Source: RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY submitted to
GENETIC IMPROVEMENT OF EASTERN OYSTER STOCKS FOR AQUACULTURE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
ANIMAL HEALTH
Reporting Frequency
Annual
Accession No.
1004475
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 2, 2014
Project End Date
Sep 30, 2019
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
Oyster aquaculture is a major industry in the US and worldwide. The sustainable development of oyster aquaculture is increasingly dependent on technological advances. Currently there are a number of problems and challenges facing the oyster aquaculture industry, where genetic research and development can contribute greatly. First, eastern oyster populations along much of the Atlantic coast have been devastated by three diseases: Dermo (caused by Perkinsus marinus), MSX (Haplosporidium nelsoni) and ROD (caused by Roseovarius crassostreae). Each of these diseases can caused severe mortalities in naïve oysters. The development of disease resistant strains is critically important for the oyster aquaculture industry. Secondly, most oyster stocks in production have only limited history of domestication, and genetic improvements are needed to produce stocks with desirable characteristics for aquaculture. The eastern oyster grows slowly and it often takes 24 - 36 months to reach market size. Stocks with superior growth will greatly benefit oyster farmers.The advent of modern breeding technologies offers new promises to the aquaculture industry. Advances in genomics may identify new genes or markers that greatly empower genetic improvement of cultured stocks. The development of sterile and fast-growing triploids (with three sets of chromosomes) can also greatly benefit oyster aquaculture. The goal of this project is to improve animal health and increase oyster production through the development of superior stocks that are disease resistant, fast growing, sterile and of high meat quality, and sterile. Specifically, we propose to: 1) test and apply marker-assisted selection for disease resistance; and 2) study and improve genome stability of tetraploid stocks for the production of superior triploids that have become a popular stock for oyster farming.
Animal Health Component
40%
Research Effort Categories
Basic
30%
Applied
40%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033799108030%
3110811108035%
3040811108035%
Knowledge Area
303 - Genetic Improvement of Animals; 311 - Animal Diseases; 304 - Animal Genome;

Subject Of Investigation
3799 - Cultured aquatic animals, general/other; 0811 - Shellfish;

Field Of Science
1080 - Genetics;
Goals / Objectives
The goal of this project is to improve animal health by producing disease-resistant oyster stocks and increase the profitability by producing the best performing triploids that are disease-resistant, fast growing and genetically stable.The specific objectives are: 1) test and add marker-assisted selection for disease resistance to our oyster breeding program; and 2) study and improve tetraploid stocks for the production of superior triploids.
Project Methods
The overall objective of our research is to produce superior oyster stocks that are disease resistant, fast growing, of high meat quality, and sterile, by using a combination of traditional and modern approaches. The specific objectives are: 1) test and add marker-assisted selection for disease resistance to our oyster breeding program; and 2) Study and improve tetraploid stocks for the production of superior triploids.For marker-assisted selection, we will use eight genetic markers that have been identified and validated in previous studies. We will genotype them in surviving oysters of three (diverse) selected lines that have gone through selection by diseases in the field. Oysters with the highest breeding value based on multi-locus genotypes will be selected to produce the next generation of selected lines. Control lines will be produced using randomly selected oysters from each line. Spat from the selected and control lines will be deployed in the field to evaluate if selected lines have better survival than the control lines. If the selected lines have significantly better survival than the control lines, we will conclude that MAS is effective, and survivors from the selected lines will be made available to the oyster culture industry.For the development of superior tetraploids and triploids, our hypothesis is that genome instability in tetraploids observed in somatic tissue also exists to some extent in germline cells and results in chromosome loss in gametes and triploid progeny, which negatively affect the performance of triploids. We further hypothesize that genome stability of tetraploids is variable, inheritable and can be improved through selection. We will test these hypotheses by producing a set of triploid and tetraploid families using tetraploids with different levels of somatic reversion. We will study the relationship among somatic chromosome loss, germline chromosome loss, chromosome integrity of triploids, and the performance of triploid and tetraploid progeny. We hope to identify the most stable tetraploid families that produce the best performing triploids for the oyster industry.Oyster lines will be evaluated in our field studies. Results of the evaluation will be made available to the oyster research and farming community at meetings and through publications and extension programs.

