José Manuel Yañez

Genomic signals of local adaptation in Eleginops maclovinus from Northern Chilean Patagonia

This study identifies genomic signals of local adaptation in Eleginops maclovinus by analyzing SNP data and environmental variables to find adaptive loci associated with temperature, salinity, and oxygen.

100 years domestication of penaeid shrimp and meta-analysis of breeding traits

This paper reviews the domestication of penaeid shrimp, discusses breeding traits, and highlights the role of genomic selection and AI in improving shrimp farming sustainability.

Meta-analysis of GWAS for sea lice load in Atlantic salmon

This study performs a meta-GWAS on Atlantic salmon to identify genetic variants associated with sea lice load, finding significant genomic regions and candidate genes involved in immune and tissue repair responses.

Prioritized imputed sequence variants from multi-population GWAS improve prediction accuracy for sea lice count in Atlantic salmon (Salmo salar)

The paper improves genomic prediction accuracy for sea lice count in Atlantic salmon by prioritizing imputed SNPs from multi-population GWAS meta-analysis.

GWAS meta-analysis of resistance against Piscirickettsia salmonis in Atlantic salmon

This study performs a GWAS meta-analysis of SRS resistance in Atlantic salmon, identifying a QTL on Ssa02 and 16 shared genes associated with resistance traits.

Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

The paper uses genome-wide data to infer isolation-by-distance and population size history in coho salmon, identifying genes associated with latitude and potential osmoregulation roles.

The impact of Piscirickettsia Salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon

This study examines how Piscirickettsia salmonis infection affects DNA methylation in Atlantic salmon, identifying differentially methylated sites and their association with immune-related processes.

The impact of genetic relationship between training and validation populations on genomic prediction accuracy in Atlantic salmon

This study evaluates how genetic relationship between training and validation populations affects genomic prediction accuracy in Atlantic salmon for body weight and sea lice resistance.

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

This study identifies candidate genes for sea lice resistance in Atlantic salmon and rainbow trout through genome-wide association studies.

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

The paper investigates genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing, identifying polygenic traits and immune-related pathways associated with resistance.

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

This study identifies selection signatures in farmed coho salmon using genome-wide SNP data and detects genes associated with growth and disease resistance traits.

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

The paper identifies selection signatures in three farmed Nile tilapia strains using whole-genome sequencing and SNP analysis.

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

The paper estimates autozygosity in farmed coho salmon using runs of homozygosity (ROH) and compares genomic and pedigree-based inbreeding methods.

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

This study compares optimum contribution selection and mate selection in simulated aquaculture breeding programs, finding similar long-term genetic progress and inbreeding rates between the two strategies.

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

The paper discovers and validates 50,000 high-quality SNPs in Nile tilapia through whole-genome resequencing of 326 individuals, useful for genomic selection and trait analysis.

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

The paper identifies selection signatures in Atlantic salmon populations adapted to different environments using haplotype-based statistics, highlighting candidate genes related to growth traits.

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

This study analyzes population structure, linkage disequilibrium, and effective population size in three farmed Nile tilapia populations using SNP data from whole-genome sequencing.

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

The paper uses whole-genome sequencing to fine-map sex determination genes in Nile tilapia, identifying anti-Mullerian hormone as a major gene.

Comparative genomic analysis of three salmonid species identifies functional candidate genes involved in resistance to the intracellular bacteria Piscirickettsia salmonis

The paper identifies 120 candidate genes associated with resistance to Piscirickettsia salmonis in three salmonid species using GWAS and comparative genomics.

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)

This study identifies genomic regions associated with resistance to IPNV in rainbow trout using GWAS and finds candidate genes related to viral replication and immune response.

Genome-wide association study and low-cost genomic predictions for growth and fillet yield in Nile tilapia (Oreochromis niloticus)

This study performs GWAS and evaluates genomic selection for growth and fillet yield in Nile tilapia using imputed SNP panels, finding imputation improves genomic prediction accuracy.

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

This paper estimates linkage disequilibrium and effective population size in coho salmon using ddRAD markers, suggesting 75,000 SNPs for association studies and an effective population size of 100 ten generations ago.

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

This study identifies genomic regions and candidate genes associated with resistance to Piscirickettsia salmonis in rainbow trout using a single-step genome-wide association analysis.

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

This study identifies and characterizes quantitative trait loci (QTL) affecting resistance to sea lice in Atlantic salmon using genomic and transcriptomic data from a commercial breeding population.

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

The paper analyzes population structure and linkage disequilibrium in Chilean farmed Atlantic salmon using SNP genotypes, finding genetic differentiation and varying LD decay across populations.

Novel insights into the genetic relationship between growth and disease resistance in Pacific salmon

This study examines genetic correlations between growth and disease resistance traits in Pacific salmon, finding favorable genetic links between early growth and survival during infection.

Gene expression response to sea lice in Atlantic salmon skin: an RNA-Seq comparison between resistant and susceptible animals

Genome-Wide Association Study And Genomic Predictions For Resistance Against Piscirickettsia salmonis In Coho Salmon (Oncorhynchus kisutch) Using ddRAD Sequencing

The paper identifies a SNP associated with resistance to P. salmonis in coho salmon and shows genomic selection models perform similarly to pedigree-based methods.

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

The paper introduces FAASG, an initiative to study salmonid genomes to understand phenotypic variation and improve aquaculture and conservation.