Progress 01/01/98 to 09/30/04
Outputs
This project is part of a USDA regional project (NE-186) aimed at developing genetic maps for aquaculture species. The regional project holds annual meetings to coordinate and promote research in aquaculture genomics. The shellfish genetics laboratory at the Haskin Shellfish Research Laboratory at Rutgers is a participant of NE-186 and has maintained an active research program in oyster genomics since 1998. During the past six years, research at Rutgers University has focused on three areas of oyster genomics: 1) cytogenetic mapping of chromosomes using fluorescence in situ hybridization (FISH); 2) marker development and linkage mapping; and 3) identification and mapping of important genes and QTLs. A number of genes, repetitive DNA and large insert clones were mapped chromosomes of oysters, clams and scallops using FISH. A preliminary cytogenetic map was developed for the eastern oyster. Studies find some evidence that chromosomal change has played an important role
in bivalve evolution, and at least one-round of genome duplication has occurred. In mapping, we constructed genetic linkage maps for eastern and Pacific oysters. In the eastern oyster, the female map consisted of 84 markers in 12 linkage groups with a length of 904 cM, and the male map had 114 markers in 12 linkage groups, covering 647 cM. The estimated genome length of the eastern oyster was 858 cM for the male map and 1296 cM for the female map. Several recessive lethal genes have been mapped in the eastern and Pacific oysters. We also studied gene expression in oysters in response of pathogen exposure and triploidy. Nine subtractive libraries were constructed; over 800 ESTs were sequenced; and 170 up-regulated oyster genes were identified in response to pathogen exposure.
Impacts
The linkage and cytogenetic maps of the eastern oyster were the first published genetic maps for a mollusc. These genetic maps provide some insight to the genome of oysters. Genetic maps are critical for our understanding of the genome and the genetic improvement of oysters. With genetic maps, we can potentially map important QTLs and use marker-assisted selection for genetic improvement. Although the genetic maps developed here are preliminary, they provide an important first step for the development of a comprehensive genetic map and QTL mapping in the eastern oyster. The identification of oyster genes expressed in response of pathogen challenge is important to our understanding of disease-resistance.
Publications
- Wang, Y. and X. Guo, 2004. Chromosomal rearrangement in Pectinidae revealed by rRNA loci and implications for bivalve evolution. Biol. Bull., 207:247-256.
- Wang, H. X. Guo, G. Zhang and F. Zhang. 2004. Classification of jinjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis. Aquaculture, 242:137-155.
- Tanguy, A., X. Guo and S.E. Ford. 2004. Discovery of genes expressed in response to Perkinsus marinus challenge in eastern (Crassostrea virginica) and Pacific (C. gigas) oysters. Gene, 338:121-131.
- Gong, N., H. Yang, G. Zhang, B.J. Landau and X. Guo. 2004. Chromosome inheritance in autotriploid Pacific oyster Crassostrea gigas Thunberg. Heredity, 93:408-415.
- Li, L. and X. Guo. 2004. AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology 6:26-36.
- Wang, Y., Z. Xu and X. Guo. 2004. Differences in the rDNA-bearing chromosome divide the Asian-Pacific and Atlantic species of Crassostrea (Bivalvia, Mollusca). Biol. Bull., 206:46-54.
- Yu, Z., X. Kong, L. Zhang, X. Guo, J. Xiang. 2003. Taxonomic status of four Crassostrea oysters from China as inferred from mitochondrial DNA sequences. J. Shellfish Res., 22(1):31-38.
- Yu, Z. and X. Guo. 2003. Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. Biol. Bull. 204: 327-338.
- Wang, Y. and X. Guo. 2001. Chromosomal mapping of the vertebrate telomere sequence (TTAGGG)n in four bivalve Molluscs by fluorescence in situ hybridization. J. Shellfish Res., 20(3):1187-1190.
- Wang, Y., Z. Xu and X. Guo. 2001. A centromeric satellite sequence in the Pacific oyster, Crassostrea gigas (Thunberg) identified by fluorescence in situ hybridization. Marine Biotechnology, 3:486-492.
- Xu, Z., X. Guo, J. Pierce and P.M. Gaffney, 2001. Chromosomal location of the major ribosomal RNA genes in the eastern and Pacific oysters. The Veliger, 44:79-83.
