Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bringing next-generation breeding into aquaculture

ABSTRACT: Low-coverage whole-genome sequencing with genotype imputation identifies noncoding genetic variants associated with cold stress adaptation in Nile tilapia, highlighting candidate lncRNA and miRNA interactions for selective breeding applications.

INSTRUMENT(S): -

ORGANISM(S): Oreochromis Niloticus

SUBMITTER: EBI

PROVIDER: PRJEB102261 | EVA | 2025-11-07

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	G0723-06-UMD_73-samples.accessioned.vcf.contigs	Other
	G0723-06-UMD_73-samples.accessioned.vcf.variants	Other
	G0723-06-UMD_73-samples.vcf.csi	Other
	G0723-06-UMD_73-samples.vcf.gz	Vcf

Items per page:

1 - 4 of 4

Similar Datasets

Neuronal ire-1 coordinates an organism-wide cold stress response by regulating fat metabolism - Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ire-1(ok799) Transcriptomes During Cold Stress.

Project description:Cold affects many aspects of biology, medicine, agriculture and industry. Here, we identify a conserved endoplasmic reticulum (ER) stress response, distinct from the canonical unfolded protein response, which maintains lipid homeostasis during extreme cold stress. We establish that the ER stress sensor IRE-1 is critical for resistance to extreme cold and is activated by cold temperature. Specifically, neuronal IRE-1 signals via JNK-1 and neuropeptide-mediated signalling to regulate lipid composition throughout the animal. The requirement of this cold-response pathway can be bypassed by supplementation with unsaturated fatty acids or by altering the diet . Altogether, our findings define an ER-centric conserved organism-wide cold stress response pathway, consisting of sensors, effectors and signalling moieties, which control adaptation to cold throughout the organism. Better understanding of the molecular basis of cold adaptation is crucial for the design of safe and optimal use of cold conditions on live organisms and samples, and for the development of better treatments for hypothermia. Conclusions: Our study represents a detailed analysis of C.elegans transcriptomes during cold stress, with biological replicates, generated by RNA-seq technology.

2022-11-15 | GSE193923 | GEO

Next generation sequencing technologies for next generation plant breeding.

Project description: Not available

| S-EPMC4115663 | biostudies-literature

Protein expression profiles of cold stress in red tilapia

Project description:The cold stress is considered the bottleneck problem limiting the development of red tilapia industry. Fish (initial weight: 72.71±1.32 g) was divided into the cold stressed group (C) and the control normal water temperature group (N). The water temperature was reduced by 2℃ per day from 20℃ to 8℃ in cold group, and the control group kept the water temperature at 20℃ during the experiment. At the end of the experiment, the gill(G)、liver(L) and skin(S) tissues from the fish of cold(C) group and control normal water temperature (N) group were taken. The DIA proteome analysis of 18 samples was completed, and 6341 trusted proteins containing quantitative information were obtained. Our aim is to understand the protein expression profiles of cold stress in red tilapia.

2024-08-15 | PXD052625 | Pride

Space Breeding: The Next-Generation Crops.

Project description: Not available

| S-EPMC8579881 | biostudies-literature

Harnessing Crop Biodiversity and Genomics Assisted Pre-Breeding Approaches for Next Generation Climate-Smart Varieties

Project description:Integration of genome wide association studies (GWAS), metabolomics and transcriptomics reveals phenolic acids and flavonoids associated genes and their regulatory elements under drought stress in rapeseed flowers

2024-01-31 | GSE250611 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Streptococcus agalactiae and Nitrite Exposure Leukocyte Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived head kidney leukocytes transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: The leukocytes of tilapia were treated with PBS(A), heat-killed S.agalactiae(B), sodium nitrite(C) or heat-killed S.agalactiae and sodium nitrite co-treatment(D),respectively. Then the mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the tilapia genome in the head kidney leukocytes of tilapia.10 candidate genes were randomly selected to quantify their mRNA expression levels of treatment and control groups by q-PCR. Results showed that the Pearson’s correlation coefficient between q-PCR and RNA-seq was 0.939. Total of 6173 transcripts were differently expressed, with a fold change ≥2 and p value <0.05. Conclusions: Our study represents the first detailed analysis of tilapia head kidney leukocytes transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a fish cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2019-07-27 | GSE134931 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ern1f/f and Ern1f/f AKO iWAT transcriptomes

Project description:Bulk RNA-seq has uncovered the the function of adipocyte IRE1α in cold-induced thermogenic program in inguinal white adipose tissue. The GO analysis shows that adipocyte IRE1α supressed inflammatory responds when the mice were maintained at 30oC and adipocyte IRE1α abrogation facilated cold-induced thermogenic program after challenged with cold stress. In addition, the transcription factor (TF) analysis indicates that adipocyte IRE1α repressed lots of temperature-dependent TFs, including PGC1α.

2022-07-21 | GSE180524 | GEO

Transcriptomic stress responses in Vaccinium spp. F1 hybrids: Implications for temperature-resilient cranberry breeding using a crop wild relative

Project description:Cranberry (Vaccinium macrocarpon) is an important North American fruit crop with vulnerability to temperature extremes and a relatively recent domestication history. Hybridization with a cold-adapted crop wild relative (CWR), V. oxycoccos, offers a strategy for improving temperature stress tolerance. We conducted RNA sequencing (RNA-seq) on V. macrocarpon and F1 hybrids between V. macrocarpon and V. oxycoccos subjected to acute heat and cold stress, capturing early transcriptional responses up to 30 minutes (heat) and 95 minutes (cold) after treatment onset. We then evaluated differences in responses across genotypes and stress conditions. Differential expression analysis and functional profiling revealed cold-induced differences in pathways related to photosynthesis, ribosomes, defense, and hormone signaling. No subgenome-specific functional specialization was observed. Two F1 hybrids exhibited suggestive cold resilience, with expression changes elevated at 60 minutes but declining by 95 minutes. Hybrids also displayed substantial regulatory variation under stress and transgressive downregulation of photosynthesis genes under ambient conditions. These findings suggest that V. oxycoccos introgression could be utilized in breeding cold-tolerant cranberry cultivars. Variation observed between F1 hybrids reflects the diversity introduced through CWR germplasm and provides opportunities for selection. Conservation of V. oxycoccos and other CWRs remains critical for future crop improvement.

2025-07-07 | GSE301608 | GEO

Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish

Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28Â°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8Â°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8Â°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.Â Examination of gene expressional divergence in gill between zebrafish and tilapia

2016-07-03 | E-GEOD-69965 | biostudies-arrayexpress

Solanum tuberosum

Project description:Heat, Cold and Stress adaptation in Potato

| PRJNA91633 | ENA