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PROVIDER: PRJNA1060490 | 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: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:Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.
2021-05-24 | GSE161308 | 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
2012-11-30 | GSE42628 | GEO
Project description:To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express. Seeldings were treated with low-K hydroponic (containing 0.1 mmol.L-1 K+) and after 0 (CK), 8, 24 and 72 h exposure to low -K stress, the roots of sugarcane were collected. Four independent experiments were performed using roots collected at different time points
2014-10-02 | E-GEOD-61935 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. niger comparing WT strain vs. ΔXlnR strain treated with steam-exploded sugarcane bagasse (SESB) for 6, 12 and 24 h. The main objective was to identifiy genes related to cellulases and hemicellulases, comparing the differences between WT strain and the strain with the disrupted xylanolytic transcriptional activator gene, XlnR, after treatment with steam-exploded sugarcane. The experiment was further validated by real-time PCR, mass spectrometry of secreted proteins and enzymatic assays.
2010-10-20 | GSE24798 | GEO