Source: RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY submitted to NRP
NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0202842
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
NRSP-_OLD8
Project Start Date
Oct 1, 2008
Project End Date
Sep 30, 2013
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY
3 RUTGERS PLZA
NEW BRUNSWICK,NJ 08901-8559
Performing Department
Inst of Marine & Coastal Sci - DO NOT USE
Non Technical Summary
The eastern oyster is a major aquaculture species in the United States. It has been seriously affected by three major diseases: MSX caused by Haplosporidium nelsoni, Dermo caused by Perkinsus marinus and JOD caused by Roseovarius crassostreae. Each of these three diseases can cause up to 90% mortality of cultured oysters. The development of disease-resistant stocks is a major priority for the oyster research and culture community. The identification and mapping of disease-resistance genes may greatly contribute to our understanding of disease-resistance and lead to significant advances in oyster breeding.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30437231080100%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3723 - Oysters;

Field Of Science
1080 - Genetics;
Goals / Objectives
Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.
Project Methods
We will focus on the disease-resistance genes in the eastern oyster. We will develop mapping families targeting resistance to specific pathogens. We will develop microsatellite and single nucleotide polymorphism (SNP) markers. Genetic linkage maps will be constructed and used to map disease-resistance QTLs and genes. The identified disease-resistance genes or markers will be tested and used for marker-assisted selection.