Progress 10/02/14 to 09/30/19

Outputs
Target Audience: Shellfish farmers, shellfish breeders, aquaculturists, geneticists, biologists, educators and people who are interested in shellfish aquaculture and the environment. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project provided training opportunities to 9 undergraduate students, 5 graduate students and 4postdoctoral researchers. They received training and working experience in spawning oysters, culturing oyster larvae, conducting sampling and genetic analyses. How have the results been disseminated to communities of interest?Results of this project have been published in peer-reviewed journals and presented at professional conferences. Improved disease-resistant oyster strains have been distributed to hatcheries for production. New tetraploid oyster lines have been transferred to oyster hatcheries for commercial production of improved triploid oysters. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Diseases pose a serious challenge to shellfish aquaculture. The development of disease-resistant strains is critically important to the shellfish industry. In addition to disease resistance, triploid oysters grow significantly faster than normal diploids. Fast growth means that triploids reach market size earlier than diploids, which reduces production cost and losses to disease. The demand for disease-resistant and triploid oysters is on the rise. This project improved the performance of disease-resistant eastern oyster strains ofRutgers University, which are widely used for aquaculture in the Northeastern region. This project producednew and improved tetraploid oysters which have been transferred to hatcheries for commercial production of triploid oysters. This project has also led to progress in our understanding of genomics,immunity and evolution of molluscan shellfish, paving the way for further genetic improvement of aquacultural shellfish. Objective 1: Markers and Marker-assisted selection for disease resistance The identification of disease-resistance markers can benefit from a better understanding of the immune system of oysters. We analyzed and reviewed transcriptome datasets to improve our understanding of oyster's immune related genes and pathways. Our analyses show that oysters have a sophisticated immune system that is equipped with a large number of genes. Many immune related genes are expanded and highly diverse. The great paralogous and allelic diversity of immune response genesmay be essential for oyster's defense against diverse pathogens in the absence of adaptive immunity. To identify candidate disease-resistant markers, we assembled a set of 1002 candidate genes of the eastern oyster that are involved in immune and stress responses based on gene function and transcriptome profile. We sequenced them in before- and after-mortality samples to identify single-nucleotide polymorphisms (SNPs) that consistently shifted allele frequencies. SNPs in 21 genes showed significant (>20%) frequency shift in all three populations, suggesting they are likely associated with disease resistance. They include some well-known immune response genes encoding c-type lectins, tissue necrosis factor receptor-associated factor and interferon induced protein, as well as proteins whose involvement in immune response is less clear such as epidermal growth factor, G-protein coupled receptor, hemicentin, L-ascorbate oxidase and glutamate decarboxylase. These genes and markers provide good candidates for further studies and marker-assisted selection. We identified additional genetic markers for disease resistance and used them for marker-assisted selection in the eastern oyster. Seven groups were produced by marker-assisted selection, based parental genotypes at five disease-resistant loci. The seven groups were produced in summer 2017 and evaluated. We have provided improved oyster broodstock for commercial production. We discovered a novel variant of alternative oxidase gene in the eastern oyster that is created by alternative splicing of a duplicate exon. The new variant is preferentially expressed when oysters are under stress and likely adaptive to stressful conditions. This finding provides insight into how exon duplicate and alternative splicing together contribute to genome complexity and stress adaptation. For hard clams, five markers associated with QPX-resistance or high survival were identified and used for marker-assisted selection. About 400 hard clams were genotyped and breeding value was determined for each clam based on relative fitness of their genotypes at the five loci. Fifteen clams with the highest, lowest and average breeding values were selected and used as parents to produce the next generation. Clams of the three groups are being cultured for field evaluation. As part of this project, we participated the sequencing of the eastern oyster genome, which provides a foundation forgenome-based breeding. Our lab and several other labs have obtained a major grant for genomic selection targeting disease resistance and other production traits in the eastern oyster. The grant is funded by NOAA through Atlantic States Marine Fisheries Commission. Objective 2: Improving tetraploid and triploid oysters Triploid oysters have three sets of chromosomes instead of two sets found in normal