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 Cool and Cold Water Aquaculture Research: Leetown, WV
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Roger  Vallejo    Computational Biologist /ARSUserFiles/37662/2017 RVallejo-2015-2.jpg  **U.S. Department of Agriculture** **Agricultural Research Service** **National Center for Cool & Cold Water Aquaculture** **11861 Leetown Road** **Kearneysville, WV 25430** **Voice: (304) 724-8340 x2141** **CV-PDF**  **EDUCATION** 1993   Ph.D. Plant Breeding & Genetics  North Carolina State University, Raleigh, NC, USA 1983   M.S. Plant Breeding & Statistics Universidad Nacional Agraria La Molina, Lima, Peru 1981   B.S. Agronomy Universidad Nacional Agraria La Molina, Lima, Peru **** **ACADEMIC & PROFESSIONAL EXPERIENCE** 2005-          Computational Biologist & Geneticist, NCCCWA, ARS-USDA, Kearneysville, WV 2009-2019 Adjunct Professor, Aquaculture Graduate School, Universidad Nacional Agraria La Molina, Lima, PERU 2000-2004  Assist. Professor of Genomics & Bioinformatics, Department of Animal Science, Pennsylvania State University, State College, PA 1997-2000  Senior Research Fellow in Statistical Genetics, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 1995-1997  Research Geneticist, Avian Disease & Oncology Laboratory, ARS-USDA, East Lansing, MI 1993-1994  Postdoctoral Fellow, GCREC, IFAS, University of Florida, Bradenton, FL 1990-1993  Graduate Research Assistant, North Carolina State University, Raleigh, NC 1983-1990  Associate Geneticist, Breeding & Genetics Depart, International Potato Center, Lima, PERU  **ACCOMPLISHMENTS** Performed Genome‐wide association analysis and implemented genome‐enabled selection (GS) for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population, Clear Springs Foods Inc., Buhl, ID, USA, 2019
Designed, performed statistical data analysis and implemented genomic selection (GS) for BCWD resistance using single-step GBLUP and Bayesian multiple regression methods in NCCCWA rainbow trout breeding program, ARS-USDA, Kearneysville, WV, USA, 2016
Designed, performed statistical data analysis and implemented genomic selection (GS) for BCWD resistance using single-step GBLUP and Bayesian multiple regression methods in a commercial rainbow trout breeding program, Troutlodge, Inc., Sumner, WA, USA, 2017
Performed GWAS and quantitative trait loci (QTL) mapping for complex traits in rainbow trout including BCWD, CD, IHNV, IFG and fillet yield using single-step GBLUP and Bayesian multiple regression methods in NCCWA, ARS, USDA, Kearneysville, WV, USA, 2010-2019
Performed population genetic analysis in rainbow trout populations including assessment of the extent and distribution of linkage disequilibrium (LD), genetic diversity, population structure, admixture, genome-wide scans for signatures of selection for BCWD resistance and phylogenomic analysis in NCCWA, ARS, USDA, Kearneysville, WV, USA, 2009-2016
Determined the extent and distribution of linkage disequilibrium in North American Holstein dairy cattle populations and conducted research on the genetics of resistance to clinical mastitis in dairy cattle. Department of Animal Science, Pennsylvania State University, University Park, PA, 2000-2004
Performed mapping of QTL affecting vulnerability to alcoholism and psychiatric disorders comorbid with alcoholism in human populations. Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, USA, 1997-2000
Conducted mapping of QTL affecting susceptibility to Marek’s disease in chicken populations. Avian Disease and Oncology Laboratory, ARS, USDA, East Lansing, MI, USA, 1995-1997