Progress 10/01/08 to 09/30/13

Outputs
Target Audience: Geneticists, biologists, shellfish researchers and breeders Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Provided training to five graduate students and three postdoctoral researchers. How have the results been disseminated to communities of interest? Results have been published and presented at conferences. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We conducted the following research that are related to the goals of NRSP-8: 1) we developed genetic markers, ESTs and improved genetic maps for the eastern oyster; 2) we identified, mapped and characterized disease-resistance markers and genes in the eastern oyster; 3) we developed genetic marker, ESTs and genetic maps for other shellfish species including the pearl oyster, hard clam, surfclam and scallops; 4) we sequenced and characterized the mitochondrial genome of several oyster species; 5) we participated in the sequencing, assembly and annotation of the Pacific oyster genome; 6) we sequenced and characterized the transcriptome of the eastern oyster and identified 657 genes related to innate immunity; 7) we attended meetings of NRSP-8 and aquaculture genomics workshops.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Zhang, L., L. Li, Y. Zhu, G. Zhang and X. Guo. 2013. Transcriptome analysis reveals a rich gene set related to innate immunity in the eastern oyster (Crassostrea virginica). Marine Biotechnology, 10.1007/s10126-013-9526-z.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Guevelou, E., A. Huvet, R. Sussarellu, M. Milan, X. Guo, L. Li, G. Zhang, V. Quillien, J.-Y. Daniel, C. Quere, P. Boudry, and C. Corporeau. 2013. Regulation of a truncated isoform of AMP-activated protein kinase alpha (AMPK alpha) in response to hypoxia in the muscle of Pacific oyster Crassostrea gigas. Journal of Comparative Physiology B-Biochemical Systemic and Environmental Physiology 183:597-611.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Zhang, G., X. Fang, X. Guo, L. Li, R. Luo, F. Xu, P. Yang, L. Zhang, X. Wang, H. Qi, Z. Xiong, H. Que, Y. Xie, P. W. H. Holland, J. Paps, Y. Zhu, F. Wu, Y. Chen, J. Wang, C. Peng, J. Meng, L. Yang, J. Liu, B. Wen, N. Zhang, Z. Huang, Q. Zhu, Y. Feng, A. Mount, D. Hedgecock, Z. Xu, Y. Liu, T. Domazet-Loso, Y. Du, X. Sun, S. Zhang, B. Liu, P. Cheng, X. Jiang, J. Li, D. Fan, W. Wang, W. Fu, T. Wang, B. Wang, J. Zhang, Z. Peng, Y. Li, N. Li, J. Wang, M. Chen, Y. He, F. Tan, X. Song, Q. Zheng, R. Huang, H. Yang, X. Du, L. Chen, M. Yang, P. M. Gaffney, S. Wang, L. Luo, Z. She, Y. Ming, W. Huang, S. Zhang, B. Huang, Y. Zhang, T. Qu, P. Ni, G. Miao, J. Wang, Q. Wang, C. E. W. Steinberg, H. Wang, N. Li, L. Qian, G. Zhang, Y. Li, H. Yang, X. Liu, J. Wang, Y. Yin & J. Wang. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490:49-54.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: He, Y., H. Yu, Z. Bao, Q. Zhang and X. Guo. 2012. Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica). Fish & Shellfish Immunology 33:411-417.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Yu, H., Y. He, X. Wang, Q. Zhang, Z. Bao and X. Guo. 2011. Polymorphism in a serine protease inhibitor gene and its association with disease resistance in the eastern oyster (Crassostrea virginica Gmelin). Fish and Shellfish Immunology, 30:757-762.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2011 Citation: Zhang, G., X. Guo, L. Li, F. Xu, X. Wang. H. Qi, L. Zhang, H. Que, H. Wu, S. Wang, D. Hedgecock, P.M. Gaffney, R. Luo, X. Fang and J. Wang. 2011. The oyster genome project: an update on assembly and annotation. J. Shellfish Res., 30(2):567-567. (abstract)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2011 Citation: Bao, Y., Z. Lin and X. Guo. 2011. Cloning, characterization of glutamine synthetase gene from bloody clam Tegillarca granosa. J. Shellfish Res., 30(2):485-485. (abstract)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2011 Citation: Hedgecock, D., P.M. Gaffney, X. Guo, G. Shin, A. Gracey, H. Qi, L. Li, G. Zhang, M.P. Samanta. 2011. GIGASNP: integrating genetic, physical and cytogenetic maps of the Pacific oyster Crassostrea gigas. J. Shellfish Res., 30(2):515-151. (abstract)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2011 Citation: Wang, S., P.M. Gaffney, D. Hedgecock, Z. Bao and X. Guo. 2011. Construction of a cytogenetic map for the Pacific oyster (Crassostrea gigas). J. Shellfish Res., 30(2):561-561. (abstract)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2011 Citation: Yu. H., H. Yan, X. Wang, Q. Zhang, Z. Bao and X. Guo. 2011. Association between the serine protease inhibitor gene and disease resistance in the eastern oyster. J. Shellfish Res., 30(2):565-565. (abstract)
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Wang, L, L. Song, J. Zhao, L. Qiu, H. Zhang, W. Xu, H. Li, C. Li, L. Wu, and X. Guo. 2009. Expressed sequence tags from the zhikong scallop (Chlamys farreri): Discovery and annotation of host-defense genes. Fish & Shellfish Immunology 26: 744-750.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Ren, J., X. Liu, F. Jiang, X. Guo and B Liu. 2010. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology, 10:394.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z. 2010. Microarray analysis of gene expression in eastern Oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol., 29: 921-929.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Kucuktas, H., S. Wang, S, P. Li, C. He, P. Xu, Z. Sha, H. Liu, Y. Jiang, P. Baoprasertkul, B. Somridhivej, Y. Wang, J. Abernathy, X. Guo, L. Liu, W. Muir & Z. Liu. 2009. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 181: 1649-1660.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Wang, Y., A. Wang and X. Guo. 2009. Development and characterization of 30 polymorphic microsatellite markers for the Atlantic surfclam, Spisula solidissima (Dillwyn, 1817). Mol. Ecol. Res., 9(4):1264-1267.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Shi, Y., H. Kui, X. Guo, Z. Gu, Y. Wang and A. Wang. 2009. Genetic linkage map of the pearl oyster, Pinctada martensii (Dunker). Aqua. Res. 41:35-44.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Wang, Y., Y. Shi and X. Guo. 2009. Identification and characterization of 66 EST-SSR markers in the eastern oyster Crassostrea virginica (Gmelin). J. Shellfish Res., 28(2):227-234.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Ren, J., X. Liu, G. Zhang, B. Liu and X. Guo. 2009. "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. BMC Genomics, 10:84.
  • Type: Journal Articles Status: Published Year Published: 2009 Citation: Shi, Y., Y. Wang, K. Hong, Z. Hou, A. Wang and X. Guo. 2009. Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker). Mol. Ecol. Res., 9:177-179.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Zhang, L. and X. Guo. 2010. Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture, 302:124-129.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Wang, Y., X. Wang, A. Wang and X. Guo. 2010. A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica). Aquaculture, 308:S28-S33.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Powell1, E.N., J.M. Klinck, X. Guo, E.E. Hofmann, S.E. Ford and David Bushek. 2012. Can oysters Crassostrea virginica develop resistance to dermo disease in the field: The impediment posed by climate cycles. . J. Mar. Res., 70:309355.


