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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » People & Locations » Guangtu Gao
Guangtu Gao
Cool and Cold Water Aquaculture Research
Computational Biologist

Phone: (304) 724-8340 ext. 2143
Fax: (304) 725-0351

USDA,REE,ARS,NEA,NCCCWA
11861 LEETOWN ROAD
KEARNEYSVILLE, WV 25430

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

Projects
Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout
In-House Appropriated (D)
  Accession Number: 437699
High-quality Reference Assembly And Annotation Of The Rainbow Trout Genome
Reimbursable Cooperative Agreement (R)
  Accession Number: 438288

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genomic selection models substantially improve the accuracy of genetic merit predictions for fillet yield and body weight in rainbow trout using a multi-trait model and multi-generation progeny testing Reprint Icon - (Peer Reviewed Journal)
L. S. Garcia, A., Tsuruta, S., Gao, G., Palti, Y., Lourenco, T., Leeds, T.D. Genomic selection models substantially improve the accuracy of genetic merit predictions for fillet yield and body weight in rainbow trout using a multi-trait model and multi-generation progeny testing. Genetics Selection Evolution. 55:11 (2013). https://doi.org/10.1186/s12711-023-00782-6.
Genome-wide mapping of quantitative trait loci that can be used in marker-assisted selection for resistance to bacterial cold water disease in two commercial rainbow trout breeding populations - (Peer Reviewed Journal)
Development of a high-density SNP array for rainbow trout genome-wide genotyping Reprint Icon - (Peer Reviewed Journal)
Bernard, M., Dehaullon, A., Gao, G., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Palti, Y., Lallias, D., Phocas, F. 2022. Development of a high-density SNP array for rainbow trout genome-wide genotyping. Frontiers in Genetics. 13:941340. https://doi.org/10.3389/fgene.2022.941340.
Identification of haplotypes associated with resistance to bacterial cold water disease in rainbow trout using whole-genome resequencing Reprint Icon - (Peer Reviewed Journal)
Liu, S., Martin, K.E., Gao, G., Long, R., Evenhuis, J., Leeds, T.D., Wiens, G.D., Palti, Y. 2022. Identification of haplotypes associated with resistance to bacterial cold water disease in rainbow trout using whole-genome resequencing. Frontiers in Genetics. 13:936806. https://doi.org/10.3389/fgene.2022.936806.
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping Reprint Icon - (Pre-print Publication)
Bernard, M., Dehaullon, A., Gao, G., Palti, Y., Phocas, F., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Lallia, D. 2022. Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. bioRxiv. 488574. https://doi.org/10.1101/2022.04.17.488574.
Maternal transcript profiles associated with egg viability in rainbow trout, Oncorhynchus mykiss, and comparisons among populations - (Abstract Only)
Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability Reprint Icon - (Peer Reviewed Journal)
Weber, G.M., Birkett, J.E., Martin, K., Dixon, II, D., Gao, G., Leeds, T.D., Vallejo, R.L., Ma, H. 2021. Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability. Biomed Central (BMC) Genomics. 22. Article 448. https://doi.org/10.1186/s12864-021-07773-1.
A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout Reprint Icon - (Peer Reviewed Journal)
Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Thorgaard, G., Palti, Y. 2021. A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout. Genes, Genomes, and Genomics. https://doi.org/10.1093/g3journal/jkab052.
Identification of high confidence structural variants in domesticated rainbow trout using whole-genome sequencing Reprint Icon - (Peer Reviewed Journal)
Liu, S., Gao, G., Layer, R.M., Thorgaard, G.H., Wiens, G.D., Leeds, T.D., Martin, K.E., Palti, Y. 2021. Identification of high confidence structural variants in domesticated rainbow trout using whole-genome sequencing. Frontiers in Genetics. 12:639355. https://doi.org/10.3389/fgene.2021.639355.
Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire Reprint Icon - (Peer Reviewed Journal)
Magadan, S., Mondot, S., Palti, Y., Gao, G., Lefranc, M., Boudinot, P. 2021. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. Developmental and Comparative Immunology. 118: 103998. https://doi.org/10.1016/j.dci.2021.103998.
A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout Reprint Icon - (Pre-print Publication)
Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Thorgaard, G., Palti, Y. 2021. A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout. bioRxiv. https://doi.org/10.1101/2020.12.28.424581.
Structure and regulation of the NK-lysin (1-4) and NK-lysin like (a and b) antimicrobial genes in rainbow trout (Oncorhynchus mykiss) Reprint Icon - (Peer Reviewed Journal)
Shepherd, B.S., Ma, H., Han, Y., Palti, Y., Gao, G., Liu, S., Wiens, G.D. 2020. Structure and regulation of the NK-lysin (1-4) and NK-lysin like (a and b) antimicrobial genes in rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology. 116 (103961). https://doi.org/10.1016/j.dci.2020.103961.