Developed potato populations adapted to tropical and temperate climates with resistance to fungal, bacterial and viral diseases using quantitative genetics and traditional selective breeding methods. Department of Breeding and Genetics, International Potato Center, Lima, PERU, 1983-1990  **SCIENTIFIC & ACADEMIC ACTIVITIES** Associate Editor: *BMC Genetics; Genetics Selection Evolution*
Review Editor: *Frontiers in Genetics*
Ad Hoc Science Journal Reviewer: *Genetics; G3; PLOS One; Heredity; BMC Genomics; Genomics; Journal of Animal Breeding & Genetics; Animal Genetics; Journal of Animal Science; Marine Biotechnology; Aquaculture*
Grant Panel Reviewer: USDA-NRICGP; USDA-NIFA-AFRI
Ad Hoc Grant Reviewer: National Science Foundation; Israel Science Foundation; US-Israel Binational Agric. Res. & Develop.  **PEER REVIEWED PUBLICATIONS (Last 10 years)** **Vallejo, R.L.,** H. Cheng, B.O. Fragomeni, K. Shewbridge, G. Gao, J.R. MacMillan, R. Towner, Y. Palti. 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. *Genetic Selection Evolution* 51:47 Silva, R.M.O, J.P. Evenhuis, **R.L. Vallejo**, G. Gao, K.E. Martin, T.D. Leeds, Y. Palti, D.A.L. Lourenco. 2019. Whole‐genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. *Genetics Selection Evolution (2019 51:42* Silva, R.M.O., J.P. Evenhuis, **R.L. Vallejo**, S. Tsuruta, G.D. Wiens, K.E. Martin, J.E. Parsons, Y. Palti, D.A.L. Lourenco, T.D. Leeds. 2018. Variance and covariance estimates for resistance to bacterial cold water disease and columnaris disease in two rainbow trout breeding populations. *Journal of Animal Science*97(3):1124-1132 **Vallejo RL,**RMO Silva, JP Evenhuis, G Gao, S Liu, JE Parsons, KE Martin, GD Wiens, DAL Lourenco, TD Leeds, Y Palti. 2018. Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor. *J. Animal Breeding & Genetics* 135:263-274 Sixin L, **RL Vallejo**, PE Evenhuis, KE Martin, A Hamilton, G Gao, TD Leeds, GD Wiens, Y Palti. 2018. Retrospective Evaluation of Marker-Assisted Selection for Resistance to Bacterial Cold Water Disease in Three Generations of a Commercial Rainbow Trout Breeding Population. *Frontiers in Genetics*9:286 **Vallejo RL,**TD Leeds, G Gao, JE Parsons, KE Martin, JP Evenhuis, BO Fragomeni, GD Wiens and Y Palti.  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 **Vallejo RL**, S Liu, G Gao, BO Fragomeni, AG Hernandez, TD Leeds, JE Parsons, KE Martin, JP Evenhuis, TJ Welch, GD Wiens, Y Palti. 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 Abdelrahman H, M ElHady, A Alcivar-Warren, T Leeds, Y Palti, C Rexroad, **R Vallejo**, et al.  2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. *BMC Genomics* 18:191 **Vallejo RL**, TD Leeds, BO Fragomeni, G Gao, AG Hernandez, I Misztal, TJ Welch, GD Wiens, Y Palti. 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 Genetics* 7: 96 Leeds TD, **RL Vallejo**, GM Weber, D Gonzalez-Pena, JT Silverstein. 2016. Response to five generations of selection for growth performance traits in rainbow trout (Oncorhynchus mykiss). *Aquaculture*465: 341-351 Gonzalez-Pena D, G Gao, M Baranski, T Moen, BM Cleveland, B Kenney, **RL Vallejo**, Y Palti, TD Leeds. 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 Liu S, **RL Vallejo**, G Gao, Y Palti, G Weber, A Hernandez, CE Rexroad III. 2015. Identification of Single-Nucleotide Polymorphism Markers Associated with Cortisol Response to Crowding in Rainbow Trout. *Marine Biotechnology* 17: 328-337 Palti Y, **RL Vallejo,** G Gao, S Liu, AG Hernandez, CE Rexroad III, GD Wiens. 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 Liu S, **RL Vallejo**, Y Palti, G Gao, DP Marancik, AG Hernandez, GD Wiens. 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 **Vallejo RL,**Y Palti, S Liu, DP Marancik, GD Wiens. 