Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23654646_1.fastq.gz | Fastqsanger.gz | |||
| SRR23654646_2.fastq.gz | Fastqsanger.gz | |||
| SRR23654647_1.fastq.gz | Fastqsanger.gz | |||
| SRR23654647_2.fastq.gz | Fastqsanger.gz | |||
| SRR23654648_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Green manure is widely advocated as a sustainable alternative to chemical fertilizers in crop systems, yet the mechanisms underlying its yield benefits remain unclear. Moreover, vigorous vegetative growth under green manure can elevate lodging risk, undermining yield and harvest efficiency. Here, we describe mechanisms by which hairy vetch–based green manure enhances yield and evaluate the practical value of deploying functionally weak alleles of gibberellin 20-oxidase (GA20ox) in this management context. We conducted field comparisons of green manure and conventional chemical fertilization to evaluate effects on rice productivity, grain appearance quality, and canopy physiology. Green manure significantly increased grain yield and grain appearance quality in the leading Japanese cultivar ‘Koshihikari’, accompanied by higher lodging. By contrast, high-yielding cultivars homozygous for a single-copy GA20ox1 allele and/or a non-functional GA20ox2 allele maintained superior lodging resistance under green manure treatment while improving yield and grain appearance quality, indicating an effective combination of its treatment and genotypes. Physiologically, green manure increased chlorophyll index during vegetative growth and at the reproductive stage, and nitrogen (N) concentration on the whole plant. Furthermore, green manure increased flag-leaf width and tiller number; these canopy changes were associated with reduced panicle temperature at the ripening stage. Green manure treatment induced upregulation of OsNADH-GOGAT2, a known gene associated with increased N loading to grains, and more grain storage proteins, providing a positive link to improved grain appearance quality. Collectively, this study demonstrates that integrating hairy vetch with functionally weak GA20ox alleles can enhance productivity and grain appearance quality while mitigating lodging risk. This sheds light on the importance of aligning green-manure treatment with targeted allelic selection to stabilize performance across intensive-farming systems and reduce chemical fertilizer dependency.
2026-01-19 | GSE313855 | GEO
Project description:Reproductive-stage heat stress reduces rice yield and grain appearance quality, even in modern heat-resilient cultivars. Although our previous work showed that green manure can lessen ripening heat damage in the widely grown but heat-susceptible Japanese cultivar Koshihikari, it remains unclear whether similar benefits occur in heat-resilient cultivars and how green manure influences source–sink molecular responses during ripening. Here, using the heat-resilient cultivar Nijinokirameki, we tested whether green manure alleviates ripening heat stress by modifying panicle thermal status, nitrogen assimilation, and early endosperm stress responses. Green manure increased flag-leaf size and tiller (panicle) number and enhanced ripening-stage heat resilience by lowering panicle temperature without a meaningful phenological shift. Consistent with reduced heat load at the target organ, endosperm RNA-seq at 5 days after flowering (DAF) revealed weaker induction of heat-responsive programs under green manure, accompanied by increased grain protein content and reduced chalkiness classes (e.g., white milky, and white belly and back kernels). In parallel, shoot nitrogen contents at panicle formation stage were increased and flag-leaf RNA-seq at 5 DAF showed upregulation of ASN1 and NADH-GOGAT2, suggesting contribution to nitrogen assimilation in source organs and nitrogen allocation to grains. Together, these results link a sustainable fertility practice to tissue-scale heat stress mitigation and coordinated source–sink transcriptional responses at ripening that reflects enhanced grain protein accumulation and appearance quality under green manure treatment.
2026-06-01 | GSE331540 | GEO
Project description:Bile acids are steroid compounds from the digestive tracts of vertebrates that enter agricultural environments in unusual high amounts with manure. Bacteria degrading bile acids can readily be isolated from soils and waters including agricultural areas. Under laboratory conditions, these bacteria transiently release steroid compounds as degradation intermediates into the environment. These compounds include androstadienediones (ADDs), which are C19-steroids with potential hormonal effects. Experiments with Caenorhabditis elegans showed that ADDs derived from bacterial bile acid degradation had effects on its tactile response, reproduction rate, and developmental speed. Additional experiments with a deletion mutant as well as transcriptomic analyses revealed that these effects might be conveyed by the putative testosterone receptor NHR-69. Soil microcosms showed that the natural microflora of agricultural soil is readily induced for bile acid degradation accompanied by the transient release of steroid intermediates. Establishment of a model system with a Pseudomonas strain and C. elegans in sand microcosms indicated transient release of ADDs during the course of bile acid degradation and negative effects on the reproduction rate of the nematode. This proof-of-principle study points at bacterial degradation of manure-derived bile acids as a potential and so-far overlooked risk for invertebrates in agricultural soils.
2019-02-08 | GSE126214 | GEO
Project description:Bacteria from manure of free-range chickens
| PRJEB89434 | ENA
Project description:Meta-proteomics analysis approach in the application of biogas production from anaerobic digestion has many advantages that has not been fully uncovered yet. This study aims to investigate biogas production from a stable 2-stage chicken manure fermentation system in chemical and biological perspective. The diversity and functional protein changes from the 1st stage to 2nd stage is a good indication to expose the differential metabolic processes in anaerobic digestion. The highlight of identified functional proteins explain the causation of accumulated ammonia and carbon sources for methane production. Due to the ammonia stress and nutrient limitation, the hydrogenotrophic methanogenic pathway is adopted as indicative of meta-proteomics data involving the key methanogenic substrates (formate and acetate). Unlike traditional meta-genomic analysis, this study could provide both species names of microorganism and enzymes to directly point the generation pathway of methane and carbon dioxide in investigating biogas production of chicken manure.
2021-02-08 | PXD022498 | Pride
Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design factorial design; 2 potato cultivars (Sante, Lady Balfour); 2 fertilizers (dairy manure compost, chicken manure pellets); 3 plant protection treatments (copper oxychloride, comcat, water), 3 biological replicates, 48 samples
2009-02-01 | E-GEOD-11875 | biostudies-arrayexpress
Project description:Metaproteomics analysis of the evolution of protein expression profile during cattle manure composting
2025-01-07 | PXD059527 |