diploids. Triploid oysters are ideal for aquaculture because of their sterility, fast growth and improved meat quality in summer. Triploids are produced by mating normal diploids and tetraploids with four sets of chromosomes. However, the tetraploid genome is unstable. Tetraploid oysters may lose chromosomes and affect the quality of triploids they produce. The project aims to produce stable tetraploids that can produce superior triploids for aquaculture. We obtained a research grant from USDA NIFA aquaculture program for genetic improvement of tetraploid oysters. We produced new generations of tetraploid oysters that will serve as the base population for making and selecting best-performing tetraploid families. To determine if triploid eastern oysters can be improved by selecting tetraploids, we produced two classes of triploids by crossing the same diploid females with the largest (L) or smallest (S) tetraploid males from the same cohort. At 6-month post-fertilization and in both experiments, L-triploids were significantly (p<0.001) larger than S-triploids, and both triploids were significantly (p<0.001) larger than diploids. In Experiment 1 where the largest and smallest 10% tetraploids were used, L-triploids were 79% heavier than S-triploids, which in turn were 50% heavier than diploids. In Experiment 2 where the largest and smallest 20% tetraploids were used, L-triploids were 21% heavier than S-triploids, and the latter were 54% heavier than diploids. These results show that despite genome instability tetraploids have a large influence on the performance of their triploid progeny, and superior triploids can be produced by selecting and using the best- performing tetraploids. By selecting the best-performing triploids and tetraploids, new lines of tetraploids were produced. These new lines have been transferred to the industry for commercial production of improved triploids. A new strategy for genetic improvement of tetraploids was developed which may have wide applications in improving tetraploids and triploids of oysters and other shellfish species.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Whiteside, W. and X. Guo. 2019. Identification of genes potentially associated with shell color in the eastern oyster Crassostrea virginica. Presented at Aquaculture 2019, March 7-11, 2019, New Orleans, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Wang, Z. and X. Guo. 2019. Gene editing with CRISPR/Cas9 in the eastern oyster Crassostrea virginica. Presented at Aquaculture 2019, March 7-11, 2019, New Orleans, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Guo, X. 2019. Progress in genetic improvement of eastern oysters. Presented at the Northeast Aquaculture Conference & Exposition and the Milford Aquaculture Seminar in Boston, Massachusetts, January 9-11, 2019.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Turley, B., K. Reece, J. Shen, J.-H. Lee, X. Guo and J. McDowell. 2019. Multiple drivers of interannual oyster settlement and recruitment in the lower Chesapeake Bay. Conservation Genetics, 20(5):10571071.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Hu, L., H. Wang, Z. Zhang, C. Li and X. Guo. 2019. Classification of small flat oysters of Ostrea stentina species complex and a new species Ostrea neostentina sp. nov. (Bivalvia: Ostreidae). Journal of Shellfish Research, 38(2):295-308.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Lafont, M., P. Goncalves, X. Guo, C. Montagnani, D. Raftos & T. Green. 2019. Transgenerational plasticity and antiviral immunity in the Pacific oyster (Crassostrea gigas) against Ostreid herpesvirus 1 (OsHV-1). Developmental & Comparative Immunology, 91:17-25.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Bayne, B., M. Angl�s d'Auriac, T. Backeljau, P. Beninger, P. Boudry, R. Carnegie, J. Davis, X. Guo, D. Hedgecock, M. Krause, C. Langdon, S. Lap�gue, D. Manahan, R. Mann, E. Powell & S. Shumway. 2019. A scientific name for Pacific oysters. Aquaculture 499:373.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Guo, X. 2019. Telomere sequences in shrimp and bivalves. Presented at Aquaculture 2019, March 7-11, 2019, New Orleans, USA.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Shellfish farmers, shellfish breeders, aquaculturists, geneticists, biologists, educators and people who are interested in shellfish aquaculture and the environment. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provided training opportunities to threeundergraduate students, two graduate students and one postdoctoral researcher. They received training and working experience in spawning oysters, culturing oyster larvae, conducting sampling and genotyping analyses. How have the results been disseminated to communities of interest?Results of this project havebeen presented at local and national meetings and published in peer-reviewed journals. The tetraploid oysters developed in this project have been transferred to hatcheries (one in New Jersey and two in Maine) for commercial production. Oyster farmers in New Jersey received excess triploid seed from this projects for their own evaluation. What do you plan to do during the next reporting period to accomplish the goals?Continue with data analysis and completion of the project goals and pursue the next stage of oyster research upon terminiation of this project.

