenesis.
2022-08-02 | GSE140801 | GEO
Project description:Sugarcane is a very efficient crop to produce ethanol. In recent years, extensive efforts have been made in order to increase sugarcane yields. To reach this goal, molecular biology tools have been used comprehensively, identifying genes, pathways and genetic polymorphisms. However, some important molecular components, like microRNAs, have not been deeply investigated. MicroRNAs are an important class of endogenous small, noncoding RNAs that regulate gene expression at the post-transcription level and play fundamental roles in diverse aspects of animal and plant biology. Plant genomes harbor numerous miRNA genes that regulate many protein-coding genes to influence key processes ranging from development, metabolism, and responses to abiotic and biotic stresses. There is wide range of pests and diseases that affect sugarcane, yet the mechanisms that regulate pathogen interactions with sugarcane have not been thoroughly investigated. To gain knowledge on the physiological responses to pathogens mediated by microRNAs in sugarcane, we screened the transcriptoma of sugarcane plants infected with Acidovorax avenae subsp avenae, the causal agent of red stripe disease in sugarcane, and detected several microRNAs modulated in the presence of the pathogen. Furthermore, we validated with qPCR a number of microRNA expression patterns observed by bioinformatics analysis. In addition, we observed high expression levels of several star microRNAs, in numbers larger than the mature microRNAs in some cases. Interestingly, sof-miR408 was consistently down-regulated in the presence of several pathogens, but not in the presence beneficial microbes. This result indicates that the sugarcane senses pathogenic or beneficial microorganisms differentially and triggers specific epigenetic regulatory mechanisms accordingly Screenning of sRNA transcriptome of sugarcane plants infected with Acidovorax avenae subsp avenae after seven days
2012-11-30 | E-GEOD-42628 | biostudies-arrayexpress
Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome. Examination of small RNA populations in the sugarcane leaves that show matches against sugarcane LTR-RTs.
2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress
Project description:Sugarcane is a very efficient crop to produce ethanol. In recent years, extensive efforts have been made in order to increase sugarcane yields. To reach this goal, molecular biology tools have been used comprehensively, identifying genes, pathways and genetic polymorphisms. However, some important molecular components, like microRNAs, have not been deeply investigated. MicroRNAs are an important class of endogenous small, noncoding RNAs that regulate gene expression at the post-transcription level and play fundamental roles in diverse aspects of animal and plant biology. Plant genomes harbor numerous miRNA genes that regulate many protein-coding genes to influence key processes ranging from development, metabolism, and responses to abiotic and biotic stresses. There is wide range of pests and diseases that affect sugarcane, yet the mechanisms that regulate pathogen interactions with sugarcane have not been thoroughly investigated. To gain knowledge on the physiological responses to pathogens mediated by microRNAs in sugarcane, we screened the transcriptoma of sugarcane plants infected with Acidovorax avenae subsp avenae, the causal agent of red stripe disease in sugarcane, and detected several microRNAs modulated in the presence of the pathogen. Furthermore, we validated with qPCR a number of microRNA expression patterns observed by bioinformatics analysis. In addition, we observed high expression levels of several star microRNAs, in numbers larger than the mature microRNAs in some cases. Interestingly, sof-miR408 was consistently down-regulated in the presence of several pathogens, but not in the presence beneficial microbes. This result indicates that the sugarcane senses pathogenic or beneficial microorganisms differentially and triggers specific epigenetic regulatory mechanisms accordingly
2012-11-30 | GSE42628 | GEO
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: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:Transcriptional profile of sugarcane plants variety SP80-3280 inoculated with the pathogen Leifsonia xyli subsp. xyli (Lxx) compared with mocked inoculated ones 30 and 60 days after inoculation (DAI). Goal was to determine the effects of the increase in Lxx title on global sugarcane gene expression.
2017-11-13 | GSE87826 | GEO