RESEARCH

The Laboratory of Applied Genetics and Genomics is a multidisciplinary research laboratory dedicated to understanding the biological processes that shape life in aquatic environments. Through the integration of marine biology, genetics, genomics, ecology, and biotechnology, we investigate how aquatic organisms adapt, evolve, and respond to environmental and biological challenges across natural and human-modified ecosystems.

1.- Domestication and adaptation of aquatic organisms to changing environments: In this area, we investigate the genetic, genomic, physiological, and evolutionary mechanisms that allow aquatic organisms to adapt to environmental challenges and domestication processes. We are interested in traits related to growth, reproduction, disease resistance, hypoxia tolerance, environmental stress response, and resilience to climate change.

How do we do it: we perform quantitative genetic analyses, genomic association studies (GWAS), genomic selection, whole genome sequencing (WGS), transcriptomic analyses (RNAseq), population genomics, and physiological characterization of adaptive traits. We also evaluate genotype-by-environment interactions and the molecular mechanisms underlying adaptation to changing environmental conditions.

2.- Health and resilience of aquatic organisms facing environmental and biological challenges: In this area, we study the interactions among hosts, pathogens, microbiota, and the environment to understand the mechanisms that determine health, disease resistance, and resilience in aquatic organisms. We are particularly interested in the effects of pathogens, coinfections, environmental stressors, and climate-related challenges on immune function and host performance.

How do we do it: we conduct controlled pathogen challenges, vaccine efficacy evaluations, microbiome analyses, immune response characterization, transcriptomic studies (RNAseq), cell culture experiments, and functional genomic analyses. We combine classical microbiological and immunological approaches with modern genomic, biotechnological, and bioinformatic tools to identify mechanisms that promote resilience and health in aquatic organisms.

3. Origin and early evolution of life in extreme environments: We investigate the origin of life, the evolution of early organisms, and the limits of life in extreme environments. Our research focuses on microbial mats, stromatolites, and hypersaline ecosystems of southern Patagonia, particularly Torres del Paine and Tierra del Fuego, as modern analogues of early Earth environments.

How do we do it: we combine field studies, environmental monitoring, microbial ecology, molecular biology, genomics, metagenomics, phylogenetics, and bioinformatics to investigate the diversity, function, and evolution of microbial communities inhabiting extreme environments. We also use these systems as models to study adaptation, resilience, and the limits of life on Earth.

International grants

PCI Chile – Sweden NºCS2018 -7993. Genomics of Coinfection of Pathogens in Salmonid Fish. 2019-2023. Principal investigator (PI).

OCDE CO-OPERATIVE RESEARCH PROGRAMME. Disease Resistance in Atlantic salmon: Analysis of immune responses to coinfection of the sea lice Caligus rogercresseyi and the bacteria Piscirickettsia salmonis using RNAseq technology (2015). Principal investigator (PI).

CYTED Nº 111RT0420. Ibero-american network of genetics and immunology to control pathogens in aquaculture. (2011-2014). Principal investigator (PI).

National grants

Proyecto ANID-VIU 24P0043. Producción Escalable de Inmunoestimulantes Nanoestructurados para el Control de Piscirickettsiosis en Salmón del Atlántico. Daniela López: Director de proyecto; José Gallardo Matus: profesor guía. 2024-2025

Proyecto Fondecyt postdoctorado Nº 3240697. Tolerancia a la hipoxia en salmón del Atlántico: Caracterización sanguínea de familias tolerantes y susceptibles a la hipoxia. Nicolás Salinas: Investigador principal; José Gallardo Matus: Patrocinante. ANID. 2024-2026

Proyecto Fondecyt regular (Nº 1231206). Gill immunity under hypoxia conditions in Salmo salar. 2023-2026. Luis Mercado: Investigador principal; José Gallardo Matus: Coinvestigador.