Progress 10/01/11 to 09/30/12

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by USDA, NSF and Rutgers University. We conducted the following research in our lab and in collaboration with colleagues in 2012: 1) we identified and mapped disease resistance genes and makers, and used them to model disease resistance in eastern oyster populations; 2) we worked on the development of a cytogenetic map for the Pacific oyster; and 3) we worked on assembly and annotation of the Pacific oyster genome as members of an international team, which was published in Nature in October 2012. The outputs have been disseminated to the research community through meeting presentations and publications. PARTICIPANTS: Guofan Zhang, Chinese Academy of Sciences; Yan He, Ocean University of China TARGET AUDIENCES: Geneticists, shellfish biologists, breeders, shellfish farmers. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We identified loci for Dermo disease resistance, which improved our understanding of genetics of Dermo resistance. A preliminary cytogenetic map has been developed for the Pacific oyster, which is the first for this species. We have published the Pacific oyster genome, which provides a valuable resource for the scientific community.

Publications

  • Zhang, G., X. Fang, X. Guo, L. Li, R. Luo, F. Xu, P. Yang, L. Zhang, X. Wang, H. Qi, Z. Xiong, H. Que, Y. Xie, P. W. H. Holland, J. Paps, Y. Zhu, F. Wu, Y. Chen, J. Wang, C. Peng, J. Meng, L. Yang, J. Liu, B. Wen, N. Zhang, Z. Huang, Q. Zhu, Y. Feng, A. Mount, D. Hedgecock, Z. Xu, Y. Liu, T. Domazet-Loso, Y. Du, X. Sun, S. Zhang, B. Liu, P. Cheng, X. Jiang, J. Li, D. Fan, W. Wang, W. Fu, T. Wang, B. Wang, J. Zhang, Z. Peng, Y. Li, N. Li, J. Wang, M. Chen, Y. He, F. Tan, X. Song, Q. Zheng, R. Huang, H. Yang, X. Du, L. Chen, M. Yang, P. M. Gaffney, S. Wang, L. Luo, Z. She, Y. Ming, W. Huang, S. Zhang, B. Huang, Y. Zhang, T. Qu, P. Ni, G. Miao, J. Wang, Q. Wang, C. E. W. Steinberg, H. Wang, N. Li, L. Qian, G. Zhang, Y. Li, H. Yang, X. Liu, J. Wang, Y. Yin & J. Wang. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490:49-54.
  • He, Y., H. Yu, Z. Bao, Q. Zhang and X. Guo. 2012. Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica). Fish & Shellfish Immunology 33:411-417.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant, USDA, NSF and Rutgers University. We conducted the following research in our lab and in collaboration with colleagues in 2011: 1) we identified and mapped disease resistance genes and makers, and used them to model disease resistance in eastern oyster populations; 2) we worked on the development of SNP marker and a cytogenetic map for the Pacific oyster; 3) we worked on assembly and annotation of the Pacific oyster genome; and 4) we attended the annual meeting of NRSP-8 held in San Diego, January 2011. The outputs have been disseminated to the research community through workshops, meeting presentations and publications. PARTICIPANTS: Ximing Guo, Principal Investigator; Shan Wang, graduate student; Yan He, graduate student; Daniel Bradbury, undergraduate student; Susan Ford, collaborator, Rutgers University; Eric Powell, collaborator, Rutgers University; Dennis Hedgecock, University of Southern California, CA. Yongbo Bao, collaborator, Wanli University, China; Guofan Zhang, Chinese Academy of Sciences, China. TARGET AUDIENCES: Researchers and shellfish farmers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
We identified 14 loci for Dermo disease resistance, which improved our understanding of genetics of Dermo resistance. A preliminary cytogenetic map has been developed for the Pacific oyster, which is the first for this species. This map will provide physical anchors of the genetic and sequence maps of this species. We have assembled and annotated the Pacific oyster genome, which will provide a valuable resource for the scientific community

