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Ximing Guo - One of the best experts on this subject based on the ideXlab platform.

  • development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea Virginica gmelin by mining ests and resequencing
    Aquaculture, 2010
    Co-Authors: Liusuo Zhang, Ximing Guo
    Abstract:

    Single nucleotide polymorphisms (SNPs) are useful markers for genetic and genomic studies. They are needed in the eastern oyster (Crassostrea Virginica), a major aquaculture species, for the mapping of genes affecting economically important quantitative traits such as disease resistance. Here we report the discovery and characterization of 46 SNPs in the eastern oyster by mining expressed sequence tags (ESTs) and resequencing. Sixty-three putative SNPs were identified from existing ESTs, of which 27 were validated. Three hundred and thirty-six putative SNPs were discovered by resequencing 6.8 Kb from 19 genes, corresponding to a remarkably high density of one SNP per 20 bp. Twenty-one of the candidate SNPs identified by resequencing were tested, and 19 were validated. Thirty-three of the 46 validated SNPs segregated in two mapping families, with 28 (85%) in accordance to expected Mendelian ratios. These markers are derived from expressed genes and should be useful for genetic analyses including the mapping and characterization of the genes that they represent.

  • a 16 microsatellite multiplex assay for parentage assignment in the eastern oyster Crassostrea Virginica gmelin
    Aquaculture, 2010
    Co-Authors: Xiaoxue Wang, Yan Wang, Aimin Wang, Ximing Guo
    Abstract:

    We tested a high level multiplex PCR for efficient microsatellite genotyping in the eastern oyster (Crassostrea Virginica). Sixteen microsatellites were selected based on polymorphism, allele size range, and reliability. They were divided into four groups according to their allele sizes and labeled with four different fluorescence dyes, so that loci in the same color did not overlap in size. A multiplex PCR protocol with eight levels of primer concentrations and four phases of touchdown reactions was developed for simultaneous amplification of all 16 loci and subsequent genotyping on a genetic analyzer. One hundred sixty progeny from a putative pool of 81 full-sib families were successfully genotyped at all 16 loci after one PCR, and all were unambiguously assigned to their perspective families. Our results show that high level multiplexing of 16 microsatellites is possible and can be used for rapid and highly efficient parentage assignment in the eastern oyster.

  • identification and characterization of 66 est ssr markers in the eastern oyster Crassostrea Virginica gmelin
    Journal of Shellfish Research, 2009
    Co-Authors: Yongping Wang, Yaohua Shi, Ximing Guo
    Abstract:

    Large numbers of genetic markers are needed for genomic analyses in the eastern oyster (Crassostrea Virginica). We previously identified 53 simple sequence repeat (SSR) markers from an expressed sequence tag (EST) database using a high selection standard. We mined the same EST database again using a lower threshold (>5 di-nucleotide and 4 other repeats) and identified 330 new SSR-containing ESTs. Primers were designed for 201 suitable sequences, and PCR was successful for 137. The screening of 113 primer pairs that produced fragments shorter than 800 bp produced 66 polymorphic SSR markers, which were characterized in 30 oysters from three populations and a full-sib family. The SSRs had an average of 5.4 alleles per locus, ranging from 2-12. Thirty- four loci segregated in the family, with seven showing significant deviation from Mendelian ratios after Bonferroni correction. Null- alleles were observed at 17 loci. The EST-derived SSRs are part of expressed genes, and most of them should be useful for gene and genome mapping. This study shows that more SSR markers can be developed from ESTs using lower selection standards.

  • generation and analysis of ests from the eastern oyster Crassostrea Virginica gmelin and identification of microsatellite and snp markers
    BMC Genomics, 2007
    Co-Authors: Yongping Wang, Shaolin Wang, Eric Peatman, Jonas P Quilang, Richard K Wallace, Jason Abernathy, Lingling Wang, Yaohua Shi, Ximing Guo
    Abstract:

    Background The eastern oyster, Crassostrea Virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. Virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST) resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs).

  • identification and mapping of disease resistance qtls in the eastern oyster Crassostrea Virginica gmelin
    Aquaculture, 2006
    Co-Authors: Ximing Guo
    Abstract:

    Identification and mapping of disease-resistance QTLs (quantitative trait loci) is important for our understanding of genetic mechanisms of disease-resistance and for our ability to genetically improve cultured stocks. Disease-resistance is the most important trait for farmers of the eastern oyster (Crassostrea Virginica Gmelin), which is affected by two major diseases: MSX and Dermo. In this study, the genome of the eastern oyster was scanned with a large number of amplified fragment length polymorphism (AFLP) markers before and after Dermo-inflicted mortalities (53% and 67%) in two reference families. Significant post-mortality shifts in genotype frequency were detected at a large number of loci. Linkage analysis revealed that most markers showing frequency shifts are closely linked to each other on the genetic map, and all markers within a cluster had frequency shifts in the same direction according to their linkage phase. This finding suggests that post-mortality shifts in genotype frequency were not random, but linked to Dermo/summer mortality-resistance QTLs. Twelve putative Dermo/summer mortality-resistance QTLs were identified on female and male maps from two families, providing candidate genome regions for further analysis. © 2005 Elsevier B.V. All rights reserved.