Proyecto tesis de doctorado en el sector productivo 2022 (Nº TDP220008). Producción de una vacuna en base a nanoproteínas quiméricas altamente antigénicas para combatir brotes de Piscirickettsia salmonis. ANID 2022-2025

Proyecto Fondecyt postdoctorado Nº 3210502. Cuerpos de inclusión como inmunoestimulantes de administración oral para el control de Piscirickettsia salmonis en Salmón del Atlántico. José Gallardo Matus (Advisor of Dra. Débora Torrealba). ANID. 2021-2024

Proyecto súmate a innovar Código Nº 20SN-151304. Producción de proteínas nanoestructuradas como inmunoestimulantes contra Piscirickettsiosis. José Gallardo Matus (Coinvestigador), Luis Mercado, Claudia Altamirano. INNOVA CORFO. 2021-2021

FIC ATACAMA Nº40013444-0. ConCiencia Lab Caldera: Innovación, Desarrollo Local y Productividad. Ettienne Choupay Magna, Alejandra Tapia Avalos, Claudia Zuleta Peralta, Dra. Gabriele Lara, Dra. Silvia Gómez. 2019-2021.

Proyecto FONDEQUIP (EQM170214). OCEANO: Plataforma de Alto desempeño computacional para la sostenibilidad de los ecosistemas acuáticos y sus recursos. (2017-2019). Principal investigator (PI).

Proyecto FONDECYT POSTDOCTORADO (3170744). Disease Resistance in Atlantic Salmon: Understanding mechanisms that explain resistance and tolerance to co-infection of the Sea Lice Caligus rogercresseyi and the bacteria Piscirickettsia salmonis. (Advisor of Dra. Carolina Figueroa). Anid 2017-2019).

FONDECYT. Disease Resistance in Salmonids: Genetic analysis of co-infection of the Sea Lice Caligus rogercresseyi and the bacteria Piscirickettsia salmonis. (2014-2017). Principal investigator (PI).

FIC-R. Marine Integrated Aquaculture-Agriculture: Innovation for sustainable development of Valparaíso. (2013-2014). Principal investigator (PI).

INNOVA-CORFO. Nº 07CN13PBT-61. Development of a new methodology for the identification and selection of salmonids genetically resistant to the ectoparasite Caligus rogercresseyi. Principal investigator (PI).

INNOVA-CORFO. Nº 206-5047. Business consortium of genetics and biotechnology development for the salmon industry. Coinvestigator.

University grants

PUCV. N°39.365/2023. Immunity and stress: Risk assessment and adaptability of farmed salmon to hypoxia / Inmunidad y estrés Principal investigator (PI).

PUCV. Postdoc project. Efecto inmunomodulador de citoquinas recombinantes nanoestructuradas de Salmo salar sobre cultivo primario y línea celular de macrófagos de salmónidos desafiados contra dos patógenos bacterianos de salmón. Advisor of Dr. Nicolas Salinas.

PUCV. Nº 037.472/2013. Generation of a marker-assisted selection related to sex in Atlantic salmon. Principal investigator (PI).

PUCV Nº02/2013. Study of patentability «Method for identifying and selecting fish resistant / susceptible to parasites of fish. Principal investigator (PI).

PUCV 037.358/2011. Generation of antibodies for detection, quantification and regulation of molecular markers in aquaculture production Systems. Coinvestigator.

PUCV 037.101/2008. Biotechnology applied to the development of oral vaccines for salmon. Coinvestigator.