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Progress 01/01/03 to 12/31/03
Outputs
This project is part of a multi-institution, USDA regional project aimed at developing genetic maps for aquaculture species. Our team at Rutgers is to conduct genomic studies on oysters. In 2003, research at Rutgers University focused on linkage mapping in the eastern and Pacific oysters, two most important molluscs cultured in the US and worldwide. We developed a large number of amplified fragment length polymorphism (AFLP) markers and constructed two genetic linkage maps for each oyster species. In the eastern oyster, 396 polymorphic AFLP markers were obtained, and two genetic linkage maps were constructed: one for the female and one for the male. The female map consisted of 84 markers in 12 linkage groups with a length of 904 cM, and the male map had 114 markers in 12 linkage groups, covering 647 cM. The estimated genome length of the eastern oyster was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and
female map when all linked markers were considered. In the Pacific oyster, 384 AFLP markers were developed and two (female and male) maps were constructed. The female map consisted of 119 markers in 11 linkage groups, spanning 1030.7 cM with an average interval of 9.5 cM per marker. The male map contained 96 markers in 10 linkage groups, covering 758.4 cM with 8.8 cM per marker. The estimate genome length of the Pacific oyster was 1258 cM for the female and 933 cM for the male, and the observed coverage was 82.0% for the female and 81.3% for male map. Several recessive lethal genes have been mapped in the eastern and Pacific oysters. We also studied gene expression in oysters in response of pathogen exposure and triploidy. Nine subtractive libraries were constructed, and over 500 ESTs were sequenced. Some of the sequenced genes are apparently associated with host-defense in oysters. Using the molecular markers and maps, we analyzed marker frequency shifts after disease-inflicted
mortality and identified markers putatively associated with resistance genes.
Impacts
This is the first time that genetic linkage maps are developed for the eastern oyster. These genetic maps provide some insight to the genome of oysters. Genetic maps are critical for our understanding of the genome and the genetic improvement of oysters. With genetic maps, we can potentially map important QTLs and use marker-assisted selection for genetic improvement. Although the genetic maps developed here are preliminary, they provide an important first step for the development of a comprehensive genetic map and QTL mapping in the eastern oyster.
Publications
- Li, L. and X. Guo. 2003. AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology, in press.
- Yu, Z. and X. Guo. 2003. Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. Biol. Bull. 204: 327-338.
- Wang, Y. and X. Guo. 2003. Chromosomal mapping of ribosomal RNA genes and telomeric repeats in zhikong and bay scallops. J. Shellfish Res., 22(1):360 (Abstract).
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Progress 01/01/02 to 12/31/02
Outputs
This project is part of a multi-institution, USDA regional project aimed at developing genetic maps for aquaculture species. In 2002, research at Rutgers University focused on linkage mapping in the eastern and Pacific oysters, two most important molluscs cultured in the US and worldwide. We developed a large number of amplified fragment length polymorphism (AFLP) markers and constructed two genetic linkage maps for each oyster species. In the eastern oyster, 396 polymorphic AFLP markers were obtained, and two genetic linkage maps were constructed: one for the female and one for the male. The female map consisted of 84 markers in 12 linkage groups with a length of 904 cM, and the male map had 114 markers in 12 linkage groups, covering 647 cM. The estimated genome length of the eastern oyster was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and female map when all linked markers were considered. In the
Pacific oyster, 384 AFLP markers were developed and two (female and male) maps were constructed. The female map consisted of 119 markers in 11 linkage groups, spanning 1030.7 cM with an average interval of 9.5 cM per marker. The male map contained 96 markers in 10 linkage groups, covering 758.4 cM with 8.8 cM per marker. The estimate genome length of the Pacific oyster was 1258 cM for the female and 933 cM for the male, and the observed coverage was 82.0% for the female and 81.3% for male map. Several recessive lethal genes have been mapped in the eastern and Pacific oysters. We also studied gene expression in oysters in response of pathogen exposure and triploidy. Nine subtractive libraries were constructed, and over 500 ESTs were sequenced. Some of the sequenced genes are apparently associated with host-defense in oysters.
Impacts
This is the first time that genetic linkage maps are developed for the eastern oyster. These genetic maps provide some insight to the genome of oysters. Genetic maps are critical for our understanding of the genome and the genetic improvement of oysters. With genetic maps, we can potentially map important QTLs and use marker-assisted selection for genetic improvement. Although the genetic maps developed here are preliminary, they provide an important first step for the development of a comprehensive genetic map and QTL mapping in the eastern oyster.
Publications
- Landau, B.J., A. Tanguy and X. Guo. 2002. Searching for differentially expressed genes in diploid and triploid Pacific oyster, Crassostrea virginica Gmelin. J. Shellfish Res., 21(1):382.
- Li, L. and X. Guo. 2002. A Preliminary linkage map for the Pacific oyster Crassostrea gigas, constructed with RAPD and AFLP markers. J. Shellfish Res., 21(1):433.