Publications

  • Zhang, G., X. Guo, L. Li, F. Xu, X. Wang. H. Qi, L. Zhang, H. Que, H. Wu, S. Wang, D. Hedgecock, P.M. Gaffney, R. Luo, X. Fang and J. Wang. 2011. The oyster genome project: an update on assembly and annotation. J. Shellfish Res., 30(2):567-567. (abstract)
  • Powell, E.N., J.M. Klinck, X. Guo, E.E. Hofmann, S.E. Ford, D. Bushek. 2011. Can oysters develop resistance to Dermo disease: evaluation using a gene-based population dynamics model. J. Shellfish Res., 30(2):544-544. (abstract)
  • Bao, Y., Z. Lin and X. Guo. 2011. Cloning, characterization of glutamine synthetase gene from bloody clam Tegillarca granosa. J. Shellfish Res., 30(2):485-485. (abstract)
  • Hedgecock, D., P.M. Gaffney, X. Guo, G. Shin, A. Gracey, H. Qi, L. Li, G. Zhang, M.P. Samanta. 2011. GIGASNP: integrating genetic, physical and cytogenetic maps of the Pacific oyster Crassostrea gigas. J. Shellfish Res., 30(2):515-151. (abstract)
  • Wang, S., P.M. Gaffney, D. Hedgecock, Z. Bao and X. Guo. 2011. Construction of a cytogenetic map for the Pacific oyster (Crassostrea gigas). J. Shellfish Res., 30(2):561-561. (abstract)
  • Yu. H., H. Yan, X. Wang, Q. Zhang, Z. Bao and X. Guo. 2011. Association between the serine protease inhibitor gene and disease resistance in the eastern oyster. J. Shellfish Res., 30(2):565-565. (abstract)


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant, USDA, NSF and Rutgers University. We conducted the following research in our lab and in collaboration with colleagues in 2010: 1) we developed genetic markers, ESTs, genotyping protocols and improved genetic maps for the eastern oyster; 2) we identified and characterized 20 disease-resistance markers in the eastern oyster; 3) we developed genetic markers and resources for other shellfish species including the Pacific oyster, hard clam and pearl oyster; 4) we worked on the international oyster genome project which has completed shot-gun sequencing and is now finalizing assembly and annotation; and 5) we attended the 2010 annual meeting of NRSP-8 held in San Diego, January 2010. The outputs have been disseminated to the research community through workshops, meeting presentations and publications. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Shellfish research community and the aquaculture industry PROJECT MODIFICATIONS: None

Impacts
We developed genetic markers, sequences, genotyping methods and improved genetic maps for the eastern oyster. These markers and maps have been made available to the research community through publications, meeting presentations, workshops and personal communications. They are being used in other labs. The identification and mapping of disease-resistance genes with co-dominant markers is a significant development. The resistance markers are being validated through association studies and tested for marker-assisted selection. Diseases are the number one concern for the eastern oyster culture industry. Marker-assisted selection may greatly enhance selection efficiency for disease resistance in the eastern oyster. We are making progress on the oyster genome project. Once completed, the genome sequence will provide a valuable resource for the scientific community

