Ontology highlight
ABSTRACT:
PROVIDER: PRJNA542754 | ENA |
REPOSITORIES: ENA
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Project description:Thraustochytrids of the genera Schizochytrium and Aurantiochytrium accumulate oils rich in the essential, marine n3 fatty acid docosahexaenoic acid (DHA). DHA production in Aurantiochytrium sp T66 was studied with the aim to provide more knowledge about factors that affect the DHA-productivities and the contributions of the two enzyme systems used for fatty acid synthesis in thraustochytrids, fatty acid synthetase (FAS) and PUFA-synthase. Fermentations with nitrogen starvation, which is well-known to initiate lipid accumulation in oleaginous organisms, were compared to fermentations with nitrogen in excess where lipid accumulation was obtained by oxygen limitation. The specific productivities of fatty acids originating from FAS were considerably higher under nitrogen starvation than with nitrogen in excess, while the specific productivities of DHA were the same at both conditions. Global transcriptome analysis showed significant up-regulation of FAS under N-deficient conditions, while the PUFA-synthase genes were only marginally upregulated. Neither of them was upregulated under O2-limitation where nitrogen was in excess, suggesting that N-starvation mainly affects the FAS and may be less important for the PUFA-synthase. The transcriptome analysis also revealed responses likely to be related to the generation of reducing power (NADPH) for fatty acid synthesis.
2019-12-19 | GSE134374 | GEO
Project description:Here, we investigated marine thraustochytrid Schizochytrium limacinum SR21 for its ability to convert waste oil, mixture of commercial oils (mCOs) and volatile fatty acids i.e., acetic acid and butyric acid into ω-3 fatty acid; docosahexaenoic acid (DHA). Metabolic insights through whole cell transcriptomic aid in tracing the route of substrate assimilation.
2024-04-10 | GSE252403 | GEO
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:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding. To investigate the epigenetic effect on histone mark distribution of the EUE/PEG selection we performed ChIP-seq analyses. Native ChIP using an anti-H3K4me3 and no antibody (background control) was done on PEG1 and control plants.
2015-06-28 | E-GEOD-65571 | biostudies-arrayexpress
Project description:Crop breeding aims to balance disease resistance with yield; however, single resistance (R) genes can lead to resistance breakdown, and R gene pyramiding may affect growth fitness. Here we report that the rice Pigm locus contains a cluster of genes encoding nucleotide-binding leucine-rich repeat (NLR) receptors that confer durable resistance to the fungus Magnaporthe oryzae without yield penalty. Among these NLR receptors, PigmR confers broad-spectrum resistance, whereas PigmS competitively attenuates PigmR homodimerization to suppress resistance. PigmS expression, and thus PigmR-mediated resistance, are subjected to tight epigenetic regulation. PigmS increases seed production to counteract the yield cost induced by PigmR Therefore, our study reveals a mechanism balancing high disease resistance and yield through epigenetic regulation of paired antagonistic NLR receptors, providing a tool to develop elite crop varieties.
2017-06-15 | GSE83522 | GEO
Project description:Hybrid sturgeon, an ancient fish, has great economic and nutritional value as a source of caviar. Although significant differences exist in the female reproductive capacity under artificial breeding conditions, differential gene expression associated to domesticated female reproductive capacity have never been investigated. In this study, we conducted reference genome-based transcriptome sequencing of 16 individuals from high-yield (H) and low-yield (L) populations, respectively.
2024-03-19 | GSE261910 | GEO
Project description:The environment plays important role in the interaction between plant hosts and pathogens. The application of chemical fertilizer is a crucial breeding technology to enhance crop yield since last century. As the most abundant fertilizer, nitrogen often increases disease susceptibility for crop plants. The underlying mechanism for nitrogen induced disease susceptibility is elusive. Here we found that nitrogen application activate gibberellin signaling by degradation of SLR1, the repressor protein in gibberellin signaling, which result in simultaneously promoting plant growth and disease susceptibility. SLR1, physically interacts with OsNPR1 and consequently facilitate OsNPR1 mediated defense responses. Transcriptome analysis showed that OsNPR1-SLR1 module plays a vital role in transcriptional reprogramming for both disease resistance and plant growth. Increase of SLR1 protein level in gibberellin deficient rice plants neutralizes disease susceptibility but sacrifice yield enhancement under high nitrogen supply. Mutation in SD1, encoding OsGA2ox2, produced more grains than WT，and maintains disease resistance under high nitrogen supply. Taken together, our work reveals the molecular mechanism underlying nitrogen-induced disease susceptibility, and demonstrates that the application of sd1 rice varieties prevent the tradeoff between disease susceptibility and yield increase under high nitrogen supply.
2024-08-01 | GSE171646 | GEO
Project description:Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.
2021-01-09 | GSE164470 | GEO
Project description:Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence.
2016-12-05 | GSE83152 | GEO