Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1042846 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26901933.fastq.gz | Fastqsanger.gz | |||
| SRR26901934.fastq.gz | Fastqsanger.gz | |||
| SRR26901935.fastq.gz | Fastqsanger.gz | |||
| SRR26901936.fastq.gz | Fastqsanger.gz | |||
| SRR26901937.fastq.gz | Fastqsanger.gz |
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Project description:Intercropping is a vital technology in resource-limited agricultural systems with low inputs. Peanut/maize intercropping enhances iron (Fe) nutrition in calcareous soil. Proteomic studies of the differences in peanut leaves, maize leaves and maize roots between intercropping and monocropping systems indicated that peanut/maize intercropping not only improves Fe availability in the rhizosphere but also influences the levels of proteins related to carbon and nitrogen metabolism. Moreover, intercropping may enhance stress resistance in the peanut plant (Xiong et al. 2013b). Although the mechanism and molecular ecological significance of peanut/maize intercropping have been investigated, little is known about the genes and/or gene products in peanut and maize roots that mediate the benefits of intercropping. In the present study, we investigated the transcriptomes of maize roots grown in intercropping and monocropping systems by microarray analysis. The results enabled exploration differentially expressed genes in intercropped maize. Peanut (Arachis hypogaea L. cv. Luhua14) and maize (Zea mays L. cv. Nongda108) seeds were grown in calcareous sandy soil in a greenhouse. The soil was enhanced with basal fertilizers [composition (mg·kg−1 soil): N, 100 (Ca (NO3)2·4H2O); P, 150 (KH2PO4); K, 100 (KCl); Mg, 50 (MgSO4·7H2O); Cu, 5 (CuSO4·5H2O); and Zn, 5 (ZnSO4·7H2O)]. The experiment consisted of three cropping treatments: peanut monocropping, maize monocropping and intercropping of peanut and maize. After germination of peanut for 10 days, maize was sown. Maize samples were harvested after 63 days of growth of peanut plants based on the degree of Fe chlorosis in the leaves of monocropped peanut. The leaves of monocropped peanut plants exhibited symptoms of Fe-deficiency chlorosis at 63 days, while the leaves of peanut plants intercropped with maize maintained a green color.
2017-01-24 | GSE93771 | GEO
Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.
2013-07-11 | E-MTAB-4279 | biostudies-arrayexpress
Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms. The were 3 biological repliactes of each of the following groups: Control, Saffron pretreated, Photobiomodulation pretreated, Light Damage, Saffron Light Damage and Photobiomodulation Light Damage. 18 chips in total were performed.
2010-07-16 | E-GEOD-22818 | biostudies-arrayexpress
Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms.
2010-07-16 | GSE22818 | GEO
Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
2021-03-24 | GSE166350 | GEO