Publications

  1. Ortega Y, Torrealba D, Gallardo-Matus J, Fernández F, Figueroa C, Bustos P, Conejeros P, Dixon B, Mancilla M. 2026. Pathogen coinfections in wild and farmed salmonids: A systematic review. Fish Shellfish Immunol. 170:111155. doi: 10.1016/j.fsi.2026.111155. Epub 2026 Jan 23. PMID: 41581676.
  2. Domínguez-Borbor, C., Gallardo-Matus, J., Sánchez-Rodríguez, A., Salinas, J. F., Sonnenholzner, S., and Rodríguez, J. 2026. Oregano essential oil reduces the virulence of Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei. Aquaculture, vol. 613, Art. no. 743412. https://doi:10.1016/j.aquaculture.2025.743412
  3. Sergio P. Barahona, Nicolás Salinas-Parra, Rodrigo Pulgar & José Gallardo-Matus. 2026. Genetic variation of hypoxia tolerance in farmed fish: a systematic review for selective breeding purposes. Genet Sel Evol 58, 12. https://doi.org/10.1186/s12711-026-01032-1
  4. Patricia Rivera, M. Angélica Rueda-Calderón, Nicol Delgado, María Eugenia López, Anti Vasemägi, Carlos Soto, Alfonso Romero & José Gallardo-Matus. 2026. GWAS on early sexual maturation across freshwater and seawater environments in domesticated Lochy strain of Atlantic salmon. Genet Sel Evol 58, 3. https://doi.org/10.1186/s12711-025-01026-5
  5. Salinas-Parra N, Torrealba D, Ahumada A, Figueroa C, Gallardo-Matus J. 2025. Cell lines and primary cultures uses for vaccine development for bacterial pathogens of fish: a systematic review. Fish Shellfish Immunol. 2025 Nov;166:110625. doi: 10.1016/j.fsi.2025.110625. Epub 2025 Aug 5. PMID: 40769272.
  6. Karla Camacho-Méndez, Felipe Vásquez-Ponce, Felipe Ramírez, Cristian Valenzuela, Manuel Alcalde-Rico, Antonio López-Carvallo, José Gallardo-Matus, Roberto Cruz-Flores, Carlos Zarza, Luis Mercado & Jorge Olivares-Pacheco. 2025. Gut dysbiosis after successive administration of florfenicol-medicated feed alters intestinal inflammatory response and growth patterns in healthy Atlantic salmon (Salmo salar). anim microbiome 7, 122 (2025). https://doi.org/10.1186/s42523-025-00490-0
  7. Torrealba, Débora, Daniela López, Patricio Zelada, Nicolás Salinas-Parra, Paula Valenzuela-Avilés, Elena Garcia-Fruitós, Anna Arís, Luis Mercado, Claudia Altamirano, and José Gallardo-Matus. 2024. Immunomodulation Evidence of Nanostructured Recombinant Proteins in Salmonid Cells. Animals 14, no. 6: 844. https://doi.org/10.3390/ani14060844
  8. Paulina Bustos, Carolina Figueroa, Bárbara Cadiz, Tamara Santander, Brian Dixon, Jose Gallardo, Pablo Conejeros. 2023. Immune response induced by coinfection of the Sea louse Caligus rogercresseyi and the intracellular bacteria Piscirickettsia salmonis in vaccinated Atlantic salmon. Journal of Fish Diseases 46(12): 1337-1342.
  9. Débora Torrealba, Byron Morales-Lange, Victoriano Mulero, Anti Vasemägi, Luis Mercado and José Gallardo-Matus. Heritability of Immunity Traits and Resistance of Atlantic Salmon against the Sea Louse Caligus rogercresseyi. Biology 2023, 12(8), 1078  
  10. Gómez S, Hurtado C, Orellana J, Gallardo J. Salinity reduction by Sarcocornia neei in hydroponics: implications in marine aquaculture wastewater remediation.  Lat. Am. J. Aquat. Res. 2023;51(3): 414-420.
  11. Valenzuela-Aviles P, Torrealba D, Figueroa C, Mercado L, Dixon B, Conejeros P, Gallardo-Matus J. 2022. Why vaccines fail against Piscirickettsiosis in farmed salmon and trout and how to avoid it: A review. Front. Immunol. 13:1019404.
  12. Figueroa, C.; Torrealba, D.; Morales-Lange, B.; Mercado, L.; Dixon, B.; Conejeros, P.; Silva, G.; Soto, C.; Gallardo, J.A. 2022. Commercial Vaccines Do Not Confer Protection against Two Genogroups of Piscirickettsia salmonis, LF-89 and EM-90, in Atlantic Salmon. Biology 11(7) 993.
  13. Mónica Díaz-Silva, Jonathan Maldonado, Pamela Veloso, Nicol Delgado, Herman Silva, José A. Gallardo. 2022. RNA-seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification. Electronic Journal of Biotechnology, 58: 70-81.
  14. Diaz, M.R.; Araneda, J.; Osses, A.; Orellana, J.; Gallardo, J.A. 2020. Efficiency of Salicornia neei to Treat Aquaculture Effluent from a Hypersaline and Artificial Wetland. Agriculture 10(12) 621.
  15. Carolina Figueroa, Pamela Veloso, Lenin Espin, Brian Dixon, Débora Torrealba, Islam Said Elalfy, Juan Manuel Afonso, Carlos Soto, Pablo Conejeros & José A. Gallardo. 2020. Host genetic variation explains reduced protection of commercial vaccines against Piscirickettsia salmonis in Atlantic salmon. Scientific Report 10, 18252.
  16.  Verónica Rojas, Delany Sánchez, José A. Gallardo & Luis Mercado. 2018. Histopathological changes induced by Caligus rogercresseyi in rainbow trout (Oncorhynchus mykiss). Lat. Am. J. Aquat. Res., 46 [4]: 843-848.
  17. Carolina Figueroa, Paulina Bustos, Débora Torrealba, Brian Dixon, Carlos Soto, Pablo Conejeros & José A. Gallardo. 2017. Coinfection takes its toll: Sea lice override the protective effects of vaccination against a bacterial pathogen in Atlantic salmon. Scientific Reports 7: 17817
  18. Riquelme Javiera, Olaeta José Antonio, Gálvez Lena, Undurraga Pedro, Fuentealba Clauida, Osses Andrea, Orellana Jaime, Gallardo José, Pedreschi Romina. 2016. Nutritional and functional characterization of wild and cultivated Sarcocornia neei grown in Chile. Ciencia e Investigación Agraria 43 (2): 283-293.