Impacts
What was accomplished under these goals? For marker-assisted selection, we deployed seven groups of eastern oysters produced through marker-assisted selection and maintained them in the field for evaluation. Five markers associated with QPX-resistance or high survival were identified and usedfor marker-assisted selection in the hard clam. About 400 hardclams were genotyped and breeding value was determined for each clam based on relative fitness of their genotypes at the five loci. Fifteen clams with the highest, lowest and average breeding values were selected and used as parents to produce the next generation. Clams of the three groups are being cultured for field evaluation. To improve the performance of triploid and tetraploid oysters, different classes of tetraploids, large, small and average-sized, were selected to produce triploids and tetraploids, by mating with diploid and tetraploid females, respectively. The resultant triploids and tetraploids were evaluated along with their diploid controls.Triploid oysters produced from large tetraploids grew significantly faster than triploids produced from small or average-sized tetraploids. Mating of larger tetraploids also produced larger tetraploid progeny. Genotype of diploid parents also significantly affected the performance of triploids. Triploids produced with disease-resistant diploids survived better than that produced from susceptible stocks. These results indicate that genetic background of diploid and tetraploid parents is important in determining the performance of triploids. By selecting the best-performing triploids and tetraploids, new lines of tetraploids were produced. These new lines have been transferred to the industry for commercial production of improved triploids. A new strategy for genetic improvement of tetraploids was developed which may have wide applications in improving tetraploids and triploids of oysters and other shellfish species. Diseases pose a serious challenge to shellfish aquaculture. The development of disease-resistant strains is critically important to the shellfish industry.In addition to disease resistance, triploid oysters grow significantly faster than normal diploids. Fast growth means that triploids reach market size earlier than diploids, which reduces production cost and losses to disease. The demand for disease-resistant and triploid oysters is on the rise. The new and improved tetraploid oysters have been transferred to hatcheries for commercial production of triploid oysters.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Guo, X., C. Li and H. Wang. 2018. Diversity and evolution of living oysters. J. Shellfish Res., 37(4):755-771. https://doi.org/10.2983/035.037.0407
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Li, L., A. Li, K. Song, J. Meng, X. Guo, S. Li, C. Li, P. D. Wit, H. Que, F. Wu, W. Wang, H. Qi, F. Xu1, R. Cong, B. Huang, Y. Li, T. Wang, X. Tang, S. Liu, B. Li, R. Shi, Y. Liu, C. Bu, C. Zhang, W. He, S. Zhao, H. Li, S. Zhang, L. Zhang and G. Zhang. 2018. Divergence and plasticity shape adaptive potential in the Pacific oyster. Nature Ecology & Evolution, 2:1751-1760. https://doi.org/10.1038/s41559-018-0668-2
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Thongda, W., H. Zhao, D. Zhang, L. N. Jescovitch, M. Liu, X. Guo, M. Schrandt, S. P. Powers, and E. Peatman. 2018. Development of SNP panels as a new tool to assess the genetic diversity, population structure, and parentage analysis of the eastern oyster (Crassostrea virginica). Marine Biotechnology, 20:385-395. . https://doi.org/10.1007/s10126-018-9803-y
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Guo, X. 2018. Molecular adaptations of bivalve molluscs revealed by genomics analyses. Presented at 110th Annual Meeting of National Shellfisheries Association, March 18 ⿿ 22, 2018, Seattle, USA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Guo, X. 2018. Observations on tetraploid eastern oysters, Crassostrea virginica and implications in genetic improvement of triploids. Presented at 110th Annual Meeting of National Shellfisheries Association, March 18 ⿿ 22, 2018, Seattle, USA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Whiteside, M. and Guo, X. 2018. Everything from shells: Genetics of shell shape and color in the eastern oyster, Crassostrea virginica. Presented at 110th Annual Meeting of National Shellfisheries Association, March 18 ⿿ 22, 2018, Seattle, USA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Wang, Z. and Guo, X. 2018. Developing an effective transfection protocol for gene editing in the Pacific oyster, Crassostrea gigas. Presented at 110th Annual Meeting of National Shellfisheries Association, March 18 ⿿ 22, 2018, Seattle, USA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Guo, X., M. Liu, B. Xu, Y. Chen, Y. Dong, L. Lv, M. Whiteside and G. DeBrosse. 