Publications

  • Yu, H., Y. He, X. Wang, Q. Zhang, Z. Bao and X. Guo. 2011. Polymorphism in a serine protease inhibitor gene and its association with disease resistance in the eastern oyster (Crassostrea virginica Gmelin). Fish and Shellfish Immunology, in press.
  • Ren, J., X. Liu, F. Jiang, X. Guo and B Liu. 2010. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology, 10:394.
  • Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z. 2010. Microarray analysis of gene expression in eastern Oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol., 29: 921-929.
  • Wang, A., Y. Wang, Z. Gu, S. Li, Y. Shi, and X. Guo. 2010. Development of expressed sequence tags from the pearl oyster, Pinctada martensii Dunker. Marine Biotechnology, in press.
  • Wang, Y., X. Wang, A. Wang and X. Guo. 2010. A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica). Aquaculture, 308:S28-S33.
  • Zhang, L. and X. Guo. 2010. Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture, 302:124-129.
  • Wang, Y., A. Wang, X. Guo. 2010. Development and characterization of polymorphic microsatellite markers for the northern quahog Mercenaria mercenaria (Linnaeus, 1758). J. Shellfish Res., 29(1):77-88.


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant, USDA, NSF and Rutgers University. We conducted the following research in our lab and in collaboration with colleagues in 2009: 1) we developed genetic markers and improved genetic maps for the eastern oyster; 2) we identified and characterized disease-resistance markers in the eastern oyster; 3) we developed genetic markers and constructed genetic maps for the pearl oyster; 4) we developed genetic markers and resources for other shellfish species including the hard clam, surfclam and scallops; and 5) we attended the 2009 annual meeting of NRSP-8 held in San Diego, January 2009. The outputs have been disseminated to the research community through workshops, meeting presentations and publications. PARTICIPANTS: Ximing Guo, Principle Investigator; Yongping Wang, Research Associate; Liusuo Zhang, Postdoctoral Associate; Yan Wang, Research Scientist; Hong Yu, graduate student; Haiyang Yu, graduate student; Gail Bradbury, undergraduate student; John Liu, collaborator, Auburn University; Dennis Hedgecock, collaborator, University of Southern California; Patrick Gaffney, collaborator, University of Delaware. TARGET AUDIENCES: SHellfish researchers and breeders PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We developed molecular markers and improved genetic maps for the eastern oyster. These markers and maps have been made available to the research community through publications, meeting presentations, workshops and personal communications. They are being used in other labs. The identification and mapping of disease-resistance genes with co-dominant markers is a significant development. The resistance markers are being validated through association studies and tested for marker-assisted selection. Diseases are the number one concern for the eastern oyster culture industry. Marker-assisted selection may greatly enhance selection efficiency for disease resistance in the eastern oyster.

Publications

  • Kucuktas, H., S. Wang, S, P. Li, C. He, P. Xu, Z. Sha, H. Liu, Y. Jiang, P. Baoprasertkul, B. Somridhivej, Y. Wang, J. Abernathy, X. Guo, L. Liu, W. Muir & Z. Liu. 2009. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 181: 1649-1660.
  • Wang, L, L. Song, J. Zhao, L. Qiu, H. Zhang, W. Xu, H. Li, C. Li, L. Wu, and X. Guo. 2009. Expressed sequence tags from the zhikong scallop (Chlamys farreri): Discovery and annotation of host-defense genes. Fish & Shellfish Immunology 26: 744-750.
  • Wang, Y., A. Wang and X. Guo. 2009. Development and characterization of 30 polymorphic microsatellite markers for the Atlantic surfclam, Spisula solidissima (Dillwyn, 1817). Mol. Ecol. Res., 9(4):1264-1267.
  • Shi, Y., H. Kui, X. Guo, Z. Gu, Y. Wang and A. Wang. 2009. Genetic linkage map of the pearl oyster, Pinctada martensii (Dunker). Aqua. Res. 41:35-44.
  • Ren, J., X. Liu, G. Zhang, B. Liu and X. Guo. 2009. "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. BMC Genomics, 10:84.
  • Shi, Y., Y. Wang, K. Hong, Z. Hou, A. Wang and X. Guo. 2009. Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker). Mol. Ecol. Res., 9:177-179.
  • Wang, Y., Y. Shi and X. Guo. 2009. Identification and characterization of 66 EST-SSR markers in the eastern oyster Crassostrea virginica (Gmelin). J. Shellfish Res., 28(2):227-234.


Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant, USDA, NSF and Rutgers University. We conducted the following research in our lab and in collaboration with colleagues in 2008: 1) we developed 100+ microsatellite and single-nucleotide polymorphism markers for the eastern oyster; 2) we added these new genetic markers to existing genetic maps; 3) we produced and deployed F2 mapping populations for field exposure to diseases; and 4) we identified disease-resistance genes using infection intensity as an indicator. The outputs have been disseminated to the research community through workshops, meeting presentations and publications. PARTICIPANTS: Dr. Ximing Guo, principal investigator Dr. Liusuo Zhang, postdoctoral associate Dr. Yongping Wang, research associate Dr. David Bushek, collaborator Dr. Susan Ford, collaborator Haiyang Yu, graduate student Hong Yu, graduate student TARGET AUDIENCES: Shellfish researchers and breeders Shellfish farmers Students PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We developed 100+ co-dominant markers in 2008 and added most of them to existing based genetic maps. These markers and maps have been made available to the research community through publications, meeting presentations, workshops and personal communications. They are being used in other labs. The identification and mapping of disease-resistance genes with co-dominant markers is a significant development. The resistance markers are being validated through association studies and tested for marker-assisted selection. Diseases are the number one concern for the eastern oyster culture industry. Marker-assisted selection may greatly enhance selection efficiency for disease resistance in the eastern oyster.

Publications

  • Guo, X., Y. Wang, L. Wang and J-H Lee. 2008. Oysters. Pp 161-175 in: Genome Mapping and Genomics in Fishes and Aquatic Animals, Thomas D. Kocher & Chittaranjan Kole (Eds), Springer, Berlin.
  • Wang, Y. and X. Guo. 2008. Chromosomal mapping of the major ribosomal RNA genes in the Dwarf Surfclam (Mulinia lateralis Say). J. Shellfish Res., 27(2):307-311.
  • Wang, Y. and X. Guo. 2008. Mapping disease-resistance genes in the eastern oyster (Crassostrea virginica). J. Shellfish Res., 27(4): 1061-1061.
  • Zhang, L., X. Guo, D. Bushek and S.E. Ford. 2008. Mapping quantitative trait loci conferring Dermo resistance in the eastern oyster Crassostrea virginica. J. Shellfish Res., 27(4): 1067-1067.
  • Wang, X. and X. Guo. 2008. Variation in the heat shock cognate protein (Hsc70) gene of the eastern oyster, Crassostrea virginica Gmelin. J. Shellfish Res., 27(4): 1061-1061.


Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchanges of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant, USDA, NSF and Rutgers University. Summarized here are outputs from research conducted in our lab and in collaboration with other labs in 2007: 1) we developed 119 microsatellite markers from expressed sequences tag (ESTs) in the eastern oyster; 2) we developed 90+ single-nucleotide markers for the eastern oyster; and 3) we added co-dominant genetic markers to existing AFLP maps; 4) we worked with John Liu's group on the development of ESTs for the eastern oyster; and 5) we worked with colleagues in China on genome mapping in the bay scallop. The outputs have been disseminated to the research community through workshops, meeting presentations and publications. PARTICIPANTS: Ximing Guo, Principal Investigator, Rutgers University; Yongping Wang, Research Associate, Rutgers University; John Liu, Collaborator, Auburn University; Guofan Zhang, Collaborator, Chinese Academy of Sciences; Lingling Wang, Collaborator, Chinese Academy of Sciences; Greg Warr, Collaborator, Medical University of South Carolina TARGET AUDIENCES: The eastern oyster farming and research community