Assessing accuracy of genomic predictions for resistance to infectious hematopoietic necrosis virus with progeny testing of selection candidates in a commercial rainbow trout breeding population Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Fragomeni, B.O., Cheng, H., Gao, G., Long, R., Shewbridge, K., Macmillan, J.R., Towner, R., Palti, Y. 2020. Assissing accuracy of genomic predictions for resistance to infectious hematopoietic necrosis virus with progeny testing of selection candidates in a commercial rainbow trout breeding population. Frontiers in Veterinary Science. 7:590048. https://doi.org/10.3389/fvets.2020.590048.
Hepatic fatty acid and transcriptome profiles during the transition from vegetable- to fish oil-based diets in rainbow trout (Oncorhynchus mykiss) Reprint Icon - (Peer Reviewed Journal)
Cleveland, B.M., Gao, G., Radler, L.M., Picklo, M.J. 2020. Hepatic fatty acid and transcriptome profiles during the transition from vegetable- to fish oil-based diets in rainbow trout (Oncorhynchus mykiss). Lipids. https://doi.org/10.1002/lipd.12287.
Transcriptomic response to selective breeding for fast growth in rainbow trout (Oncorhynchus mykiss) Reprint Icon - (Peer Reviewed Journal)
Cleveland, B.M., Gao, G., Leeds, T.D. 2020. Transcriptomic response to selective breeding for fast growth in rainbow trout (Oncorhynchus mykiss). Marine Biotechnology. https://doi.org/10.1007/s10126-020-09974-3.
A new single nucleotide polymorphism database for North American Atlantic salmon generated through whole genome re-sequencing Reprint Icon - (Peer Reviewed Journal)
Gao, G., Pietrak, M.R., Burr, G.S., Rexroad III, C.E., Peterson, B.C., Palti, Y. 2020. A new single nucleotide polymorphism database for North American Atlantic salmon generated through whole genome re-sequencing. Frontiers in Genetics. 11:85. https://doi.org/10.3389/fgene.2020.00085.
A long reads-based De-novo assembly of the rainbow trout Arlee-line genome - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. 2020. A long reads-based De-novo assembly of the rainbow trout Arlee-line genome. In Proceedings of the Plant and Animal Genome Conference. International Plan and Animal Genome Conference,January 11, 2020, San Diego, CA. P.No.PE0432.
A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R.C., Pietrak, M.R., Scheffler, B.E., Rexroad III, C.E., Peterson, B.C., Palti, Y. 2020. A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome. Plant and Animal Genome Conference. 28th International Plant and Animal Genome Conference held in San Diego, CA, January 11, 2020. P.No.PO0425.
Identification of additional single nucleotide polymorphisms associated with resistance to bacterial cold water disease in rainbow trout using whole genome resequencing - (Abstract Only)
Liu, S., Gao, G., Long, R., Evenhuis, J., Wiens, G.D., Martin, K.E., Palti, Y. 2020. Identification of additional single nucleotide polymorphisms associated with resistance to bacterial cold water disease in rainbow trout using whole genome resequencing. Plant and Animal Genome Conference. P.NO.W065.
Heritability estimates and genome-wide association analysis of egg quality traits in commercial rainbow trout breeding populations - (Abstract Only)
Palti, Y., Vallejo, R.L., Gao, G., Long, R., Shewbridge, K., Leeds, T.D., Martin, K. 2020. Heritability estimates and genome-wide association analysis of egg quality traits in commercial rainbow trout breeding populations. Plant and Animal Genome Conference. 28th International Plant and Animal Genome Conference held in San Diego, CA, January 11, 2020. P.No.PO0433
A long reads-based De-novo assembly of the rainbow trout Arlee-line genome - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. 2019. A long reads-based De-novo assembly of the rainbow trout Arlee-line genome. International Conference on Integrative Salmonid Biology. In: Proceedings of International Conference on Integrative Salmonid Biology,November 17,2019, Edinburgh, Scotland, UK. P.No.ORAL-1.4
A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R.C., Pietrak, M.R., Scheffler, B.E., Rexroad Iii, C.E., Peterson, B.C., Palti, Y. 2019. A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome. In:Proceedings of International Conference on Integrative Salmonid Biology. Fourth International Conference on Integrative Salmonid Biology, November 17, 2019, Edinburgh, Scotland, UK. P.No.Poster - 1
Improving the functional annotation of the rainbow trout genome. - (Abstract Only)
Palti, Y., Gao, G., Zhou, H., Salem, M. 2019. Improving the functional annotation of the rainbow trout genome. In Proceedings of the International Conference on Integrative Salmonid Biology. Fourth International Conference on Integrative Salmonid Biology, November 17, 2019, Edinburgh, Scotland,UK. P.No.Poster - 18.
Sex-dependent dominance maintains migration supergene in rainbow trout Reprint Icon - (Peer Reviewed Journal)
Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadia-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Matthew, K., Minkley, D.R., Rondeau, E.B., Brieuc, M.S., Sandye, S., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology and Evolution. 3:1731–1742. https://doi.org/10.1038/s41559-019-1044-6.
Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Cheng, H., Fragomeni, B.O., Shewbridge, K., Gao, G., Macmillan, J.R., Towner, R., Palti, Y. 2019. Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population pserial online]. Genetic Selection Evolution. 51:47. https://doi.org/10.1186/s12711-019-0489-z.
Genomic regions associated with Columnaris disease in two rainbow trout breeding populations Reprint Icon - (Peer Reviewed Journal)
Silva, R., Evenhuis, J., Vallejo, R.L., Gao, G., Martin, K., Leeds, T.D., Lourenco, D., Palti, Y. 2019. Genomic regions associated with Columnaris disease in two rainbow trout breeding populations. Genetics Selection Evolution. 51:42. https://doi.org/10.1186/s12711-019-0484-4.
Sex-dependent dominance maintains migration supergene in rainbow trout Reprint Icon - (Trade Journal)
Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadia-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Kent, M., Minkley, D.R., Rondeau, E.B., Brieuc, M.O., Sandve, S., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout [serial online]. bioRxiv. https://doi.org/10.1101/504621.
Genome-wide mapping of quantitative trait loci and accuracy of genomic selection for resistance to infectious hematopoietic necrosis virus in rainbow trout using multiple regression single-step methods - (Abstract Only)
Vallejo, R.L., Cheng, H., Fragomeni, B.O., Shewbridge, K., Gao, G., Macmillan, J.R., Towner, R., Palti, Y. 2019. Genome-wide mapping of quantitative trait loci and accuracy of genomic selection for resistance to infectious hematopoietic necrosis virus in rainbow trout using multiple regression single-step methods [abstract]. Gordon Research Conferences. P29107.
Whole genome resequencing refines genomic regions associated with bacterial cold water disease resistance in rainbow trout - (Abstract Only)
Liu, S., Gao, G., Wiens, G.D., Palti, Y. 2019. Whole genome resequencing refines genomic regions associated with bacterial cold water disease resistance in rainbow trout. [abstract]. Plant and Animal Genome Conference. p. PE0262.
Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population - (Abstract Only)
Palti, Y., Vallejo, R.L., Cheng, H., Fragomeni, B., Gao, G., Macmillan, R., Towner, R. 2019. Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population [abstract]. Plant and Animal Genome Conference. P1-298.
Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout Reprint Icon - (Peer Reviewed Journal)
Salem, M., Al-Tobasei, R., Ali, A., Lourenco, D., Gao, G., Palti, Y., Kenney, B., Leeds, T.D. 2018. Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout. Frontiers in Genetics [serial online]. 9:387. doi:10.3389/fgene.2018.00387.
Evaluation of marker-assisted selection for resistance to bacterial cold water disease in three generations of a commercial rainbow trout breeding population Reprint Icon - (Peer Reviewed Journal)
Liu, S., Vallejo, R.L., Evenhuis, J., Martin, K.E., Hamilton, A., Gao, G., Leeds, T.D., Wiens, G.D., Palti, Y. 2018. Evaluation of marker-assisted selection for resistance to bacterial cold water disease in three generations of a commercial rainbow trout breeding population [serial online]. Frontiers in Genetics. 9:286. https://doi.org/10.3389/fgene.2018.00286.
Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China Reprint Icon - (Trade Journal)
Zhao, Z., Xu, J., Bai, Q., Yang, S., Jiang, L., Chen, B., Palti, Y., Gao, G., Xu, P. 2018. Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China. Journal of Fishery Sciences of China (JFSC). 25(3):485-493.
Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss) Reprint Icon - (Peer Reviewed Journal)
Shaw, C.H., Gao, G., Wiens, G.D. 2018. Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology. 87:193-203. https://doi.org/10.1016/j.dci.2018.06.003.
Lessons from the application of genomic selection to rainbow trout aquaculture - (Abstract Only)
Palti, Y., Vallejo, R.L., Evenhuis, J., Silva, R., Liu, S., Gao, G., Martin, K., Lourenco, D., Wiens, G.D., Leeds, T.D. 2018. Lessons from the application of genomic selection to rainbow trout aquaculture. International Symposium on Genetics in Aquaculture. 716:02.
Marker-assisted selection for resistance to bacterial cold water disease in a commercial rainbow trout breeding population - (Abstract Only)
Liu, S., Vallejo, R.L., Evenhuis, J., Martin, K.E., Hamilton, A., Gao, G., Leeds, T.D., Wiens, G.D., Palti, Y. 2018. Marker-assisted selection for resistance to bacterial cold water disease in a commercial rainbow trout breeding population [abstract]. International Symposium on Genetics in Aquaculture. P:1330-1345.
Rainbow trout genetic resistance to bacterial cold water disease: Contribution of interleukin-1 receptor-like 1 genes - (Abstract Only)
Shaw, C.H., Gao, G., Wiens, G.D. 2018. Rainbow trout genetic resistance to bacterial cold water disease: Contribution of interleukin-1 receptor-like 1 genes [abstract]. Society of Developmental Comparative Immunology. 14:144.
Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that strong long-range LD is a major contributing factor Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Silva, R.M., Evenhuis, J., Gao, G., Liu, S., Parsons, J.E., Martin, K.E., Wiens, G.D., Lourenco, D.A., Leeds, T.D., Palti, Y. 2018. Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that strong long-range LD is a major contributing factor. Journal of Animal Breeding and Genetics. 135:263–274. https://doi.org/10.1111/jbg.12335.
A new single-nucleotide polymorphism database for rainbow trout generated through whole genome re-sequencing Reprint Icon - (Peer Reviewed Journal)
Gao, G., Nome, T., Pearse, D.E., Moen, T., Naish, K.A., Thorgaard, G.H., Lien, S., Palti, Y. 2018. A new single-nucleotide polymorphism database for rainbow trout generated through whole genome re-sequencing. Frontiers in Genetics. 9:147. https://doi.org/10.3389/fgene.2018.00147.
Use of DAVID algorithms for gene functional classification in a non-model organism, rainbow trout Reprint Icon - (Peer Reviewed Journal)
Ma, H., Gao, G., Weber, G.M. 2018. Use of DAVID algorithms for gene functional classification in a non-model organism, rainbow trout. BMC Research Notes. 11:63. https://doi.org/10.1186/s13104-018-3154-7.
Evaluation of the utility of the new rainbow trout genome assembly for analyzing RNA-seq data from stress response experiments - (Abstract Only)
Gao, G., Weber, G.M., Liu, S., Palti, Y., Rexroad Iii, C.E. 2018. Evaluation of the utility of the new rainbow trout genome assembly for analyzing RNA-seq data from stress response experiments. Plant and Animal Genome Conference. International Plant and Animal Genome XXVI. Paper No. 102.
GWAS for detecting QTL associated with Columnaris Disease in two rainbow trout breeding populations - (Abstract Only)
Silva, R., Evenhuis, J., Vallejo, R.L., Gao, G., Martin, K., Misztal, I., Leeds, T.D., Lorenco, D., Palti, Y. 2018. GWAS for detecting QTL associated with Columnaris Disease in two rainbow trout breeding populations. Plant and Animal Genome Conference. International Plant and Animal Genome XXVI. Paper No. 101.
Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population - (Abstract Only)
Palti, Y., Liu, S., Vallejo, R.L., Martin, K., Evenhuis, J., Gao, G., Wiens, G.D., Leeds, T.D. 2018. Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population. Plant and Animal Genome Conference. International Plant and Animal Genome XXVI. Paper No. 103.
Accurate genomic predictions for bacterial cold water disease resistance using low-density SNP panels in rainbow trout - (Proceedings)
Vallejo, R.L., Silva, R., Evenhuis, J., Gao, G., Liu, S., Parsons, J., Martin, K., Lourenco, D., Leeds, T.D., Palti, Y. 2018. Accurate genomic predictions for bacterial cold water disease resistance using low-density SNP panels in rainbow trout [abstract]. World Congress of Genetics Applied in Livestock Production. Species-Aquaculture 2:334.
Prospecting genomic regions associated with columnaris disease in two rainbow trout breeding populations - (Proceedings)
Silva, R., Evenhuis, J., Vallejo, R.L., Gao, G., Martin, K., Leeds, T.D., Lourenco, D., Palti, Y. 2018. Prospecting genomic regions associated with columnaris disease in two rainbow trout breeding populations [abstract]. World Congress of Genetics Applied in Livestock Production. GP2.
Similar genetic architecture with shared and unique quantitative trait loci for bacterial cold water disease resistance in two rainbow trout breeding populations Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Liu, S., Gao, G., Fragomeni, B.O., Hernandez, A.G., Leeds, T.D., Parsons, J.E., Martin, K.E., Evenhuis, J., Welch, T.J., Wiens, G.D., Palti, Y. 2017. Similar genetic architecture with shared and unique quantitative trait loci for bacterial cold water disease resistance in two rainbow trout breeding populations. Frontiers in Genetics. 8:156. https://doi.org/10.3389/fgene.2017.00156.
Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array Reprint Icon - (Peer Reviewed Journal)
Larson, W.A., Palti, Y., Gao, G., Warheit, K.I., Seeb, J.E. 2018. Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array. Canadian Journal of Fisheries and Aquatic Sciences. 75:1160-1168. doi:10.1139/cjfas-2017-0116.
Genome-wide association studies reveal similar genetic architecture with shared and unique QTL for Bacterial Cold Water Disease resistance in two rainbow trout (Oncorhynchus mykiss) breeding populations - (Other)
Vallejo, R.L., Liu, S., Gao, G., Fragomeni, B.O., Hernandez, A.G., Leeds, T.D., Parsons, J.E., Martin, K.E., Evenhuis, J., Welch, T.J., Wiens, G.D., Palti, Y. 2017. Genome-wide association studies reveal similar genetic architecture with shared and unique QTL for Bacterial Cold Water Disease resistance in two rainbow trout (Oncorhynchus mykiss) breeding populations. bioRxiv. doi: 10.1101/163964.