2017. Superior triploid eastern oysters produced by selecting tetraploids. Accepted by 109th Annual Meeting of National Shellfisheries Association, March 26-30, 2017, Knoxville, TN, USA.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Shellfish farmers, shellfish biologists, shellfish breeders, geneticists, educators and students Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project provided training and career opportunties for two graduate students, one postdoctoral researcher, two undergraduate students and three visiting scientists. How have the results been disseminated to communities of interest?Results have been disseminated to interested communities through publications, conference presentationsand invited talks. What do you plan to do during the next reporting period to accomplish the goals?We have experimental oysters deployed in the field for evaluation. They include diploid oysters produced by marker-assisted selection, triploid oysters produced by different tetraploids, and tetraploid oysters. We will evaluate their growth and survival to market size.

Impacts
What was accomplished under these goals? We identified additional genetic markers for disease resistance and used them for marker-assisted selection in the eastern oyster. Seven groups were produced by marker-assisted selection, based parental genotypes at five disease-resistant loci. The seven groups were produced in summer 2017 and deployed in the field for evaluation. We have provided improved oyster broodstock for commercial production. We discovered a novel variant of alternative oxidase gene in the eastern oyster that is created by alternative splicing of a duplicate exon. The new variant is preferentially expressed when oysters are under stress and likely adaptive to stressful conditions. This finding provides insight into how exon duplicate and alternative splicing together contribute to genome complexity and stress adaptation. We worked in collaboration with colleagues in the sequencing of the pearl oyster, Yesso scallop and Chinese scallop. The sequencing of the three bivalve genomes provided insight into bivalve biology and evolution. In the pearl oysters, analyses identified key elements of both chitin and collagen-based matrix for biomineralization, suggesting that these two basic types of matrix may have a common evolutionary origin. The Yesso scallop genome shows remarkable conservation of the ancestral bilaterian linkage groups, indicating that the scallop karyotype is highly conserved. Analyses of the Chinese scallop genome revealed molecular adaptations to semi-sessile life and neurotoxins. We also conducted phylogenetic studies on oysters from Peru and Myanmar. Taxonomic confusion was clarified for oysters from Peru. A new subspecies was identified from Myanmar.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Li, Y., X. Sun, X. Hu, X. Xun, J. Zhang, X. Guo, W. Jiao, L. Zhang, W. Liu, J. Wang, J. Li, Y. Sun, Y. Miao, X. Zhang, T. Cheng, G. Xu, X. Fu, Y. Wang, X. Yu, X. Huang, W. Lu, J. Lv, C. Mu, D. Wang, X. Li, Y. Xia, Y. Li, Z. Yang, F. Wang, L. Zhang, Q. Xing, H. Dou, X. Ning, J. Dou, Y. Li, D. Kong, Y. Liu, Z. Jiang, R. Li, S. Wang, and Z. Bao. 2017. Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins. Nature Communications, 8:1721.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Yang, H. and X. Guo. 2017. Triploid hard clams Mercenaria mercenaria produced by inhibiting polar body I or polar body II. Aquaculture Research, 49:449-461.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, M. and X. Guo. 2017. A novel and stress adaptive alternative oxidase derived from alternative splicing of duplicated exon in oyster Crassostrea virginica. Scientific Reports, 7:10785.