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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » People » Roger Vallejo

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    North Carolina State University, Raleigh, NC  Ph.D. Plant Breeding & Genetics

1983    Universidad Nacional Agraria La Molina, Lima, Peru  M.S. Plant Breeding & Statistics

1981    Universidad Nacional Agraria La Molina, Lima, Peru  B.S. Agronomy

 

RESEARCH INTERESTS

  • Design and Implementation of genome-enabled selection or genomic selection and marker/gene-assisted selection in rainbow trout commercial breeding programs
  • Design and implementation of genome-wide mapping of quantitative trait loci (QTL) for complex traits in admixed rainbow trout breeding populations using Bayesian multiple-regression analysis
  • Genone-wide mapping of candidate causal variants by statistical fine-mapping using Bayesian methods
  • Population genetic studies in salmonids fish including assessment of genetic diversity, population structure, admixture, selection signatures, linkage disequilibrium (LD) extent-distribution and phylogenomic 

 

SCIENTIFIC AND ACADEMIC ACTIVITIES

  • Associate Editor: BMC Genetics; Genetics Selection Evolution
  • Ad Hoc Reviewer: Genetics; G3; Heredity; BMC Genetics; BMC Genomics; Animal Genetics; Journal of Animal Breeding & Genetics; Journal of Animal Science; Marine Biotechnology; Aquaculture
  • Grant Panel Reviewer: USDA-NRICGP; USDA-NIFA-AFRI
  • Ad hoc Grant Reviewer: NSF; Israel Science Foundation; US-Israel Binational Agric. Res. & Develop.
  • Adjunct Professor, Universidad Nacional Agraria La Molina, Graduate School of Aquaculture, Lima, Peru (2009- )
  • Faculty Member Pennsylvania State University, Department of Animal Science (2000-2004)

 

PEER-REVIEWED PUBLICATIONS (Last 10 years)

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

Vallejo RL, RM Silva, JP Evenhuis, G Gao, S Liu, JE Parsons, KE Martin, DAL Lourenco, TD Leeds, Y Palti. 2018. Accurate genomic predictions for bacterial cold water disease resistance using low-density SNP panels in rainbow trout. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand

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, TD Leeds, S Liu, G Gao, TJ Welch, GD Wiens, Y Palti. 2014. Accuracy of Genomic Selection for BCWD Resistance in Rainbow Trout. Proceedings of the World Congress on Genetics Applied to Livestock Production. Vancouver, BC, Canada

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 psychrophilumMarine 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. Aquacult. 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

Rexroad III CE, Y Palti, SA Gahr, RL Vallejo. 2008. A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genetics 9: 74