Evolution of three tandem copies of the interleukin-1 receptor-like 1 gene in salmonid fish and their contribution to rainbow trout bacterial cold water disease resistant phenotype - (Abstract Only)
Shaw, C.H., Liu, S., Gao, G., Palti, Y., Wiens, G.D. 2017. Evolution of three tandem copies of the interleukin-1 receptor-like 1 gene in salmonid fish and their contribution to rainbow trout bacterial cold water disease resistant phenotype. Society of Developmental Comparative Immunology. P51.
Genome-enabled selection doubles the accuracy of predicted breeding values for bacterial cold water disease resistance compared to traditional family-based selection in rainbow trout aquaculture - (Proceedings)
Vallejo, R.L., Leeds, T.D., Gao, G., Parsons, J.E., Kyle, M.E., Evenhuis, J., Fragomeni, B.O., Wiens, G.D., Palti, Y. 2017. Genome-enabled selection doubles the accuracy of predicted breeding values for bacterial cold water disease resistance compared to traditional family-based selection in rainbow trout aquaculture. Genetics in Aquaculture Symposium. Proceedings of the 44th U.S.-Japan Aquaculture Panel Symposium:33-43.
Prospecting genomic regions associated with Columnaris disease in two commercially important rainbow trout breeding populations - (Abstract Only)
Silva, R., Vallejo, R.L., Evenhuis, J., Leeds, T.D., Gao, G., Parsons, J., Martin, K., Lourenco, D., Palti, Y. 2017. Prospecting genomic regions associated with Columnaris disease in two commercially important rainbow trout breeding populations [absctract]. American Society of Animal Science Annual Meeting. 95:103.P209.
Evolution of interleukin-1 receptor-like 1 and its role in rainbow trout (Oncorhynchus mykiss) resistance to Flavobacterium psychrophilum - (Abstract Only)
Shaw, C.H., Palti, Y., Gao, G., Wiens, G.D. 2017. Evolution of interleukin-1 receptor-like 1 and its role in rainbow trout (Oncorhynchus mykiss) resistance to Flavobacterium psychrophilum [abstract]. Immunology. 198(1 Supplement). 201.22.
Genome-wide association studies identify 25 genetic loci associated with resistance to Bacterial Cold Water Disease in rainbow trout - (Abstract Only)
Vallejo, R.L., Liu, S., Gao, G., Fragomeni, B.O., Hernandez, A.G., Leeds, T.D., Parsons, J., Martin, K., Evenhuis, J., Welch, T.J., Wiens, G.D., Palti, Y. 2017. Genome-wide association studies identify 25 genetic loci associated with resistance to Bacterial Cold Water Disease in rainbow trout [abstract]. Gordon Research Conferences. P245.
Genomic selection exploits within-family genetic variation for disease resistance in rainbow trout - (Abstract Only)
Evenhuis, J., Leeds, T.D., Palti, Y., Vallejo, R.L., Gao, G., Martin, K., Parsons, J., Wiens, G.D. 2017. Genomic selection exploits within-family genetic variation for disease resistance in rainbow trout [abstract]. Aquaculture America. p. 116.
Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Leeds, T.D., Gao, G., Parsons, J.E., Martin, K.E., Evenhuis, J., Fragomeni, B.O., Wiens, G.D., Palti, Y. 2017. Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genetics Selection Evolution. 49(17):1-33. doi: 10.1186/s12711-017-0293-6.
Transcriptome response to hormonal manipulation of follicle-enclosed oocytes in rainbow trout - (Abstract Only)
Ma, H., Gao, G., Weber, G.M. 2017. Transcriptome response to hormonal manipulation of follicle-enclosed oocytes in rainbow trout. [abstract] Plant and Animal Genome Conference. P1005.
Genome-wide association analysis of bacterial cold water disease resistance in rainbow trout reveals the potential of a hybrid approach between genomic selection and marker assisted selection - (Abstract Only)
Palti, Y., Vallejo, R.L., Martin, K., Evenhuis, J., Gao, G., Liu, S., Wiens, G.D., Leeds, T.D., Parsons, J. 2017. Genome-wide association analysis of bacterial cold water disease resistance in rainbow trout reveals the potential of a hybrid approach between genomic selection and marker assisted selection [abstract]. Plant and Animal Genome Conference. WO40(P1011).
Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss) Reprint Icon - (Peer Reviewed Journal)
Gonazlez-Pena, D., Gao, G., Baranski, M., Moen, T., Cleveland, B.M., Kenney, B., Vallejo, R.L., Palti, Y., Leeds, T.D. 2016. Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss). Frontiers in Genetics. 7(203):1-14. doi:10.3389/fgen.2016.00203.
A new single-nucleotide polymorphisms database for rainbow trout generated through whole genome resequencing of selected samples - (Abstract Only)
Gao, G., Lien, S., Nome, T., Moen, T., Pearse, D., Thorgaard, G., Palti, Y. 2017. A new single-nucleotide polymorphisms database for rainbow trout generated through whole genome resequencing of selected samples [abstract]. Plant and Animal Genome Conference. P1007.
