Peer-reviewed papers



72. Application of a novel 50K SNP genotyping array to assess the genetic diversity and linkage disequilibrium in a farmed Pacific white shrimp (Litopenaeus vannamei) population.

Garcia BF, Bonaguro A, Araya C, Carvalheiro R, Yáñez JM*.

Aquaculture Reports (In Press)

71. Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data.n Atlantic salmon and rainbow trout

Yoshida GM, Yáñez JM.

Evolutionary Applications (In Press)

70. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information.

López ME, Cádiz MI, Rondeau E, Koop BF, Yáñez JM*

Scientific Reports (In press).

69. Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing.

Moraleda CP, Robledo D, Gutierrez AP, del-Pozo J, Yáñez JM*, Houston RD.

BMC Genomics 22, 156

68. Genetics of growth and survival under chronic heat stress and trade-offs with growth-and robustness-related traits in rainbow trout. 

Gallardo-Hidalgo J, Barría A, Yoshida GM, Yáñéz JM*.

Aquaculture 531, 735685.


66. Genomics to accelerate genetic improvement in tilapia. 

JM Yáñez* JM, Joshi R, Yoshida GM.

Animal Genetics 51, 658-674. 

65. Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus).

Mastrochirico-Filho VA, Borges CH, Freitas MV, Ariede RB, Pilarski F, Utsunomia R, Carvalheiro R, Gutierrez AP, Peñaloza C, Yáñez JM, Houston RD, Hashimoto DT 

BMC Genomics 21, 1-13. 

64. Pharmacological iron-chelation as an assisted nutritional immunity strategy against Piscirickettsia salmonis infection. 

Caruffo M, Mandakovic D, Mejías M, Chávez-Báez I, Salgado P, Ortiz D, Montt L, Pérez-Valenzuela J, Vera-Tamargo F, Yánez JM, Wacyk J, Pulgar R. 

Veterinary Research 51, 1-12.  

63. Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus). 

Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Yoshida GM, Gomez-Uchida D, Yáñez JM*.

Genes 11, 490 

62. Mate selection provides similar genetic progress and average inbreeding than optimum contribution selection in the long-term.

Yoshida GM, Yáñez JM, de Queiroz SA, Carvalheiro R.

Aquaculture, 526, 735376.

61. Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon.

Naval-Sanchez M, McWilliam S, Evans B, Yáñez JM, Houston RD, Kijas J.

Frontiers in Genetics 11, 264.

60. Opportunities and challenges of phenomics applied to livestock and aquaculture breeding in South America.

Ventura RV, Silva FF, Yáñez JM, Brito LF

Animal Frontiers. 10: 45-52.

59. Quantitative genetic variation for resistance to the parasite Ichthyophthirius multifiliis in the Neotropical fish tambaqui (Colossoma macropomum). 

Lira LV, Ariede RB, Freitas MV, Mastrochirico-Filho VA, Agudelo JF, Barría A, Yáñez JM, Hashimoto DT

Aquaculture Reports, 17: 100338

58. Genetic (co)variation between resistance to Aeromonas hydrophila and growth in tambaqui (Colossoma macropomum).

Ariede RB, Freitas MV, Agudelo JFG, Borges CHS, Lira LVG, Yoshida GM, Pilarski F, Yáñez JM, Hashimoto DT 

Aquaculture. 523: 35225.

57. Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar).

Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, Maisey K, Yáñez JM, Cea PA, Castro-Fernandez V, Tort L, Sandino AM, Imarai M, Reyes-López FE.  

Frontiers in Genetics. 10: 1406  

56. High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus).

Yáñez JM*, Yoshida G, Barria A, Palma-Véjares R, Travisany D, Díaz D, Cáceres G, Cádiz MI, López ME, Lhorente JP, Jedlicki A, Soto J, Salas D, Maass A.  

Marine Biotechnology. 22, 109-117


54. Genetic parameters for resistance to Aeromonas hydrophila in the Neotropical fish pacu (Piaractus mesopotamicus)

Mastrochirico-Filho VA, Ariede RB, Freitas MV, Lira LV, Agudelo JF, Pilarski F, Reis Neto R, Yáñez JM, Hashimoto DT.

Aquaculture, 513:734442

53. Fine mapping using whole-genome sequencing confirms anti Mullerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.)

Cáceres G, López ME, Cadiz MIYoshida GM, Jedlicki AM, Palma-Véjares R, Travisany D, Díaz-Domínguez D, Maass A, Lhorente JP, Soto J, Salas D, Yáñez JM*.

G3 – Genes, Genomes, Genetics, 9:3213-3223

52. Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array

Barría A, Christensen KA, Yoshida GM, Jedlicki A, Lhorente JP, Davidson WS, Yáñez JM*.