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Du, X., G. Fan, Y. Jiao, H. Zhang, X. Guo, R. Huang, C. Bian, Y. Deng, Q. Wang, Z. Zheng, Z. Wang, X. Liang, H. Liang, C. Shi, X. Zhao, F. Sun, R. Hao, J. Bai, J. Liu, W. Chen, J. Liang, W. Liu, Z. Xu, Q. Shi, X. Xu, G. Zhang & Xin Liu. 2017. The pearl oyster genome and multi-omic analyses provide insights into biomineralization. GigaScience, 6(8):1-12.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, S., J. Zhang, W. Jiao, J. Li, X. Xun, Y. Sun, X. Guo, P. Huan, B. Dong, L. Zhang, X. Hu, X. Sun, J. Wang, C. Zhao, Y. Wang, D. Wang, X. Huang, R. Wang, J. Lv, Y. Li, Z. Zhang, B. Liu, W. Lu, Y. Hui, J. Liang, Z. Zhou, R. Hou, X. Li, Y. Liu, H. Li, X. Ning, Y. Lin, L. Zhao, Q. Xing, J. Dou, Y. Li, J. Mao, H. Guo, H. Dou, T. Li, C. Mu, W. Jiang, Q. Fu, X. Fu, Y. Miao, J. Liu, Q. Yu, R. Li, H. Liao, X. Li, Y. Kong, Z. Jiang, D. Chourrout, R. Li & Z. Bao. 2017. Scallop genome provides insights into evolution of bilaterian karyotype and development. Nature Ecology & Evolution, 1:0120.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Li, C., H. Wang and X. Guo. 2017. Classification and taxonomic revision of two oyster species from Peru: Ostrea megodon (Hanley, 1846) and Crassostrea talonata (Li & Qi, 1994). J. Shellfish Res., 36(2):359364.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Li, C., M. Haws, H. Wang and X. Guo. 2017. Taxonomic classification of three oyster (Ostreidae) species from Myanmar. J. Shellfish Res., 36(2):365-371.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Abdelrahman, H., M. ElHady, A. Alcivar-Warren, S. Allen, R. Al-Tobasei, L. Bao, B. Beck, H. Blackburn, B. Bosworth, J. Buchanan, J. Chappell, W. Daniels, S. Dong, R. Dunham, E. Durland, A. Elaswad, M. Gomez-Chiarri, K. Gosh, X. Guo, P. Hackett, T. Hanson, D. Hedgecock, T. Howard, L. Holland, M. Jackson, Y. Jin, K. Khalil, T. Kocher, T. Leeds, N. Li, L. Lindsey, S. Liu, Z. Liu, K. Martin, R. Novriadi, R. Odin, Y. Palti, E. Peatman, D. Proestou, G. Qin, B. Reading, C. Rexroad, S. Roberts, M. Salem, A. Severin, H. Shi, C. Shoemaker, S. Stiles, S. Tan, K. F. J. Tang, W. Thongda, T. Tiersch, J. Tomasso, W. T. Prabowo, R. Vallejo, H. van der Steen, K. Vo, G. Waldbieser, H. Wang, X. Wang, J. Xiang, Y. Yang, R. Yant, Z. Yuan, Q. Zeng & T. Zhou. 2017. Aquaculture genomics, genetics and breeding in the united states: Current status, challenges, and priorities for future research. BMC Genomics, 18:191.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bidegain, G., E.N. Powell, J.M. Klinck, E.E. Hofmann, T. Ben-Horin, D. Bushek, S.E. Ford, D.M. Munroe and X. Guo. 2017. Modeling the transmission of Perkinsus marinus in the Eastern oyster Crassostrea virginica. Fisheries Research, 186:82-93.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Guo, X., G. Wang, C.D. Castillo, E.P. Espinosa, A. Tanguy, J. Kraeuter and B. Allam. 2016. Identification of QPX-resistance markers by genome-wide candidate-gene association study in the hard clam. Presented at Aquaculture 2016, February 22  26, 2016, Las Vegas, USA.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Riviere, G., Y. He, S. Tecchio, E. Crowell, M. Gras, P. Sourdaine, X. Guo and P. Favrel. 2017. Dynamics of DNA methylomes underlie oyster development and support a new model of transcription regulation by DNA methylation in an invertebrate. PLOS Genetics, 13(6): e1006807.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Shellfish farmers,shellfish biologists,shellfish breeders, geneticists, educators and students. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training and professional development opportunities were provided to two graduate students, one postdoctoral researcher and four visiting scientists. How have the results been disseminated to communities of interest?Results have been disseminated to interested communities through publications, conference presentations and the oyster grower forum. What do you plan to do during the next reporting period to accomplish the goals?We will continue marker-assisted selection of disease-resistantoysters and evaluate them in the field. We will produce the next generation oftetraploids by selecting the best-performing and most-stable ones, and evaluate their performance and the performance of their triploid progeny. We plan to makethese improved oyster stocks available to the oyster farming community.