Identification of mitochondrial genome-encoded small RNAs related to egg deterioration caused by postovulatory aging in rainbow trout Reprint Icon - (Peer Reviewed Journal)
Ma, H., Weber, G.M., Gao, G., Wei, H., Yao, J. 2016. Identification of mitochondrial genome-encoded small RNAs related to egg deterioration caused by postovulatory aging in rainbow trout. Marine Biotechnology. 18(5):584-597. doi:10.1007/s10126-016-9719-3.
Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in Rainbow Trout: Insights on genotyping methods and genomic prediction models - (Peer Reviewed Journal)
Vallejo, R.L., Leeds, T.D., Fragomeni, B.O., Gao, G., Hernandez, A.G., Misztal, I., Welch, T.J., Wiens, G.D., Palti, Y. 2016. Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in Rainbow Trout: Insights on genotyping methods and genomic prediction models. Frontiers in Livestock Genomics. doi: 10.3389/fgene.2016.00096.
A New and Improved Rainbow Trout (Oncorhynchus mykiss) Reference Genome Assembly - (Abstract Only)
Gao, G. 2016. A New and Improved Rainbow Trout (Oncorhynchus mykiss) Reference Genome Assembly. International Conference on Integrative Salmonid Biology. 1: 40.
A new rainbow trout (Oncorhynchus mykiss) reference genome assembly - (Abstract Only)
Gao, G., Lien, S., Baranski, M., Moen, T., Miller, M., Liu, S., Hernandez, A., Thorgaard, G., Kent, M., Palti, Y. 2016. A new rainbow trout (Oncorhynchus mykiss) reference genome assembly [abstract]. Plant and Animal Genome. P0467.
Genome-wide association study for identifying genome loci that affect fillet yield in rainbow trout (Oncorhynchus mykiss) - (Abstract Only)
Gonzalez-Pena, D., Leeds, T.D., Gao, G., Vallejo, R.L., Palti, Y. 2016. Genome-wide association study for identifying genome loci that affect fillet yield in rainbow trout (Oncorhynchus mykiss) [abstract]. Plant and Animal Genome. P075.
Genomic Selection For Bacterial Cold Water Disease Resistance In Rainbow Trout Reveals Large Within-Family Variation That Cannot Be Exploited In Traditional Family-based Selective Breeding - (Abstract Only)
Vallejo, R.L., Leeds, T.D., Martin, K., Evenhuis, J., Gao, G., Wiens, G.D., Parsons, J., Palti, Y. 2016. Genomic Selection For Bacterial Cold Water Disease Resistance In Rainbow Trout Reveals Large Within-Family Variation That Cannot Be Exploited In Traditional Family-based Selective Breeding [abstract]. Plant and Animal Genome. P0470.
Development and validation of a SNP panel for parentage assignment in rainbow trout - (Peer Reviewed Journal)
Liu, S., Palti, Y., Gao, G., Rexroad III, C.E. 2015. Development and validation of a SNP panel for parentage assignment in rainbow trout. Aquaculture. 452:178–182. doi: 10.1016/j.aquaculture.2015.11.001.
Identification of mitochondrial genome-encoded small RNAs related to egg quality deterioration caused by post-ovulatory aging in rainbow trout - (Abstract Only)
Ma, H., Weber, G.M., Gao, G., Wei, H., Yao, J. 2016. Identification of mitochondrial genome-encoded small RNAs related to egg quality deterioration caused by post-ovulatory aging in rainbow trout [abstract]. Aquaculture America Conference. p. 19.
Changes in gene expression during follicle maturation in rainbow trout Oncorhynchus mykiss - (Abstract Only)
Weber, G.M., Ma, H., Hoff De Souza, C.J., Leeds, T.D., Gao, G. 2016. Changes in gene expression during follicle maturation in rainbow trout Oncorhynchus mykiss [abstract]. Aquaculture America Conference. p. 19.
A panel of single nucleotide ploymorphism for parentage assignment in rainbow trout - (Abstract Only)
Liu, S., Palti, Y., Gao, G., Rexroad Iii, C.E. 2016. A panel of single nucleotide ploymorphism for parentage assignment in rainbow trout. Aquaculture America Conference. Paper No. A-345.
Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout - (Peer Reviewed Journal)
Liu, S., Vallejo, R.L., Palti, Y., Gao, G., Marancik, D.P., Hernandez, A.G., Wiens, G.D. 2015. Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout. Frontiers in Genetics. 6:298. doi:10.3389/fgene.2015.00298.
Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing - (Peer Reviewed Journal)
Palti, Y., Vallejo, R.L., Gao, G., Liu, S., Hernandenz, A., Rexroad III, C.E., Wiens, G.D. 2015. Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing. PLoS One. 10(9):e0138435. doi: 10.1371/journal.pone.0138435.
Genomic selection for BCWD resistance in Rainbow trout using RADSNP and SNP genotyping platforms, single-step GBLUP and Bayesian variable selection models - (Abstract Only)
Vallejo, R.L., Leeds, T.D., Liu, S., Gao, G., Welch, T.J., Wiens, G.D., Palti, Y. 2015. Genomic selection for BCWD resistance in Rainbow trout using RADSNP and SNP genotyping platforms, single-step GBLUP and Bayesian variable selection models [abstract]. International Symposium on Genetics in Aquaculture. P05796.