Frontiers Genetics. 10: 498

51. Novel insights into the genetic relationship between growth and disease resistance in an aquaculture strain of Coho salmon (Oncorhynchus kisutch)

Barría A, Doeschl-Wilson AB, Lhorente JP, Houston RD, Yáñez JM*.

Aquaculture, 511:734207

50. Novel insights into the genetic relationship between growth and disease resistance in an aquaculture strain of Coho salmon (Oncorhynchus kisutch)

Barría A, Doeschl-Wilson AB, Lhorente JP, Houston RD, Yáñez JM*.

Aquaculture, 511:734207

48. Single-step genome-wide association study for resistance to Piscirickettsia salmonis in rainbow trout (Oncorhynchus mykiss)

Marín-Nahuelpi, R., Barría, A., Cáceres, P., López, M. E., Bassini, L. N., Lhorente, J. P., Yáñez, J. M.

G3 – Genes, Genomes, Genetics, 9:3833-3841.

47. Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

López, M. E., Linderoth, T., Norris, A., Lhorente, J. P., Neira, R., and Yáñez, J. M.

Frontiers Genetics 10, 901

46. Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia ( Oreochromis niloticus )

Yoshida, G. M., Lhorente, J. P., Correa, K., Soto, J., Salas, D., and Yáñez, J. M.

G3 – Genes, Genomes, Genetics, 8:2597-2607

45. Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

Yoshida, G. M., Barria, A., Cáceres, G., Correa, K., Jedlicki, A., Cadiz, M. I., et al.

Frontiers Genetics, 10:745

44. Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis

Yáñez, J. M., Yoshida, G. M., Parra, Á., Correa, K., Barría, A., Bassini, L. N., et al.

Frontiers Genetics, 10:665.

43. Genome-Wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout (Oncorhynchus mykiss)

Rodríguez Francisco H., Flores-Mara Raúl, Yoshida Grazyella M., Barría Agustín, Jedlicki Ana M., Lhorente Jean P., Reyes-López Felipe, Yáñez José M.
G3 – Genes, Genomes, Genetics, 9(9):2897-2904.

42. Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

Lhorente, J. P., Araneda, M., Neira, R., and Yáñez, J. M.
Reviews in Aquaculture


41. Population genomic structure and genome-wide linkage disequilibrium in farmed Atlantic salmon (Salmo salar L. ) using dense SNP genotypes

Barria A, Lopez ME, Yoshida GM, Carvalheiro R, Lhorente JP, Yáñez JM
Frontiers Genetics

40. Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L) populations with different geographical origins

López ME, Benestan L, Moore JS, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente JP, Correa K, Neira R, Bernatchez L, Yáñez JM
Evolutionary Applications

38. Genetic (co) variation in skin pigmentation patterns and growth in rainbow trout

Rodríguez FH, Cáceres G, Lhorente JP, Newman S, Bangera R, Tadich T, Neira R, Yáñez JM.
Animal, 13(4):675-682

37. Gene expression response to sea lice in Atlantic salmon skin: RNA sequencing comparison between resistant and susceptible animals

Robledo D, Gutiérrez AP, Barría A, Yáñez JM, Houston RD.
Frontiers Genetics 9:287

36. Mate selection allows changing the genetic variability of the progeny while optimizing genetic response and controlling inbreeding

Yoshida GMYáñez JM, Lopes de Oliveira CA, Ribeiro RP, Lhorente JP, Aidar de Queiroz A, Carvalheiro R.
Aquaculture 495,409-414

35. Accuracy of genotype imputation in a two-generation farmed Atlantic salmon population using high-density and low-density SNP panels

Yoshida GM, Carvalheiro R, Lhorente JP, Correa K, Figueroa R, Houston R, Yáñez JM.
Aquaculture 491: 147-154

34. Genomic predictions and genome-wide association study for resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAd sequencing

Barría A, Christensen KA, Correa K, Jedlicki A, Lhorente JP, Davidson WS, Yáñez JM.
G3-Genes, Genomes, Genetics 8: 1183-1194

32. Genomic prediction accuracy for resistance against Piscirickettsia salmonis in farmed rainbow trout

Yoshida GM, Bangera R, Carvalheiro R, Correa K, Figueroa R, Lhorente JP, Yáñez JM.
G3-Genes, Genomes, Genetics, 8: 719-726.