Impacts
What was accomplished under these goals? To identify candidate disease-resistant markers, we assembled a set of 1002 candidate genes of the eastern oyster that are involved in immune and stress responses based on gene function and transcriptome profile. We sequenced them in before- and after-mortality samples to identify single-nucleotide polymorphisms (SNPs) that consistently shifted allele frequencies. SNPs in 21 genes showed significant (>20%) frequency shift in all three populations, suggesting they are likely associated with disease resistance. They include some well-known immune response genes encoding c-type lectins, tissue necrosis factor receptor-associated factor and interferon induced protein, as well as proteins whose involvement in immune response is less clear such as epidermal growth factor, G-protein coupled receptor, hemicentin, L-ascorbate oxidase and glutamate decarboxylase. These genes and markers provide good candidates for further studies and marker-assisted selection. We obtained grant support from the USDA NIFAAquaculture Research Program to work on the improvement of tetraploids and their triploid progeny.To determine if triploid eastern oysterscan be improved by selecting tetraploids, we produced two classes of triploids by crossing the same diploid females with the largest (L) or smallest (S) tetraploid males from the same cohort.At 6-month post-fertilization and in both experiments, L-triploids were significantly (p<0.001) larger than S-triploids, and both triploids were significantly (p<0.001) larger than diploids. In Experiment 1 where the largest and smallest 10% tetraploids were used, L-triploids were 79% heavier than S-triploids, which in turn were 50% heavier than diploids. In Experiment 2 where the largest and smallest 20% tetraploids were used, L-triploids were 21% heavier than S-triploids, and the latter were 54% heavier than diploids. These results show that despite genome instability tetraploids have a large influence on the performance of their triploid progeny, and superior triploids can be produced by selecting and using the best-performing tetraploids.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Guo, X. and S.E. Ford. 2016. Infectious diseases of marine molluscs and host responses as revealed by genomic tools. Phil. Trans. R. Soc. Lond. B, 371: 20150206. http://dx.doi.org/10.1098/rstb.2015.0206
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Proestoua, D.A., B.T. Vinyard, R.J. Corbett, J. Piesz, S.K. Allen Jr., J.M. Small, C. Li, M. Liu, G. DeBrosse, X. Guo, P. Rawson and M. G�mez-Chiarri. 2016. Performance of selectively-bred lines of eastern oyster, Crassostrea virginica, across eastern US estuaries. Aquaculture, 464:17-27. http://dx.doi.org/10.1016/j.aquaculture.2016.06.012
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ren, J., Z. Hou, H. Wang, M. Sun, X. Liu, B. Liu and X. Guo. 2016. Intraspecific variation in mitogenomes of five Crassostrea species provides insight into oyster diversification and speciation. Marine Biotechnology, 18(2):242-254. http://dx.doi.org/10.1007/s10126-016-9686-8
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Rawson, P., S. Lindell, X. Guo and I. Sunila. 2015. Disease-resistance and improved performance for genetically improved and crossbred eastern oysters, Crassostrea virginica: results from a decade of field trials in New England. J. Shellfish Res., 34(2):718-719.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Liu, M., C. Li, G. Wang and X. Guo. 2016. Identification of disease-resistance markers by next-generation sequencing in the eastern oyster. Presented at Aquaculture 2016, February 22  26, 2016, Las Vegas, USA.


