PUBLICATIONS

Peer-reviewed papers

Pre-prints

58. Comparison of Mortality and Viral Load in Rainbow Trout (Oncorhynchus mykiss) infected with Infectious Pancreatic Necrosis Virus (IPNV) Genogroups 1 and 5

Tapia, D., Barría, A., and Yáñez, J. M.
BioRxiv

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57. 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., et al.
BioRxiv

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56. 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 in Genetics 10, 901

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55. Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

Cáceres, P., Barría, A., Christensen, K. A., Bassini, L. N., Correa, K., Lhorente, J. P., et al.
BioRxiv

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2019

54. 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 (DOI: https://doi:10.1534/g3.119.400116)

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53. 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 in genetics (DOI: https://doi:10.3389/FGENE.2019.00745)

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52. 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 in genetics (DOI: doi:10.3389/fgene.2019.00665)

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51. 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 (DOI: https://doi.org/10.1534/g3.119.400463)

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50.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 (DOI: https://doi:10.1111/raq.12335.)

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49.Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)

Giovanna Cáceres, María E. López, María I. Cádiz, Grazyella M. Yoshida, Ana M. Jedlicki, Ricardo Palma-Véjares, Dante Travisany, Diego Díaz-Domínguez, Alejandro Maass, Jean P. Lhorente, Jose Soto, Diego Salas and José M. Yáñez
G3: Genes, Genomes, Genetics (DOI: https://doi.org/10.1534/g3.119.400297.)

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48.Genetic parameters for Piscirickettsia salmonis resistance, sea lice (Caligus rogercresseyi) susceptibility and harvest weight in rainbow trout (Oncorhynchus mykiss)

Bassini, L. N., Lhorente, J. P., Oyarzún, M., Bangera, R., Yáñez, J. M., and Neira, R.
Aquaculture (DOI: https://doi:10.1016/J.AQUACULTURE.2019.05.008.)

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

Barría, A., Doeschl-Wilson, A. B., Lhorente, J. P., Houston, R. D., and Yáñez, J. M.
Aquaculture (DOI: https://doi:10.1016/J.AQUACULTURE.2019.734207.)

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46.Whole genome linkage disequilibrium and effective population size in a coho salmon (Oncorhynchus kisutch) breeding population using a high density SNP array

Barría Agustín, Christensen Kris A., Yoshida Grazyella, Jedlicki Ana, Leong Jong S., Rondeau Eric B., Lhorente Jean P., Koop Ben F., Davidson William S., Yáñez José M.
Frontiers in Genetics (DOI: https://doi:10.3389/FGENE.2019.00498)

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45. Discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in Atlantic salmon

Robledo D, Gutierrez AP, Barría A, Lhorente JP, Houston RD, Yáñez JM
Frontiers in Genetics 10:56

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44. Whole genome linkage disequilibrium and effective population size in a coho salmon (Oncorhynchus kisutch) breeding population

Barría A, Christensen KA, Yoshida GM, Jedlicki A, Leong JS, Rondeau EB, Lhorente JP, Koop B, Davidson WS, Yáñez JM
Frontiers in Genetics (DOI: https://doi.org/10.3389/fgene.2019.00498)

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43. Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)

Neto RVR, Yoshida GM, Lhorente JP, Yáñez JM
Molecular Genetics and Genomics (In Press)

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2018

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 in Genetics (In Press)

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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 (In press)

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39. Determination of the Genetic Component of Fur-Chewing in Chinchillas (Chinchilla lanigera) and Its Economic Impact

González C, Yáñez JM, Tadich T
Animals 8: 144

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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 1-8

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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 in genetics 9: 287

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

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

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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

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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

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33. Single-step genomic evaluation improves accuracy of breeding value predictions for resistance to infectious pancreatic necrosis virus in rainbow trout

Yoshida GM, Carvalheiro R, Rodriguez F, Lhorente JP, Yáñez JM.
Genomics (In Press) https://doi.org/10.1016/j.ygeno.2018.01.008

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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

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2017

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

29. Resistance against infectious pancreatic necrosis exhibits significant genetic variation and is not genetically correlated with harvest weight in rainbow trout (Oncorhynchus mykiss).

Flores-Mara R, Rodríguez FH, Bangera R, Lhorente JP, Neira R, Newman S, Yáñez JM.

Aquaculture 479: 155-160

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

27. The use of genomic information increases the reliability of breeding value predictions for sea louse (Caligus rogercresseyi) resistance in Atlantic salmon (Salmo salar).

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

Genetics Selection Evolution 49: 15

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

2016

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

2015

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

2014

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

8. Genetic co-variation between resistance against both Caligus rogercresseyi and Piscirickettsia salmonis, and body weight in Atlantic salmon (Salmo salar).

Yáñez JM, Lhorente JP, Bassini LN, Oyarzún M, Neira R, Newman S.

Aquaculture 433:295-298

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

2013

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

5. Characterization of Mycobacterium salmoniphilum as causal agent of mycobacteriosis in Atlantic salmon, Salmo salar L., from a freshwater recirculation system.

Aro L, Correa K, Martínez A, Ildefonso R, Yáñez JM.

Journal of Fish Diseases 37: 341-348

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

2007-2010

3. Genetic factors involved in resistance to infectious diseases in salmonids and their application in breeding programmes.

Yáñez JM, Martínez V.

Archivos de Medicina Veterinaria 42: 1-15

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). VER

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Gutierrez AP, Yañez JM, Fukui S, Swift B, Davidson WS. 2014.

Genome-wide association study (GWAS) for growth rate and sexual maturation in Atlantic salmon (Salmo salar). 10th World Congress on Genetics Applied to Livestock Production. Vancouver, Canada (17-22 ago). VER

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Tolone M, Yáñez JM, Sutera AM, Scatassa ML, Portolano B. 2014.

Assessment of genetic variation for resistance to mastitis in Valle del Belice dairy sheep: a survival analysis approach. 10th World Congress on Genetics Applied to Livestock Production. Vancouver, Canada (17-22 ago). VER

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Neira R, Lhorente JP, Newman S, Yáñez JM, Araneda M, Filp M. 2014.

Evolution of Coho Salmon (Oncorhynchus kisutch) Breeding Programs. 10th World Congress on Genetics Applied to Livestock Production. Vancouver, Canada (17-22 ago). VER

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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). VER

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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).

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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.

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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. VER

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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. VER

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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.VER

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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. VER

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Invited Conferences (selected, 10 out of 31)

Abstracts in International Conferences (selected, 10 out of 34)

Abstracts in Chilean Conferences (selected, 10 out of 25)