31. Bayesian Genome-wide association study for body weight and average daily gain in Atlantic salmon (Salmo salar).

Yoshida GM, Lhorente JP, Carvalheiro R,Yáñez JM

Animal Genetics 48: 698-703

30. Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

Macqueen DJ, Primmer, C, Houston R, Nowak B, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop B, Lien S, Maass A, Martin S, McGinnity P, Montecino M, Naish K, Nichols K, Ólafsson K, Omholt S, Palti Y, Plastow G, Rexroad 3rd C, Rise M, Ritchie R, Sandve SR, Schulte P, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM.

BMC Genomics 18: 484

28. Mate selection in aquaculture breeding using differential evolution algorithm.

Yoshida GM, Yáñez JM, Lopes de Oliveira CA, Ribeiro RP, Lhorente JP, Aidar de Queiroz S, Carvalheiro R.

Aquaculture Research 48: 5490–5497

25. Genomic predictions can accelerate selection for resistance against Piscirickettsia salmonis Atlantic salmon (Salmo salar).

Bangera R, Correa K, Lhorente JP, Figueroa R, Yáñez JM.

BMC Genomics 18: 121

24. Genome wide association study for resistance to Caligus rogercresseyi in Atlantic salmon (Salmo salar L. ) using a 50K SNP genotyping array.

Correa K, Lhorente JP, Bassini L, López ME, Di Génova A, Maass A, Davidson WS, Yáñez JM.

Aquaculture 472-S1: 61-65

23. Correlated response of flesh color to selection for harvest weight in coho salmon (Oncorhynchus kisutch).

Dufflocq P, Lhorente JP, Bangera R, Neira R, Newman S, Yáñez JM.

Aquaculture 472-S1: 38-43


22. Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep.

Tolone M, Larrondo C, Yáñez JM, Newman S, Sardina MT, Portolano B.

BMC Veterinary Research 12: 158

21. Negative genetic correlation between harvest weight and resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch).

Yáñez JM, Bangera R, Lhorente JP, Barría A, Oyarzún M, Neira R, Newman S.

Aquaculture 459: 8-13

20. Genome wide single nucleotide polymorphism (SNP) discovery in Atlantic salmon (Salmo salar): validation in farmed and wild American and European populations.

Yáñez JM, , Naswa S, López ME, Bassini L, Correa K, Gilbey J, Bernatchez L, Norris A, Neira R, Lhorente JP, Schnable P, Newman N, Mileham A, Deeb N, Di Genova A, Maass A.

Molecular Ecology Resources 16: 1002-1011

19. Evidence of recent signatures of selection during domestication in an Atlantic salmon population.

Gutierrez AP, Yáñez JM, Davidson WS.

Marine Genomics 26: 41-50

18. Characterization of antimicrobial susceptibility and its association to virulence genes related with adherence, invasion and citotoxicity in Campylobacter jejuni and Campylobacter coli isolates from animals, meat and humans.

Lapierre L, Gatica MA, Riquelme V, Vergara C, Yáñez JM, San Martín B, Sáenz L, Vidal M, Martínez MC, Araya P, Flores R.

Microbial Drug Resistance 22: 432-444

17. Evaluation of the growth and carcass quality of diallel crosses of four strains of Nile tilapia (Oerochromis niloticus).

Neira R, García X, Lhorente JP, Filp M, Yáñez JM, Cascante AM.

Aquaculture 451: 213-222


16. Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes.

Correa K, Lhorente JP, López ME, Bassini L, Naswa S, Deeb N, Di Genova A, Maass A, Davidson WS, Yáñez JM.

BMC Genomics 16: 854

15. High-throughput transcriptome analysis of ISAV-infected Atlantic salmon Salmo salar unravels divergent immune responses associated to head-kidney, liver and gills tissues.

Valenzuela-Miranda D, Cabrejos ME, Cisterna D, Yáñez JM, Gallardo-Escárate C.

Fish and Shellfish Immunology 45: 367-377

14. Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Yáñez JM, Houston R, Newman S.

Frontiers in Genetics 6: 128

13. Genome-wide association study (GWAS) for growth rate and sexual maturation in Atlantic salmon (Salmo salar).

Gutierrez AP, Yáñez JM, Fukui S, Swift B, Davidson WS.

PLOS One 10: e0119730

12. Applications in the search for genomic selection signatures in fish.

López ME, Neira R, Yáñez JM.

Frontiers in Genetics 5: 458

11. From the viral perspective: Infectious salmon anemia virus (ISAV) transcriptome during the infective process in Atlantic salmon (Salmo salar).

Valenzuela-Miranda D, Cabrejos ME, Yáñez JM, Gallardo-Escárate C.

Marine Genomics 20: 39-43


10. Genetics and genomics of disease resistance in salmonid species.

Yáñez JM, Houston R, Newman S.