Progress 10/02/14 to 09/30/15

Outputs
Target Audience:Geneticists, shellfish biologists, shellfish breeders, oyster farmers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunity is provided to a postdoctoral associate, two graduate students and two undergraduate students. How have the results been disseminated to communities of interest?Results of this project has been published in peer-reviewed journals and presented in the annual meeting of theNational Shellfish Association. What do you plan to do during the next reporting period to accomplish the goals?For the identification of disease-resistance markers, we will select candidate immune-related genes and test if variation in these genes are associated with disease resistance in oysters. We will produce a set of tetraploid families and their triploid sib-families to identifytetraploid families that are stable and produce best-performing triploids.

Impacts
What was accomplished under these goals? The eastern oyster is a fishery and aquaculture species in the United States. It has been under the threat of two major diseases. Rutgers University has been breeding oysters for disease resistance since 1960. Rutgers strains have demonstrated strong resistance to one of the diseases, but not to the other. The development of dual-resistance has been slow and the use of marker-assisted selection may greatly increase selection efficiency. One of the goals of this project is to identify markers for disease resistance and use it for marker-assisted selection. The identification of disease-resistance markers can benefit from a better understanding of the immune system of oysters. We analyzed and reviewed transcriptome datasets to improve our understanding of oyster's immune related genes and pathways. Our analyses show that oysters have a sophisticated immune system that is equipped with alarge number of genes. Many immune related genes are expanded and highly diverse. The great paralogous and allelic diversity of immune response genes may be essential for oyster's defense against diverse pathogens in the absence of adaptive immunity. Triploid oysters have three sets of chromosomes instead of two sets found in normal diploids. Triploid oysters are ideal for aquaculture because of their sterility, fast growth and improved meat quality in summer. Triploids are produced by mating normal diploids and tetraploids with four sets of chromosomes. However, the tetraploid genome is unstable. Tetraploid oysters may lose chromosomes and affect the quality of triploids they produce. The project aims to produce stable tetraploids that can produce superior triploids for aquaculture. We obtained a research grant from USDA NIFA aquaculture program for genetic improvement of tetraploid oysters. In summer of 2015, we produced a new generation of tetraploid oysters that will serve as the base population for making and selecting best-performing tetraploid families.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guo, X., Y. He, L. Zhang, C. Lelong and A. Jouaux. 2015. Immune and stress responses in oysters with insights on adaptation. Fish & Shellfish Immunology, 46:107-119.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: He, Y., A. Jouaux, S.E. Ford, C. Lelong, P. Sourdaine, M. Mathieu and X. Guo. 2015. Transcriptome analysis reveals strong and complex antiviral response in a mollusc. Fish & Shellfish Immunology, 46:131-144.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: G�mez-Chiarri, M., W.C. Warren, X. Guo and D. Proestou. 2015. Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica. Fish & Shellfish Immunology, 46:2-4.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Yang, H., Y. Wang, X. Guo and T.R. Tiersch. 2015. Production of inbred larvae through self-fertilization using oocytes and cryopreserved sperm from the same individuals after sex reversal in eastern oyster Crassostrea virginica. Aquaculture Research, 46:2153-2165.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Guo, X. 2015. Resilience of the oyster seen through its genome. J. Shellfish Res., 34(2):637-638.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Li, C. and X. Guo. 2015. Transcriptome analysis of the response to air exposure and cold stress by the eastern oyster. J. Shellfish Res., 34(2):652-653.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Liu, M., S.E. Ford, D. Bushek and X. Guo. 2015. Genetic variation in eastern oysters susceptibility to Perkinsus marinus. J. Shellfish Res., 34(2):654-654.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: G�mez-Chiarri, M., X. Guo, A. Tanguy, Y. He and D. Proestou. 2015. The use of -omic tools in the study of disease processes in marine bivalve mollusks. Journal of Invertebrate Pathology, 131:137-154.