A high density genetic linkage map for rainbow trout (Onchorynchus mykiss) containing 47,839 SNPS - (Abstract Only)
Baranski, M., Palti, Y., Moen, T., Lien, S., Gao, G., Liu, S., Kent, M., Rexroad Iii, C.E. 2015. A high density genetic linkage map for rainbow trout (Onchorynchus mykiss) containing 47,839 SNPS [abstract]. International Symposium on Genetics in Aquaculture. P04263.
Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout - (Abstract Only)
Liu, S., Vallejo, R.L., Palti, Y., Gao, G., Marancik, D.P., Wiens, G.D. 2015. Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout. International Symposium on Genetics in Aquaculture. 624.P403.
Accuracy of genomic prediction for BCWD resistance in rainbow trout using different genotyping platforms and genomic selection models - (Abstract Only)
Vallejo, R.L., Leeds, T.D., Liu, S., Gao, G., Welch, T.J., Wiens, G.D., Palti, Y. 2015. Accuracy of genomic prediction for BCWD resistance in rainbow trout using different genotyping platforms and genomic selection models. Plant and Animal Genome Conference. P726.
Identification of single nucleotide polymorphism markers associated with cortisol response to crowding in Rainbow Trout - (Peer Reviewed Journal)
Liu, S., Vallejo, R.L., Gao, G., Palti, Y., Weber, G.M., Hernandez, A., Rexroad III, C.E. 2015. Identification of single nucleotide polymorphism markers associated with cortisol response to crowding in Rainbow Trout. Marine Biotechnology. DOI: 10.1007\s10126-015-9621-4.
Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum - (Peer Reviewed Journal)
Marancik, D.P., Gao, G., Paneru, B., Ma, H., Hernandez, A.G., Salem, M., Yao, J., Palti, Y., Wiens, G.D. 2015. Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Frontiers in Genetics. 5(243):1-15. DOI:10.3389/fgene.2014.00453.
The development and characterization of a 57K SNP array for Rainbow Trout - (Abstract Only)
Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad Iii, C.E. 2015. The development and characterization of a 57K SNP array for Rainbow Trout. Plant and Animal Genome Conference. P354.
Development of a Fluidigm SNP panel for genetic analysis in rainbow trout - (Abstract Only)
Liu, S., Rexroad Iii, C.E., Gao, G., Palti, Y. 2015. Development of a Fluidigm SNP panel for genetic analysis in rainbow trout. Plant and Animal Genome Conference. P287.
The development and characterization of a 57K SNP array for rainbow trout - (Peer Reviewed Journal)
Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad III, C.E. 2015. The development and characterization of a 57K SNP array for rainbow trout. Molecular Ecology Resources. 15:662-672.
Exploring mechanisms of survival in rainbow trout selectively bred for increased resistance to Flavobacterium psychrophilum - (Abstract Only)
Marancik, D.P., Camus, M.S., Camus, A.C., Leeds, T.D., Gao, G., Wiens, G.D. 2014. Exploring mechanisms of survival in rainbow trout selectively bred for increased resistance to Flavobacterium psychrophilum [abstract]. International Aquatic Animal Health Symposium Proceedings. Paper No. 102.
The development and characterization of a 57K SNP Chip for rainbow trout - (Proceedings)
Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad Iii, C.E. 2014. The development and characterization of a 57K SNP Chip for rainbow trout [abstract]. World Congress of Genetics Applied in Livestock Production. Paper No. 268.
Accuracy of genomic selection for BCWD resistance in rainbow trout - (Proceedings)
Vallejo, R.L., Leeds, T.D., Liu, S., Gao, G., Welch, T.J., Wiens, G.D., Palti, Y. 2014. Accuracy of genomic selection for BCWD resistance in rainbow trout [abstract]. World Congress of Genetics Applied in Livestock Production. Paper No. 788.
RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout - (Peer Reviewed Journal)
Liu, S., Gao, G., Palti, Y., Cleveland, B.M., Weber, G.M., Rexroad III, C.E. 2014. RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout. PLoS One. 9(2). e88492. DOI: 10.1371/journal.pone.0088492.
Use of RADs to identify canidate genes for response to crowding stress in rainbow trout - (Abstract Only)
Rexroad III, C.E., Liu, S., Vallejo, R.L., Gao, G., Palti, Y., Weber, G.M. 2014. Use of RADs to identify canidate genes for response to crowding stress in rainbow trout. Aquaculture America Conference. 168.
Identification of positional candidate genes for response to crowding stress in rainbow trout - (Abstract Only)
Liu, S., Rexroad III, C.E., Vallejo, R.L., Gao, G., Palti, Y., Weber, G.M. 2014. Identification of positional candidate genes for response to crowding stress in rainbow trout. Plant and Animal Genome Conference. 148.