  19. Lhorente JP, Gallardo JA, Villanueva B, Carabaño MJ, Neira R (2014) Disease Resistance in Atlantic Salmon (Salmo salar): Coinfection of the Intracellular Bacterial Pathogen Piscirickettsia salmonis and the Sea Louse Caligus rogercresseyi. PLoS ONE 9(4): e95397.
  20. Gallardo JA, Brante A, Cancino JM (2013) The effect of light intensity and tidal cycle on the hatching and larval behaviour of the muricid gastropod Chorus giganteus. Journal Experimental Marine Biology an Ecology 440, 69-73.
  21. Rojas V, Morales-Lange B, Guzmán F, Gallardo JA, Mercado L (2012) Immunological strategy for detecting the pro-inflammatory cytokine TNF-alpha in salmonids. Electronic journal of Biotechnology 15 (5): 19.
  22. Santana P, Palacios C, Narváez E, Guzmán F, Gallardo JA, Mercado L (2012) Anti-peptide antibodies: A tool for detecting IL-8 in salmonids. Electronic journal of Biotechnology 15 (5): 15.
  23. Bethke J, Rojas V, Berendsen J, Cárdenas C, Guzmán F, Gallardo JA, Mercado L (2012)Development of a new antibody for detecting natural killer enhancing factor (NKEF)-like in infected salmonids. Journal of Fish Diseases 35: 379–388.
  24. Lhorente JP, Gallardo JA, Villanueva B, Araya A, Torrealba DA, Toledo XE, Neira R (2012)Quantitative genetic basis for resistance to Caligus rogercresseyi sea lice in a breeding population of Atlantic salmon (Salmo salar). Aquaculture 324-325: 55–59.
  25. Araya A, Mancilla M, Lhorente JP, Neira R, Gallardo JA (2012). Experimental challenges of Atlantic salmon Salmo salar with incremental levels of copepodids of sea louse Caligus rogercresseyi: effects on infestation and early development. Aquaculture research 43: 1904–1908.
  26. Torrealba DA, Toledo XE, Gallardo JA (2011). Artificial settlement of sea lice, Caligus rogercresseyi Boxshall & Bravo, 2000 (Copepoda, Caligidae), on tissues of fish used as substrate. Crustaceana 84 (8): 939-9481.
  27. Ferrada S, Canales-Aguirre CB, Galleguillos R, Barrera A, Gallardo JA (2011) Characterization of microsatellite loci in the chilean sea lice Caligus rogercresseyi. Crustaceana 84: 375-381.
  28. Cancino JM, Gallardo JA, Brante A (2011) The relationship between temperature, oxygen conditions and embryo encapsulation in the marine gastropod Chorus giganteus. Journal of the Marine Biological Association of the UK : 91(3), 727–733.
  29. Gallardo JA, Lhorente JP, Neira R (2010). The consequences of including non-additive effects on the genetic evaluation of harvest body weight in Coho salmon. Genetics, Selection and Evolution  42:19.
  30. Narvaez EA, Berendsen JA, Guzmán F, Gallardo JA, Mercado LA (2010) An immunological method for quantifying antibacterial activity in Salmo salar (Linnaeus, 1758) skin mucus. Fish & Shellfish Immunology 28: 235-239.
  31. Gallardo JA, Cancino JM (2009) Effects of temperature on development and survival of embryos and on larval production of Chorus giganteus (Lesson, 1829) (Gastropoda: Muricidae). Revista de Oceanografía y Biología Marina 44(3): 595-602.
  32. Neira R, Díaz N, Gall G, Gallardo JA, Lhorente JP, Manterola R (2006) Genetic improvement in Coho salmon (Oncorhynchus kisutch). I: Selection response and inbreeding depression on harvest weight. Aquaculture 257: 9-17.
  33. Neira R, Diaz N, Gall G, Gallardo JA, Lhorente JP, Alert A (2006). Genetic improvement in Coho salmon (Oncorhynchus kisutch).  II: Selection response on early spawning date. Aquaculture 257: 1-8.
  34. Gallardo JA, Neira R (2005). Environmental dependence of inbreeding depression in cultured Coho salmon: aggressiveness, dominance and intraespecific competition. Heredity 95: 449-456.
  35. Gallardo JA, Lhorente JP, García X, Neira R (2004) Effect of nonrandom mating schemes to delay the inbreeding accumulation in cultured populations of Coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Science 61: 547-553.
  36. Gallardo JA, García X, Lhorente JP, Neira R (2004) Inbreeding and inbreeding depression of female reproductive traits in two populations of Coho salmon selected using BLUP predictors of breeding values. Aquaculture 234: 111-122.
  37. Cancino J, Gallardo JA (2004). Effects of delaying settlement of the life expectancy of the bryozoan Bugula flabellate (Bryozoa: Gymnolaemata). Revista Chilena de Historia Natural 71: 303-311.
  38. Cancino JM, Gallardo JA, Torres F (2003). Combined effects of dissolved oxygen concentration and water temperature on embryonic development and larval shell secretion in the marine snail Chorus giganteus (Gastropoda: Muricidae). Marine Biology 142: 133-139.
  39. Cancino JM, Gallardo JA, Torres F, Leiva G, Navarro J (2000). Effects of sessile protozoan on intracapsular dissolved oxygen concentration and embryonic shell calcification in the muricid Chorus giganteus. Marine Ecology Progress Series 200: 265-276.
  40. Hernandez C, Contreras S, Gallardo JA, Cancino JM (1998). Community structure of macroinfauna along sandy beach of Central Chile: Lenga, San Vicente Bay. Revista Chilena de Historia Natural 71: 303-311.

