Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Discovery and genomic characterization of a novel hepadnavirus from asymptomatic anadromous alewife (Alosa pseudoharengus) - (Peer Reviewed Journal)
Raines, C.D., Iwanowicz, L.R., Lovy, J., Phelps, N., Mor, S., Ng, T. 2024. Discovery and genomic characterization of a novel metahepadnavirus from clinically normal anadromous alewives (Alosa pseudoharengus). Viruses. 16(6), 824. https://doi.org/10.3390/v16060824.

Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two aquaculture rainbow trout strains confirms oligogenic architecture with several moderate effect quantitative trait loci - (Peer Reviewed Journal)
Palti, Y., Vallejo, R.L., Purcell, M., Gao, G., Shewbridge, K., Long, R., Setzke, C., Fragomeni, B., Cheng, H., Martin, K., Naish, K. 2024. Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two aquaculture rainbow trout strains confirms oligogenic architecture with several moderate effect quantitative trait loci. Frontiers in Genetics. 15:1394656. https://doi.org/10.3389/fgene.2024.1394656.

Genetic architecture and accuracy of predicted genomic breeding values for sea lice resistance in the St John River aquaculture strain of North American Atlantic salmon - (Peer Reviewed Journal)
Vallejo, R.L., Pietrak, M.R., Milligan, M.T., Gao, G., Tsuruta, S., Fragomeni, B.O., Long, R., Peterson, B.C., Palti, Y. 2024. Genetic architecture and accuracy of predicted genomic breeding values for sea lice resistance in the St John River aquaculture strain of North American Atlantic salmon. Aquaculture. 586:740819. https://doi.org/10.1016/j.aquaculture.2024.740819.

Immunomodulation in adult largemouth bass (Micropterus salmoides) exposed to a model estrogen or mixture of endocrine disrupting contaminants during early gonadal recrudescence - (Peer Reviewed Journal)
Leet, J.K., Richter, C.A., Claunch, R.A., Gale, R.W., Tilitt, D.E., Iwanowicz, L.R. 2024. Immunomodulation in adult largemouth bass (Micropterus salmoides) exposed to a model estrogen or mixture of endocrine disrupting contaminants during early gonadal recrudescence. Comparative Immunology Reports. 6 (2024) 200140. https://doi.org/10.1016/j.cirep.2024.200140.

Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago - (Database / Dataset)
Blake, L., Phillips-Savage, C., Sota, E., Oura, C., Brown-Jordan, A., Raines, Buck, C., Iwanowicz, L.R. 2024. Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago. Microbiology Resource Announcements. https://doi.org/10.1128/mra.00999-23.

Maternal Dietary Choline Levels Cause Transcriptome Shift Due to Genotype-by-Diet Interactions in Rainbow Trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Freij, K., Cleveland, B.M., Biga, P. 2024. Maternal Dietary Choline Levels Cause Transcriptome Shift Due to Genotype-by-Diet Interactions in Rainbow Trout (Oncorhynchus mykiss). Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics. 101193. https://doi.org/10.1016/j.cbd.2024.101193.

De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Narum, S., Thorgaard, G., Palti, Y. 2024. De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference. International Conference on Integrative Salmonid Biology. 0311:0314.

Haplotype association analyses to inform future fine-mapping of IHNV resistant QTLs - (Abstract Only)
Setzke, C., Palti, Y., Vallejo, R.L., Purcell, M., Gao, G., Liu, S., Martin, K., Naish, K. 2024. Haplotype association analyses to inform future fine-mapping of IHNV resistant QTLs. International Conference on Integrative Salmonid Biology. 0311:0314.

Genotype imputation from low-coverage whole-genome sequencing data in rainbow trout - (Abstract Only)
Liu, S., Martin, K.E., Long, R., Leeds, T.D., Vallejo, R.L., Wiens, G.D., Palti, Y. 2024. Genotype imputation from low-coverage whole-genome sequencing data in rainbow trout. Annual International Plant & Animal Genome Conference. PO0433.

De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference - (Abstract Only)
Gao, G., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Narum, S., Gary, T., Palti, Y. 2024. De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference. Annual International Plant & Animal Genome Conference. 0112:0117.

AquaMine Genomic Data Mining Warehouse and Genome Browsers for Species of Importance to US Aquaculture and Fisheries - (Abstract Only)
Konvalina, J.D., Walsh, A.T., Tripathi, V., Gao, G., Roberts, S.B., Palti, Y., Elsik, C.T. 2024. AquaMine Genomic Data Mining Warehouse and Genome Browsers for Species of Importance to US Aquaculture and Fisheries. Annual International Plant & Animal Genome Conference. 0112:0117.

RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout - (Peer Reviewed Journal)
Ahmed, R.O., Ali, A., Leeds, T.D., Salem, M. 2023. RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout. BMC Genomics. 24:579. https://doi.org/10.1186/s12864-023-09688-5.

Control of Sexual Differentiation: Applications in Aquaculture - (Book / Chapter)
Weber, G.M. 2023. Control of Sexual Differentiation: Applications in Aquaculture. Encyclopedia of Fish Physiology, From Genome to Environment. B9780323908016000690. https://doi.org/10.1016/B978-0-323-90801-6.00069-0.

Effects of IGF1 on in vitro ovarian follicle maturation in rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Weber, G.M. 2023. Effects of IGF1 on in vitro ovarian follicle maturation in rainbow trout (Oncorhynchus mykiss). Fishes. 8(7), 367. https://doi.org/10.3390/fishes8070367.

The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St John River aquaculture strain of North American Atlantic salmon - (Peer Reviewed Journal)
Gao, G., Waldbieser, G.C., Ramey, Y.C., Zaho, D., Pietrak, M.R., Stannard, J.A., Buchman, J.T., Scheffler, B.E., Peterson, B.C., Palti, Y., Rexroad III, C.E., Long, R., Burr, G.S., Milligan, M.T. 2023. The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St John River aquaculture strain of North American Atlantic salmon. G3, Genes/Genomes/Genetics. jkad138. https://doi.org/10.1093/g3journal/jkad138.

Growth, fillet yield, and muscle quality traits are not affected by a genotype by environment interaction in rainbow trout consuming diets that differ in lipid content - (Peer Reviewed Journal)
Cleveland, B.M., Radler, L.M., Leeds, T.D. 2023. Growth, fillet yield, and muscle quality traits are not affected by a genotype by environment interaction in rainbow trout consuming diets that differ in lipid content. Journal of the World Aquaculture Society. 1-15. https://doi.org/10.1111/jwas.12979.

Effects of fertilizing eggs from a summer-spawning line with cryopreserved milt from a winter-spawning line on spawning date and egg production traits in rainbow trout - (Peer Reviewed Journal)
Weber, G.M., Martin, K.E., Palti, Y., Liu, S., Beach, J.N., Birkett, J.E. 2023. Effects of fertilizing eggs from a summer-spawning line with cryopreserved milt from a winter-spawning line on spawning date and egg production traits in rainbow trout. Aquaculture Reports. 29(101495). https://doi.org/10.1016/j.aqrep.2023.101495.

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 - (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.

Spawning date of rainbow trout produced by fertilizing eggs from a summer-spawning line with cryopreserved milt from a winter-spawning line - (Abstract Only)
Weber, G.M., Martin, K.E., Palti, Y., Liu, S., Beach, J.N., Birkett, J.E. 2023. Spawning date of rainbow trout produced by fertilizing eggs from a summer-spawning line with cryopreserved milt from a winter-spawning line. Aquaculture America Conference. p. 610.

Weighted single-step GWAS identifies genes influencing fillet color in rainbow trout - (Peer Reviewed Journal)
Ahmed, R.O., Ali, A., Al-Tobasei, R., Leeds, T.D., Kenney, B., Salem, M. 2022. Weighted single-step GWAS identifies genes influencing fillet color in rainbow trout. Genes. 13(8),1331. https://doi.org/10.3390/genes13081331.

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)
Vallejo, R.L., Evenhuis, J., Cheng, H., Fragomeni, B.O., Gao, G., Liu, S., Long, R., Shewbridge, K., Silva, R.O., Wiens, G.D., Leeds, T.D., Martin, K.E., Palti, Y. 2022. 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. Aquaculture. 560(738574). https://doi.org/10.1016/j.aquaculture.2022.738574.

Development of a high-density SNP array for rainbow trout genome-wide genotyping - (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 - (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 - (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.

Evidence of Hyperphagia and Fatty Acid Mobilization in Leptin Receptor Deficient Rainbow Trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Mankiewicz, J.L., Picklo, M.J., Idso, J.P., Cleveland, B.M. 2022. Evidence of hyperphagia and fatty acid mobilization in leptin receptor deficient rainbow trout (Oncorhynchus mykiss). Biomolecules EISSN 2218-273X. 12(4):516. https://doi.org/10.3390/biom12040516.

Evidence for a leptin–insulin axis in a fish, the tilapia (Oreochromis mossambicus) - (Peer Reviewed Journal)

Effects of duration and timing of immersion in 17alpha-methyltestosterone on sex reversal of female rainbow trout - (Peer Reviewed Journal)
Weber, G.M., Leeds, T.D. 2022. Effects of duration and timing of immersion in 17alpha-methyltestosterone on sex reversal of female rainbow trout. Aquaculture Reports. 23: 101014. https://doi.org/10.1016/j.aqrep.2022.101014.