Frontiers in Genetics 5: 415

9. Effect of triploidy in the expression of immune-related genes in coho salmon (Oncorhynchus kisutch Walbaum) infected with Piscirickettsia salmonis.

Correa K, Filp M, Cisterna D, Cabrejos ME, Gallardo-Escárate C, Yáñez JM.

Aquaculture Research 46: 59-63

7. Inbreeding and effective population size in a coho salmon (Oncorhynchus kisutch) breeding nucleus in Chile.

Yáñez JM, Bassini LN, Lhorente JP, Filp M, Ponzoni R, Neira R.

Aquaculture 420-421:S15-S19


6. Quantitative genetic variation of resistance against Piscirickettsia salmonis in Atlantic salmon (Salmo salar).

Yáñez JM, Bangera R, Lhorente JP, Oyarzún M, Neira R.

Aquaculture 414-415:155-159

4. Assessing footprints of selection in commercial Atlantic salmon populations using microsatellite data.

Martinez V, Detleff P, López P, Fernández G, Jedlicki A, Yáñez JM, Davidson WS.

Animal Genetics 44: 233-236


2. Characterization of new microsatellite markers derived from sequence databases for the emu (Dromaius novaehollandiae).

Yáñez JM, González R, Angulo J, Vidal R, Santos JL, Martínez V.

Molecular Ecology Resources 8: 1442-1444

1. The CK1 gene family: expression patterning in zebrafish development.

Albornoz A*, Yáñez JM*, Foerster C, Aguirre C, Pereiro L, Burzio V, Moraga M, Reyes AE, Antonelli M.

Biological Research 40: 251-266

*Both authors contributed equally to this work

Peer-reviewed conference proceedings

Yáñez JM, Naswa S, López ME, Bassini L, Cabrejos ME, Gilbey J, Bernatchez L, Norris A, Soto C, Eisenhart J, Simpson B, Neira R, Lhorente JP, Schnable P, Newman S, Mileham A, Deeb N. 2014.

Development of a 200K SNP Array for Atlantic Salmon: Exploiting Across Continents Genetic Variation. 10th World Congress on Genetics Applied to Livestock Production. Vancouver, Canada (17-22 ago).

Yáñez JM, Smith PA, Manneschi G, Guajardo A, Rojas ME, Larenas J, Díaz S, Valdés M, Martinez V. 2010.

Unravelling genetic co-variation for resistance and tolerance against Piscirickettsia salmonis infection in Atlantic salmon (Salmo salar). 9th World Congress on Genetics Applied to Livestock Production. Leipzig, Germany (1-6 ago).

Yáñez JM, Jedlicki AM, Beristain P, Gajardo G, Lubieniecki K, Davidson WS, Martinez V. 2009.

Niveles de diferenciación genética y desequilibrio de ligamiento en el grupo de ligamiento VIII en poblaciones chilenas de salmón del Atlántico (Salmo salar). VII Simposio de Recursos Genéticos para América Latina y el Caribe (SIRGEALC 2009). Pucón, Chile (28-30 oct).

Other publications

Yáñez JM, Correa K, López ME, Bassini L, Bangera R, Lhorente JP. 2015.

Genética y genómica de la resistencia al piojo de mar (Caligus royercresseyi). Salmon Expert. N°33 2015, 80-83.

Yáñez JM, Barría A, Correa K, Bassini L, Lhorente JP. 2015.

Avances en el mejoramiento genético de la resistencia al Síndrome Rickettsial del Salmón (Pisciricketsia salmonis): integrando la información del genoma. Salmon Expert. N°4 2015, 70-74

Araneda M, Del Campo M, Correa K, Erranz F, Lhorente JP, Oyarzún M, Yáñez JM. 2015.

El rol de la genética en la condición sanitaria sustentable. AQUA. 183, 32-35.

Lhorente JP, Yáñez JM, Neira R, Araneda M. 2014.

Desarrollo de Herramientas Genómicas para mejorar el impacto económico de los Programas de Mejoramiento en Acuicultura. Revista Versión Diferente: Salmón-Acuícola. Año 11

Yáñez JM, Martínez A, Aro L, Cabrejos ME. 2012.

Aplicación de herramientas moleculares en el mejoramiento genético de peces de cultivo: Evaluación de la condición genética de reproductores. Revista Versión Diferente: Salmón-Acuícola. Año 9, N°16: 48-51.


Aquaculture Genomics Lab

Faculty of Veterinary and Animal Sciences
University of Chile
Av. Santa Rosa 11735
La Pintana, Santiago

Dr. José Manuel Yáñez
Fono: +56 2 2978 5533