Impacts
We developed 200+ co-dominant markers in 2007 and added most of them to existing AFLP based genetic maps. These markers and maps have been made available to the research community through publications, meeting presentations, workshops and personal communications. They are being used in other labs. The identification and mapping of disease-resistance genes with co-dominant markers is a significant development. The resistance markers are being validated through association studies and tested for marker-assisted selection. Diseases are the number one concern for the eastern oyster culture industry. Marker-assisted selection should greatly enhance selection efficiency for disease resistance in the eastern oyster.

Publications

  • Guo, X., Y. Wang and Z. Xu. 2007. Genomic analyses using fluorescent in situ hybridization. In: Aquaculture Genome Technologies, Zhanjiang (John) Liu (ed), Blackwell Publishing, Ames, pp. 289-311.
  • Wang, Y. and X. Guo. 2007. Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica. Marine Biotechnology, 9, 500-511.
  • Quilang, J., S. Wang, P. Li, J. Abernathy, E. Peatman, Y. Wang, L. Wang, Y. Shi, R. Wallace, X. Guo, and Z. Liu. 2007. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics, 8:157.
  • Jenny, M. J., R. W. Chapman, A. Mancia, Y.A. Chen, D. J. McKillen, H. Trent, P. Lang, J.-M. Escoubas, E. Bachere, V. Boulo, Z. J. Liu, P. S. Gross, C. Cunningham, P. M. Cupit, A. Tanguy, X. Guo, D. Moraga, I. Boutet, A. Huvet, S. D. Guise, J. S. Almeida, G. W. Warr. 2007. A cDNA microarray for Crassostrea virginica and C. gigas. Marine Biotechnology, 9, 577-591.
  • Qin, Y., X. Liu, H. Zhang, G. Zhang and X. Guo. 2007. Identification and mapping of AFLP markers linked to shell color in bay scallop, Argopecten irradians (Lamarck, 1819). Marine Biotechnology, 9:66-73.
  • Qin, Y., X. Liu, H. Zhang, G. Zhang and X. Guo. 2007. Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers. Aquaculture, 272:281-290.
  • Wang, L., L. Song, H. Zhang, Q. Gao and X. Guo. 2007. Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819). Aquaculture Research 38 (4):409-419.
  • Wang, Y. and X. Guo. 2007. Chromosomal mapping of major ribosomal rRNA genes in the hard clam (Mercenaria mercenaria) using fluorescence in situ hybridization. Marine Biology, 150:1183-1189.


Progress 01/01/06 to 12/31/06

Outputs
This project is part of the USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchange of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant and New Jersey Commission on Science and Technology. Summarized here is genomic research conducted in our lab in 2006: 1) we conducted QTL mapping and identified 12 putative QTLs related to Dermo/summer mortality resistance in the eastern oyster; 2) we published a preliminary genetic map for the Pacific abalone; 3) we developed a set of microsatellite markers from expressed sequence tags for the eastern oyster; and 4) we developed expressed sequence tags for the bay scallops.

Impacts
The identification and mapping of disease-resistance genes is a significant development in oyster genomics. This is the first time that disease-resistance QTL are mapped in a mollusc. Diseases are the number one concern for the eastern oyster culture industry. The mapping of disease-resistance QTL will help us to understand the genetic basis of disease-resistance. It will eventually lead to genetic improvement of cultured stocks through marker-assisted selection.