Isabel Malheiro - One of the best experts on this subject based on the ideXlab platform.

  • A 'G' chromosome banding study of three cupped oyster species: Crassostrea gigas, Crassostrea angulata and Crassostrea Virginica (Mollusca: Bivalvia)
    Genetics Selection Evolution, 1999
    Co-Authors: Alexandra Leitão, Catherine Thiriot-quiévreux, Isabel Malheiro
    Abstract:

    The G-banding technique was performed on chromosomes from gill tissue of three cupped oyster species: Orassostrea gigas, Cmssostrea angulata and Cmssostrea virginiea. Identification of the ten individual chromosome pairs was obtained. Comparative analysis of G-banded karyotypes of the three species showed that their banding patterns generally resembled each other, with chromosome pair 3 being similar in ail three species. However, differences from one species to another were also observed. The G-banding pattern highlighted greater similarities between C. gigas and C. ang'l!lata than between these two species and C. virginiea, thus providing an additional argument for genetic divergence between these two evolutionary lineages. C. gigas and C. angulata showed a different G-banding patterns on the two arms of chromosome pair 7, which agrees with their taxonomic separation. The application of this banding technique offers a new approach to specifie problems in oyster taxonorny and genetics. © Inra/Elsevier, Paris chI'omosome / G-banding / Crassostrea gigas / Crassostrea angulata / Crassostrea Virginica

Inna M Sokolova - One of the best experts on this subject based on the ideXlab platform.

  • the transcriptomic responses of the eastern oyster Crassostrea Virginica to environmental conditions
    Molecular Ecology, 2011
    Co-Authors: Robert W Chapman, Annalaura Mancia, Marion Beal, Artur Veloso, Charles Rathburn, Anne Blair, A F Holland, G W Warr, Guy Didinato, Inna M Sokolova
    Abstract:

    Understanding the mechanisms by which organisms adapt to environmental conditions is a fundamental question for ecology and evolution. In this study, we evaluate changes in gene expression of a marine mollusc, the eastern oyster Crassostrea Virginica, associated with the physico-chemical conditions and the levels of metals and other contaminants in their environment. The results indicate that transcript signatures can effectively disentangle the complex interactive gene expression responses to the environment and are also capable of disentangling the complex dynamic effects of environmental factors on gene expression. In this context, the mapping of environment to gene and gene to environment is reciprocal and mutually reinforcing. In general, the response of transcripts to the environment is driven by major factors known to affect oyster physiology such as temperature, pH, salinity, and dissolved oxygen, with pollutant levels playing a relatively small role, at least within the range of concentrations found in the studied oyster habitats. Further, the two environmental factors that dominate these effects (temperature and pH) interact in a dynamic and nonlinear fashion to impact gene expression. Transcriptomic data obtained in our study provide insights into the mechanisms of physiological responses to temperature and pH in oysters that are consistent with the known effects of these factors on physiological functions of ectotherms and indicate important linkages between transcriptomics and physiological outcomes. Should these linkages hold in further studies and in other organisms, they may provide a novel integrated approach for assessing the impacts of climate change, ocean acidification and anthropogenic contaminants on aquatic organisms via relatively inexpensive microarray platforms.

  • temperature dependent stress response in oysters Crassostrea Virginica pollution reduces temperature tolerance in oysters
    Aquatic Toxicology, 2006
    Co-Authors: Gisela Lannig, Jason F Flores, Inna M Sokolova
    Abstract:

    Abstract Combined effects of temperature and a toxic metal, cadmium (Cd), on energy metabolism were studied in a model marine bivalve, the eastern oyster Crassostrea Virginica , acclimated at 20, 24 and 28 °C and exposed to 50 μg l −1 of Cd. Both increasing temperature and Cd exposure led to a rise in standard metabolic rates, and combined stressors appeared to override the capability for aerobic energy production resulting in impaired stress tolerance. Oysters exposed to elevated temperature but not Cd showed no significant change in condition, survival rate and lipid peroxidation, whereas those exposed to both Cd and temperature stress suffered high mortality accompanied by low condition index and elevated lipid peroxidation. Furthermore, RNA/DNA ratios indicative of protein synthesis rate, and levels of glutathione, which is involved in metal detoxification, increased in Cd-exposed oysters at 20 °C but not at 28 °C. Implications of the synergism between elevated temperatures and cadmium stress on energy metabolism of oysters are discussed in the light of the potential effects of climate change on oyster populations in polluted areas.

