Affymetrix SNP array data for the Pacific oyster
Ontology highlight
ABSTRACT:
ORGANISM(S): Magallana gigas
PROVIDER: GSE94633 | GEO | 2017/03/22
SECONDARY ACCESSION(S): PRJNA371639
REPOSITORIES: GEO
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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:For developing the more SNPs and new high-density genetic linkage map of tea plant, two parents and their 326 progenies and 147 registered tea cultivars was sequencing by newly developed Affymetrix Axiom genotyping technology
2022-03-09 | GSE182082 | GEO
Project description:Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas.
2010-09-01 | GSE23883 | GEO
Project description:The shellfish aquaculture industry provides a sustainable food source and jobs for a growing population. Oysters are the primary aquaculture species produced in the United States and account for a significant portion of seafood exports. Shellfish hatcheries have been experiencing frequent mass mortality events over the last couple of decades that occur approximately 10-14 days after oyster settlement. Settlement is a process that shellfish such as oysters undergo in which they transform from a free-swimming pelagic larvae to a sessile juvenile oyster. In order for this energy-intensive process to be successful, the oyster has to undergo behavioral and morphological changes. This is a vulnerable period in the oyster life cycle and conditions need to be such that they aren’t creating added stress. However, due to the oysters’ vulnerability, this is often a time when bacterial infections can occur, which when occurring with environmental conditions that are unfavorable, can prove to be fatal. In order to help oysters survive this process, scientists at the Taylor Shellfish Hatchery in Quilcene, WA has experimented with altering abiotic and biotic factors such as algal diet densities, pH, water flow rate, among others. At this hatchery, Pacific oysters are typically reared at 23˚C, however preliminary research results have suggested that oysters may have a higher survival rate when held at 29˚C during the settlement period. This pilot experiment attempts to identify differences in protein expression between oyster seed held at 23˚C and 29˚C during the settlement period using novel proteomic technology. Our proteomic results, paired with survival data, suggest that holding oyster seed at 29˚C during the settlement period results in higher survival rates.
2022-03-03 | PXD015434 | Pride
Project description:Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event using a 9K cDNA microarray that we designed. This transcriptional analysis provides new indications to define markers for Quantitative Trait Loci searches and functional studies, and evaluates the potential role of each gene in the resistance to summer mortality
2009-08-15 | GSE16448 | GEO
Project description:Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas. For the microarray analysis oysters were sampled at days 0, 2, 10, and 20 after the beginning of hypoxia. On each date, the digestive gland from 6 oysters was dissected, pooled, and stored at -80°C in Extract-All Reagent (Eurobio) at a concentration of 1 mL/50 mg tissue until total RNA was extracted. For each condition (hypoxia and normoxia) and oyster line (R and S), 4 pools were sampled (biological replicates) for a total of 56 pools during the 4 days of sampling. Furthermore, the entire tissue from 10 wild oysters was collected, pooled, and homogenized in Extract-all Reagent (Eurobio) to constitute a single total RNA sample to use as a reference in all slide hybridizations and Real-Time PCR analyses. Five ?g of total RNA were directly labeled by reverse transcription using the Direct ChipShot Direct Labeling and Clean-Up Kit (Promega). The samples were labeled with Cyanine-5 (Cy5). The reference samples were labeled with Cyanine-3 (Cy3) in separate tubes following the same protocol. The Cy3-labeled cDNAs were pooled and re-divided to obtain a homogeneous reference sample. cDNA samples and references were evaporated in a SpeedVac and mixed into a single pool in equimolar amounts with the Chip Hybe hybridization buffer (Ventana Discovery). Hybridization was performed using a Ventana automatic hybridization station (Ventana Discovery).