2014. Validation of linked QTL for bacterial cold water disease resistance and spleen size on rainbow trout chromosome Omy19. *Aquaculture* 432: 139-143 **Vallejo RL**, Y Palti, S Liu, JP Evenhuis, G Gao, CE Rexroad III, GD Wiens. 2014. Detection of QTL in Rainbow Trout Affecting Survival When Challenged with *Flavobacterium psychrophilum*. *Marine Biotechnology* 16: 349-360 Palti Y, G Gao, MR Miller, **RL Vallejo**, PA Wheeler, E Quillet, J Yao, GH Thorgaard, M Salem, CE Rexroad III. 2014. A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. *Molec Ecology Resources* 14: 588-596 Rexroad III CE, **RL Vallejo**, S Liu, Y Palti, GM Weber. 2013. Quantitative Trait Loci Affecting Response to Crowding Stress in an F2 Generation of Rainbow Trout Produced Through Phenotypic Selection. *Marine Biotechnology* 15: 613-627 Wiens GD, **RL Vallejo**, TD Leeds, Y Palti, S Hadidi, S Liu, JP Evenhuis, TJ Welch, CE Rexroad III. 2013. Assessment of Genetic Correlation between Bacterial Cold Water Disease Resistance and Spleen Index in a Domesticated Population of Rainbow Trout: Identification of QTL on Chromosome Omy19. *PLoS ONE* 8(10): e75749 Wolters WR, GS Burr, Y Palti, **RL Vallejo**. 2013. Phenotypic and Genetic Variation in Two North American Arctic Charr, *Salvelinus alpinus*, Stocks Cultured in a Recirculating Aquaculture System. *J World Aquaculture Society* 44: 473-485 Rexroad III CE, **RL Vallejo**, S Liu, Y Palti, GM Weber. 2012. QTL affecting stress response to crowding in a rainbow trout broodstock population. *BMC Genetics* 13: 97 Salem M, **RL Vallejo**, TD Leeds, Y Palti, S Liu, A Sabbagh, CE Rexroad III, J Yao. 2012. RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout. *PLoS ONE* 7(5): e36264 Overturf K, **RL Vallejo**, Y Palti, FT Barrows, JE Parsons. 2012. Microarray analysis of differential utilization of plant-based diets by rainbow trout. *Aquaculture Int*. 20: 213–232 Palti Y, C Genet, MC Luo, A Charlet, G Gao, Y Hu, C Castaño-Sánchez, K Tabet-Canale, F Krieg, J Yao, **RL Vallejo**, CE Rexroad III. 2011.  A first generation integrated map of the rainbow trout genome. *BMC Genomics* 12: 180 **Vallejo RL**, GD Wiens, CE Rexroad III, TJ Welch, JP Evenhuis, TD Leeds, LLG Janss, Y Palti. 2010. Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis. *J. Animal Sci*. 88: 3814-3832 Wiens GD, **RL** **Vallejo**. 2010. Temporal and pathogen-load dependent changes in rainbow trout (*Oncorhynchus mykiss*) immune response traits following challenge with biotype 2 *Yersinia ruckeri*.  *Fish & Shellfish Immunology*29: 639-647 Leeds TD, JT Silverstein, GM Weber, **RL Vallejo**, Y Palti, CE Rexroad III, J Evenhuis, S Hadidi, TJ Welch, GD Wiens. 2010. Response to selection for bacterial cold water disease resistance in rainbow trout. *J. Animal Sci.* 88: 1936-1946 **Vallejo RL**, CE Rexroad III, JT Silverstein, LLG Janss, GM Weber. 2009. Evidence of major genes affecting stress response in rainbow trout using Bayesian methods of complex segregation analysis. *J. Animal Sci*. 87: 3490-3505 Rexroad III CE, **RL Vallejo**. 2009. Estimates of Linkage Disequilibrium and Effective Population Size in Rainbow Trout. *BMC Genetics* 10: 83 Sanchez CC, TPL Smith, RT Wiedmann, **RL Vallejo**, M Salem, J Yao, CE Rexroad III. 2009. Single Nucleotide Polymorphism discovery in Rainbow Trout by deep sequencing of a reduced representation library. *BMC Genomics* 10: 559 Palti Y, MC Luo, Y Hu, C Genet, FM You, **RL Vallejo**, GH Thorgaard, PA Wheeler, CE Rexroad III. 2009. A first generation BAC-based physical map of the rainbow trout genome. *BMC Genomics* 10: 462


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