  • temperature dependent stress response in oysters Crassostrea Virginica pollution reduces temperature tolerance in oysters
    Aquatic Toxicology, 2006
    Co-Authors: Gisela Lannig, Jason F Flores, Inna M Sokolova
    Abstract:

    Combined effects of temperature and a toxic metal, cadmium (Cd), on energy metabolism were studied in a model marine bivalve, the eastern oyster Crassostrea Virginica, acclimated at 20, 24 and 28 degrees C and exposed to 50microgl(-1) of Cd. Both increasing temperature and Cd exposure led to a rise in standard metabolic rates, and combined stressors appeared to override the capability for aerobic energy production resulting in impaired stress tolerance. Oysters exposed to elevated temperature but not Cd showed no significant change in condition, survival rate and lipid peroxidation, whereas those exposed to both Cd and temperature stress suffered high mortality accompanied by low condition index and elevated lipid peroxidation. Furthermore, RNA/DNA ratios indicative of protein synthesis rate, and levels of glutathione, which is involved in metal detoxification, increased in Cd-exposed oysters at 20 degrees C but not at 28 degrees C. Implications of the synergism between elevated temperatures and cadmium stress on energy metabolism of oysters are discussed in the light of the potential effects of climate change on oyster populations in polluted areas.

Alexandra Leitão - One of the best experts on this subject based on the ideXlab platform.

  • A 'G' chromosome banding study of three cupped oyster species: Crassostrea gigas, Crassostrea angulata and Crassostrea Virginica (Mollusca: Bivalvia)
    Genetics Selection Evolution, 1999
    Co-Authors: Alexandra Leitão, Catherine Thiriot-quiévreux, Isabel Malheiro
    Abstract:

    The G-banding technique was performed on chromosomes from gill tissue of three cupped oyster species: Orassostrea gigas, Cmssostrea angulata and Cmssostrea virginiea. Identification of the ten individual chromosome pairs was obtained. Comparative analysis of G-banded karyotypes of the three species showed that their banding patterns generally resembled each other, with chromosome pair 3 being similar in ail three species. However, differences from one species to another were also observed. The G-banding pattern highlighted greater similarities between C. gigas and C. ang'l!lata than between these two species and C. virginiea, thus providing an additional argument for genetic divergence between these two evolutionary lineages. C. gigas and C. angulata showed a different G-banding patterns on the two arms of chromosome pair 7, which agrees with their taxonomic separation. The application of this banding technique offers a new approach to specifie problems in oyster taxonorny and genetics. © Inra/Elsevier, Paris chI'omosome / G-banding / Crassostrea gigas / Crassostrea angulata / Crassostrea Virginica

Catherine Thiriot-quiévreux - One of the best experts on this subject based on the ideXlab platform.

  • A 'G' chromosome banding study of three cupped oyster species: Crassostrea gigas, Crassostrea angulata and Crassostrea Virginica (Mollusca: Bivalvia)
    Genetics Selection Evolution, 1999
    Co-Authors: Alexandra Leitão, Catherine Thiriot-quiévreux, Isabel Malheiro
    Abstract:

    The G-banding technique was performed on chromosomes from gill tissue of three cupped oyster species: Orassostrea gigas, Cmssostrea angulata and Cmssostrea virginiea. Identification of the ten individual chromosome pairs was obtained. Comparative analysis of G-banded karyotypes of the three species showed that their banding patterns generally resembled each other, with chromosome pair 3 being similar in ail three species. However, differences from one species to another were also observed. The G-banding pattern highlighted greater similarities between C. gigas and C. ang'l!lata than between these two species and C. virginiea, thus providing an additional argument for genetic divergence between these two evolutionary lineages. C. gigas and C. angulata showed a different G-banding patterns on the two arms of chromosome pair 7, which agrees with their taxonomic separation. The application of this banding technique offers a new approach to specifie problems in oyster taxonorny and genetics. © Inra/Elsevier, Paris chI'omosome / G-banding / Crassostrea gigas / Crassostrea angulata / Crassostrea Virginica

  • A 'G' chromosome banding study of three cupped oyster species: Crassostrea gigas, Crassostrea angulata and Crassostrea Virginica
    1999
    Co-Authors: Catherine Thiriot-quiévreux, M. Curie, Abel Salazar
    Abstract:

    The G-banding technique was performed on chromosomes from gill tissue of three cupped oyster species: Crassostrea gigas, Crassostrea angulata and Crassostrea Virginica. Identification of the ten individual chromosome pairs was obtained. Comparative analysis of G-banded karyotypes of the three species showed that their banding patterns generally resembled each other, with chromosome pair 3 being similar in all three species. However, differences from one species to another were also observed. The G-banding pattern highlighted greater similarities between C. gigas and C. angulata than between these two species and C. Virginica, thus providing an additional argument for genetic divergence between these two evolutionary lineages. C. gigas and C. angulata showed a different G-banding patterns on the two arms of chromosome pair 7, which agrees with their taxonomic separation. The application of this banding technique offers a new approach to specific problems in oyster taxonomy and genetics. © Inra/Elsevier, Paris