- Tanguy, A., S. Ford and X. Guo. 2002. Characterization of gene expression in response to Perkinsus marinus and Haplosporidium nelsoni infections in the eastern and pacific oysters. J. Shellfish Res., 21(1):421.
- Yu, Z. and X. Guo. 2002. A basic AFLP linkage map for the eastern oyster, Crassostrea virginica Gmelin. J. Shellfish Res., 21(1):382.
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Progress 01/01/01 to 12/31/01
Outputs
Knowledge about the genome is a key prerequisite for any sophisticated genetic manipulation and improvement. At the present time, we know little about the genome of oysters and other aquaculture species. It is only recently that genomic research in oysters has received some attention. The oyster genome research is part of the USDA regional project - Genetic Maps of Aquaculture Species. Part of our research at HSRL has been on molecular characterization of oyster chromosomes, which is needed for several types of genomic analyses and mapping. We tested fluorescence in situ hybridization (FISH) on oyster chromosomes with several types of DNA sequences and probes using chromosomes from early embryos. The vertebrate telomere probe, (T2AG3)n, was mapped in the telomere of all oyster chromosomes. The major RNA genes were assigned to the second largest chromosome (Chromosome 2) in the American oyster and the smallest chromosome (Chromosome 10) in the Pacific oyster. Several
repetitive sequences were hybridized to oyster chromosomes. Nine P1-clones have been mapped, and a basic cytogenetic map has been developed for the American oyster. Another focus of our research is on linkage mapping. In the past year, we have developed a large number of markers from amplified fragment length polymorphisms (AFLPs). We constructed the first linkage map for the American oyster and also one for the Pacific oyster. The American oyster map consists of 140 markers in 11 linkage groups, spanning 617.4 cM with an average interval of 4.4 cM per marker.
Impacts
We produced the first cytogenetic map and the first linkage map for the American oyster, which may provide useful tools for genomic mapping of quantitative trait loci (QTLs). The mapping of QTLs is important for genetic improvement by marker-assisted selection.
Publications
- Wang, Y. and X. Guo. 2001. Chromosomal mapping of the vertebrate telomere sequence (TTAGGG)n in four bivalve Molluscs by fluorescence in situ hybridization. J. Shellfish Res., 20(3):1187-1190.
- Wang, Y., Z. Xu and X. Guo. 2001. A centromeric repeat in the Pacific oyster, Crassostrea gigas (Thunberg) identified by FISH. Marine Biotechnology, 3: 486-492.
- Xu, Z., X. Guo, J. Pierce and P.M. Gaffney, 2001. Chromosomal location of the major ribosomal RNA genes in the eastern and Pacific oysters. The Veliger, 44:79-83.
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Progress 01/01/99 to 12/31/99
Outputs
Knowledge about the genome is a key prerequisite for any sophisticated genetic manipulation and improvement. At the present time, we know very little about the genome of oysters. It is only recently that genomic research in oysters has received some attention. The oyster genome research is part of the USDA regional project, "Genetic Maps of Aquaculture Species". Research in our lab has been focusing on molecular characterization of oyster chromosomes, which is needed for several types of genomic analyses and mapping. Although oysters have a low haploid number of 10, oyster chromosomes are difficult to characterize because of their similarities in size and shape. Traditional banding techniques in oysters have been difficult and unreliable. We tested fluorescence in situ hybridization (FISH) on oyster chromosomes with several types of DNA sequences and probes using chromosomes from early embryos. The vertebrate telomere probe, (T2AG3)n, was located in the telomere of
all oyster chromosomes. The major RNA genes were assigned to the second largest chromosome (Chromosome 2) in the American oyster and the smallest chromosome (Chromosome 10) in the Pacific oyster. Several repetitive sequences were hybridized to oyster chromosomes. One of the repetitive elements was mapped to the centromeres of Pacific oyster chromosomes. We are testing new detection systems that may allow direct assignment of short, single copy sequences. We are also studying phenotypic effects of different chromosomes through trisomic analyses.
Impacts
The rDNA is mapped by FISH and a centromeric DNA repeat has been identified, for the first time in oysters. All oyster chromosomes have been identified, providing a base for genomic analysis.
Publications
- Xu, Z., X. Guo, J. Pierce and P.M. Gaffney, 1999. Chromosomal location of the major ribosomal RNA genes in the eastern and Pacific oysters. Veliger, in press.
- Wang, Y., Z. Xu, X. Guo, J.C. Pierce and P.M. Gaffney. 2000. Chromosomal location of some repetitive dna in crassostrea oysters as determined by fish. J. Shellfish Res., in press.
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