A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids Reprint Icon - (Peer Reviewed Journal)
Palti, Y., Gao, G., Miller, M., Vallejo, R.L., Wheeler, P.A., Quillet, E., Yao, J., Thorgaard, G.H., Salem, M., Rexroad III, C.E. 2014. A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. Molecular Ecology Resources. 14(3):588-596. DOI:10.1111/1755-0998.12204.
Detection of QTL in rainbow trout affecting survival when challenged with Flavobacterium psychrophilum Reprint Icon - (Peer Reviewed Journal)
Vallejo, R.L., Palti, Y., Evenhuis, J., Gao, G., Liu, S., Rexroad III, C.E., Wiens, G.D. 2014. Detection of QTL in rainbow trout affecting survival when challenged with Flavobacterium psychrophilum. Marine Biotechnology. 16(3) 349-360. DOI 10.1007/s10126-013-9553-9.
RNA-seq analysis of stress response in rainbow trout - (Abstract Only)
Liu, S., Gao, G., Palti, Y., Weber, G.M., Rexroad III, C.E. 2013. RNA-seq analysis of stress response in rainbow trout. Annual International Plant & Animal Genome Conference. P0511.
Single nucleotide polymorphism (SNP) discovery in rainbow trout using restriction site associated DNA (RAD) sequencing of doubled haploids and assessment of polymorphism in a population survey - (Abstract Only)
Palti, Y., Gao, G., Miller, M., Vallejo, R.L., Wheeler, P.A., Quillet, E., Yao, J., Thorgaard, G.H., Salem, M., Rexroad III, C.E. 2013. Single nucleotide polymorphism (SNP) discovery in rainbow trout using restriction site associated DNA (RAD) sequencing of doubled haploids and assessment of polymorphism in a population survey. Annual International Plant & Animal Genome Conference. P0507.
Identifying genes affectng stress response in rainbow trout - (Abstract Only)
Rexroad Iii, C.E., Liu, S., Gao, G., Palti, Y., Weber, G.M., Vallejo, R.L. 2013. Identifying genes affectng stress response in rainbow trout. Aquaculture Conference Proceedings. P0182.
Mapping of QTL for bacterial cold water disease resistance in rainbow trout - (Abstract Only)
Palti, Y., Vallejo, R.L., Welch, T.J., Evenhuis, J., Leeds, T.D., Gao, G., Liu, S., Rexroad III, C.E., Wiens, G.D. 2013. Mapping of QTL for bacterial cold water disease resistance in rainbow trout. Aquaculture Conference Proceedings. P0296.
Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout - (Abstract Only)
Rexroad III, C.E., Liu, S., Gao, G., Palti, Y., Weber, G.M., Vallejo, R.L. 2012. Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout [abstract]. p. 185.
Use of RADs and doubled haploids to identify SNPs in rainbow trout - (Abstract Only)
Rexroad III, C.E., Salem, M., Miller, M., Yao, J., Gao, G., Liu, S., Thorgaard, G., Palti, Y. 2012. Use of RADs and doubled haploids to identify SNPs in rainbow trout [abstract]. p. 246.
Mapping of QTL for bacterial cold water disease resistance in rainbow trout - (Abstract Only)
Palti, Y., Vallejo, R.L., Welch, T.J., Leeds, T.D., Evenhuis, J., Gao, G., Liu, S., Rexroad III, C.E., Wiens, G.D. 2012. Mapping of QTL for bacterial cold water disease resistance in rainbow trout [abstract]. International Symposium on Genetics in Aquaculture. p. 354.
Analysis of differential gene expression in response to handling and confinement stress in rainbow trout using whole transcriptome RNA-seq - (Abstract Only)
Liu, S., Gao, G., Castano-Sanchez, C., Palti, Y., Rexroad III, C.E. 2012. Analysis of differential gene expression in response to handling and confinement stress in rainbow trout using whole transcriptome RNA-seq [abstract]. International Symposium on Genetics in Aquaculture. p. 367.
Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors - (Peer Reviewed Journal)
Sanchez, C., Weber, G.M., Gao, G., Cleveland, B.M., Yao, J., Rexroad III, C.E. 2011. Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. Biomed Central (BMC) Genomics. 12:626.
A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of synteny with model fish genomes - (Peer Reviewed Journal)
Palti, Y., Genet, C., Gao, G., Hu, Y., You, F., Boussaha, M., Rexroad III, C.E., Luo, M. 2012. A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of synteny with model fish genomes. Marine Biotechnology. 14:343-357.
Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes - (Peer Reviewed Journal)
Genet, C., Dehais, P., Palti, Y., Gavory, F., Wincker, P., Quillet, E., Boussaha, M., Gao, G. 2011. Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. Biomed Central (BMC) Genomics. 12:314.
A first generation integrated map of the rainbow trout genome - (Peer Reviewed Journal)
Palti, Y., Genet, C., Luo, M., Charlet, A., Gao, G., Hu, Y., Castano-Sanchez, C., Yao, J., Vallejo, R.L., Rexroad III, C.E. 2011. A first generation integrated map of the rainbow trout genome. Biomed Central (BMC) Genomics. 12:180. DOI: 10.1186/1471-2164-12-180.