    Otras publicaciones

    1. Rivera, P., Gallardo, J., Araneda, C., & Vasemägi, A. (2021). Sexual Maturation in Farmed Atlantic Salmon (Salmo salar): A Review. In (Ed.), Salmon Aquaculture. IntechOpen. https://doi.org/10.5772/intechopen.99471
    2. Gallardo JA, Lhorente JP, Neira R (2012) Resistencia genética de salmón Atlántico a Caligus rogercresseyi y Piscirickettsia salmonis. SalmonXpert: Volumen 4: 41-46.
    3. Kapuscinski AR, Hard JJ, Neira R, Paulson KM, Ponniah A, Kamonrat W, Mwanja W, Fleming IA, Gallardo JA, Devlin RH, Trisak J. (2007) Approaches to assessing gene flow. Pp. 112-150 in Kapuscinski, A. R., S. Li, K. R. Hayes, and G. Dana (editors), Environmental Risk Assessment of Genetically Modified Organisms, Vol 3: Methodologies for Transgenic Fish. CABI International, Wallingford, Oxfordshire, UK.
    4. García X., J. A. Gallardo. 2005. Predictores del valor de cría: Índices de selección y metodologías de modelos mixtos. Publicación docente Nº 17. Departamento de Producción animal. Universidad de Chile. 164 pp.
    5. 2.- Gallardo J. A., R. Neira. 2003. Consanguinidad y depresión endogámica en Animales: Una guía para la acuicultura. Publicación docente Nº 16. Departamento de Producción animal. Universidad de Chile. 85 pp.
    6. Cancino JM,  Gallardo JA (2000). Effects of light on bryozoan larval settlement. Proceeding of the 11th International Bryozoology Association Conference Nº 56: 168-175.

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