Effects of feeding level and sexual maturation on expression of genes regulating growth mechanisms in rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Weber, G.M., Ma, H., Birkett, J.E., Cleveland, B.M. 2022. Effects of feeding level and sexual maturation on expression of genes regulating growth mechanisms in rainbow trout (Oncorhynchus mykiss). Aquaculture. 551: 737917. https://doi.org/10.1016/j.aquaculture.2022.737917.

Maternal transcript profiles associated with egg viability in rainbow trout, Oncorhynchus mykiss, and comparisons among populations - (Abstract Only)

Compensatory Response of the Somatotropic Axis from IGFBP-2b Gene Editing in Rainbow Trout - (Abstract Only)

Characteriztion of a leptin receptor paralog and its response to fasting in rainbow trout(Oncorhynchus mykiss) - (Peer Reviewed Journal)
Mankiewicz, J.L., Cleveland, B.M. 2021. Characteriztion of a leptin receptor paralog and its response to fasting in rainbow trout(Oncorhynchus mykiss). International Journal of Molecular Sciences. 22: 7732. https://doi.org/10.3390/ijms22147732.

The accuracy of genomic predictions for bacterial cold water disease resistance remains higher than the pedigree-based model one generation after model training in a commercial rainbow trout breeding population - (Peer Reviewed Journal)
Vallejo, R.L., Cheng, H., Fragomeni, B.O., Silva, R.O., Martin, K.E., Evenhuis, J., Wiens, G.D., Leeds, T.D., Palti, Y. 2021. The accuracy of genomic predictions for bacterial cold water disease resistance remains higher than the pedigree-based model one generation after model training in a commercial rainbow trout breeding population. Aquaculture. 545:737164. https://doi.org/10.1016/j.aquaculture.2021.737164.

Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability - (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 - (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 - (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 predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels - (Peer Reviewed Journal)
Al-Tobasei, R., Ali, A., Garcia, A.L., Lourenco, D., Leeds, T.D., Salem, M. 2021. Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels. BMC Genomics. 22:92. https://doi.org/10.1186/s12864-021-07404-9.

Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire - (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 - (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.

Molecular mechanisms regulating muscle plasticity in fish - (Review Article)
Koganti, P., Yao, J., Cleveland, B.M. 2020. Molecular mechanisms regulating muscle plasticity in fish. Animals. 11(1):61. https://doi.org/10.3390/ani11010061.

Supplemental Microalgal DHA and Astaxanthin Affect Astaxanthin Metabolism and Redox Status of Juvenile Rainbow Trout - (Peer Reviewed Journal)
Wu, K., Portman, M., Sealey, W., Cleveland, B.M., Lei, X. 2020. Supplemental microalgal DHA and astaxanthin affect astaxanthin metabolism and redox status of juvenile rainbow trout. Antioxidants. 10(1):16. https://doi.org/10.3390/antiox10010016.

Replacing fish oil and astaxanthin by microalgal sources produced different metabolic responses in juvenile rainbow trout fed 2 types of practical diets - (Peer Reviewed Journal)
Zhu, S., Portman, M., Cleveland, B.M., Magnuson, A.D., Wu, K., Sealey, W., Lei, X. 2020. Replacing fish oil and astaxanthin by microalgal sources produced different metabolic responses in juvenile rainbow trout fed 2 types of practical diets. Journal of Animal Science. 99(1):1-14. https://doi.org/10.1093/jas/skaa403.

Compensatory response of the somatotropic axis from IGFBP-2b gene editing in rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Cleveland, B.M., Shiori, H., Jin, O., Radler, L.M., Munetaka, S. 2020. Compensatory response of the somatotropic axis from IGFBP-2b gene editing in rainbow trout (Oncorhynchus mykiss). Genes. 11, 1488. https://doi.org/10.3390/genes11121488.

Oxidative stress-related gene expression in diploid and triploid Rainbow Trout (Oncorhynchus mykiss) fed diets with organic and inorganic zinc - (Peer Reviewed Journal)
Meiler, K., Cleveland, B.M., Radler, L.M., Kumar, V. 2020. Oxidative stress-related gene expression in diploid and triploid Rainbow Trout (Oncorhynchus mykiss) fed diets with organic and inorganic zinc. Aquaculture. 533: 736149. https://doi.org/10.1016/j.aquaculture.2020.736149.

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 - (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.

Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Chapagain, P., Walker, D., Leeds, T.D., Cleveland, B.M., Salem, M. 2020. Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss). Biomed Central (BMC) Genomics. 20:788. https://doi.org/10.1186/s12864-019-6175-2.

Hepatic fatty acid and transcriptome profiles during the transition from vegetable- to fish oil-based diets in rainbow trout (Oncorhynchus mykiss) - (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.