2010-09-01 | E-GEOD-23883 | biostudies-arrayexpress
Project description:Plastics are persistent synthetic polymers that accumulate in the marine environment as waste. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Filter-feeder organisms ingest MP while feeding and are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 32 µg L-1) for two months during a reproductive cycle. Effects were investigated on transcriptomic responses, in digestive gland gonads and oocytes of exposed oysters. Transcriptomic profiles in the tissues of the exposed oyster showed endocrine disrupting signals, notably highlighting alteration in glucocorticoid response, insulin pathway and fatty-acid metabolism in response to micro-PS exposition. In oocytes from exposed females, several transcripts coding for proteins involved in Ca2+ binding were differentially expressed suggesting a disruption of the Ca2+ signaling pathway with crucial consequences on oocyte maturation.
2016-01-15 | GSE71845 | GEO
Project description:Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes Background DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. We have previously reported a comprehensive view of CNVs in the HapMap DNA collection using high density 500K EA (Early Access) SNP genotyping arrays which revealed greater than 1,000 CNVs ranging in size from 1kb to over 3Mb. Although the arrays used most commonly for GWAS predominantly interrogate SNPs, CNV identification and detection does not necessarily require the use of DNA probes centered on polymorphic nucleotides and may even be hindered by the dependence on a successful SNP genotyping assay. Results In this study, we have designed and evaluated a high density array predicated on the use of non-polymorphic oligonucleotide probes for CNV detection. This approach effectively uncouples copy number detection from SNP genotyping and thus has the potential to significantly improve probe coverage for genome-wide CNV identification. This array, in conjunction with PCR-based, complexity-reduced DNA target, queries over 1.3M independent NspI restriction enzyme fragments in the 200bp to 1100bp size range, which is a several fold increase in marker density as compared to the 500K EA array. In addition, a novel algorithm was developed and validated to extract CNV regions and boundaries. Conclusions Using a well-characterized pair of DNA samples, close to 200 CNVs were identified, of which nearly 50% appear novel yet were independently validated using quantitative PCR. The results indicate that non-polymorphic probes provide a robust approach for CNV identification, and the increasing precision of CNV boundary delineation should allow a more complete analysis of their genomic organization. Keywords: Copy number variation (CNV) detection
2008-04-24 | GSE9053 | GEO
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates. Twelve Pacific oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater, respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000.
2012-12-15 | E-GEOD-38022 | biostudies-arrayexpress
Project description:Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes Background DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. We have previously reported a comprehensive view of CNVs in the HapMap DNA collection using high density 500K EA (Early Access) SNP genotyping arrays which revealed greater than 1,000 CNVs ranging in size from 1kb to over 3Mb. Although the arrays used most commonly for GWAS predominantly interrogate SNPs, CNV identification and detection does not necessarily require the use of DNA probes centered on polymorphic nucleotides and may even be hindered by the dependence on a successful SNP genotyping assay. Results In this study, we have designed and evaluated a high density array predicated on the use of non-polymorphic oligonucleotide probes for CNV detection. This approach effectively uncouples copy number detection from SNP genotyping and thus has the potential to significantly improve probe coverage for genome-wide CNV identification. This array, in conjunction with PCR-based, complexity-reduced DNA target, queries over 1.3M independent NspI restriction enzyme fragments in the 200bp to 1100bp size range, which is a several fold increase in marker density as compared to the 500K EA array. In addition, a novel algorithm was developed and validated to extract CNV regions and boundaries. Conclusions Using a well-characterized pair of DNA samples, close to 200 CNVs were identified, of which nearly 50% appear novel yet were independently validated using quantitative PCR. The results indicate that non-polymorphic probes provide a robust approach for CNV identification, and the increasing precision of CNV boundary delineation should allow a more complete analysis of their genomic organization. A set of five genomic DNA samples containing different numbers of X chromosomes (1X to 5X sample set, including NA15510 and NA10851) were hybridized to Nsp copy number (CN) arrays in triplicate to evaluate detection of copy number variation using high density, non-polymorphic oligonucleotide probes. 6 Hapmap samples were hybridized to Nsp CN arrays to evaluate Mendelian inheritance of CNVs.
2008-04-24 | E-GEOD-9053 | biostudies-arrayexpress