Publications

  • Liu, X., X. Liu, X. Guo, Q. Gao and G. Zhang. 2006. A preliminary genetic linkage map of the Pacific abalone Haliotis discus hannai Ino. Marine Biotechnology, 8:386-397.
  • Song, L., W. Xu, C. Li, H. Li, L. Wu, J. Xiang and X. Guo. 2006. Development of expressed sequence tags from the bay scallop, Argopecten irradians irradians. Marine Biotechnology, 8(2):161-169. (Coverpage)
  • Yu, Z. and X. Guo. 2006. Identification and mapping of disease-resistance QTL in the eastern oyster, Crassostrea virginica Gmelin. Aquaculture, 254:160-170.
  • Guo, X., Y. Wang, Z. Yu, L. Wang and J.H. Lee. 2006. Genome mapping in the eastern oyster (Crassostrea virginica Gmelin). J. Shellfish Res., 25(2):733-734. (abstract)
  • Lee, J.H. and X. Guo. 2006. Mining EST database for single-nucleotide polymorphisms in the eastern oyster (Crassostrea virginica). J. Shellfish Res., 25(2):748-749. (abstract)
  • Wang, Y. and X. Guo. 2006. Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica. J. Shellfish Res., 25(2):790. (abstract)


Progress 01/01/05 to 12/31/05

Outputs
This project is part of a USDA National Research Support Project (NRSP-8) on animal genomes. The national project is designed to coordinate research efforts in animal genomics and facilitate exchange of ideas and data. Our group conducts research on genomics of molluscs under projects funded by NOAA Sea Grant and New Jersey Commission on Science and Technology. We attended the annual meeting of NRSP-8, January 15 - 16th, 2005, as part of the International Conference on Plant and Animal Genomes, San Diego, CA. Summarized here is genomic research conducted at our lab in 2005. We focused on the development of molecular markers and the mapping of disease-resistance genes in the eastern oyster. We developed 53 microsatellite markers from ESTs and genes have been developing microsatellite markers for the eastern oyster. We identified 120+ single-nucleotide polymorphisms (SNPs) and designed genotyping assays for 15 of them. Using AFLP (amplified fragment length polymorphism) and microsatellite markers, we identified and mapped 12 putative disease-resistance QTL (quantitative trait loci). These QTL are being confirmed using lab-based challenges. We also continued our work on molecular cytogenetics. We developed a preliminary cytogenetic map for the eastern oyster by mapping P1 clones. We mapped ribosomal RNA genes in several species of oysters. We published a genetic linkage map for zhikong scallop in collaboration with colleagues at Chinese Academy of Sciences.

Impacts
The identification and mapping of disease-resistance genes is a significant development in oyster genomics. This is the first time that disease-resistance QTL are mapped in a mollusc. Diseases are the number one concern for the eastern oyster culture industry. The mapping of disease-resistance QTL will help us to understand the genetic basis of disease-resistance. It will eventually lead to genetic improvement of cultured stocks through marker-assisted selection.

Publications

  • Wang, Y., Z. Xu and X. Guo. 2005. Chromosomal mapping of 5S ribosomal RNA genes in the eastern oyster, Crassostrea virginica Gmelin by fluorescence in situ hybridization. J. Shellfish Res., 24(4):959-964.
  • Hedgecock, D. P.M. Gaffney, P. Goulletquer, X. Guo, K. Reece and G. Warr. 2005. A case for sequencing the Pacific oyster genome. J. Shellfish Res., 24(2):429-441.
  • Wang, Y., Z. Xu. J.C. Pierce and X. Guo. 2005. Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones. Marine Biotechnology, 7:207-214.
  • Wang, L., L. Song, Y. Chang, W. Xu, D. Ni and X. Guo. 2005. A preliminary genetic map of zhikong scallop (Chlamys farreri, Jones et Preston 1904). Aquaculture Research, 36:643-653.
  • Wang, Y. and X. Guo. 2005. Chromosomal location of major ribosomal RNA genes in three species of Ostreidae (Bivalvia, Mollusca). J. Shellfish Res., 24(2):681-682.
  • Saout, C. and X. Guo. 2005. Cross-species amplification of expressed sequence tags in three species of Crassostrea. J. Shellfish Res., 24(2):674.
  • Yu, Z. and X. Guo. 2005. Identification and mapping of disease-resistance QTLs in the eastern oyster, Crassostrea virginica Gmelin. J. Shellfish Res., 24(2):685.