Genetic and phenotypic traits in livestock

The conservation of human functional variants and their effects across mammals

This study identifies human functional variants with conserved effects in livestock species, showing their utility for understanding disease mechanisms.

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

The paper identifies HOXB13 as a candidate gene for tail length variation in Merinolandschaf sheep through haplotype mapping and candidate variant analysis.

Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

The paper develops optimal experimental designs and a software tool to estimate SNP effects on infectious disease transmission traits like susceptibility, infectivity, and recoverability.

genomicSimulation: fast R functions for stochastic simulation of breeding programs

The paper introduces genomicSimulation, a fast R tool for stochastic simulation of breeding programs using real genotypes, showing it accurately reproduces key population features.

Evaluation of Association between CSN2 Genetic Marker 7:32016718C>A with A1/A2 Milk in Pakistani Buffaloes

The paper genotypes 50 Pakistani buffalo samples to assess the CSN2 7:32016718C>A marker's association with A1/A2 milk type, finding all samples are homozygous wild-type (CC), indicating exclusive A2 milk production.

Genetic Association of CSN2 Variant 6:85451298C>A with A1/A2 Milk Phenotype in Pakistani Cows

The paper investigates the association of the CSN2 variant 6:85451298C>A with A1/A2 milk phenotype in Pakistani cows using ARMS-PCR and Chi-square test, finding significant genotype variability.

Genetic Association of LDHA Variant g.2582481G>A with Racing Performance of Pakistani Pigeons

The paper investigates the association between the LDHA variant g.2582481G>A and racing performance in Pakistani pigeons, finding a significant genetic link.

Insight on Selective Breeding the Robustness Based on Field Survival Records: New Genetic Evaluation of Survival Traits in White-leg Shrimp (Penaeus vannamei) Breeding Line

The paper uses a linear multivariate animal model to analyze survival traits in white-leg shrimp, finding low heritability but high genetic correlations across survival time points.

A comprehensive catalogue of regulatory variants in the cattle transcriptome

The paper constructs a cattle Genotype-Tissue Expression atlas and identifies genetic regulatory variants linked to gene expression and traits in cattle.

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

The paper evaluates genetic conservation of French local chicken breeds through management programs, finding that early integration into programs reduces inbreeding and highlights the utility of molecular markers for monitoring diversity.

Genomic selection in organisms with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study

The paper applies genomic selection to sugar kelp with a biphasic life cycle, predicting breeding values for gametophytes and achieving moderate prediction accuracy for yield and morphology traits.

Phylophenomic and Phylogenomic analysis for Ovis aries reveals distinct identity of newly reported breed

The paper identifies a new sheep breed from West Bengal with distinct genetic identity using phylophenomic and phylogenomic analyses.

Molecular phylogenetic analysis for Ovis aries with whole mitochondrial genome sequencing

The paper analyzes whole mitochondrial genomes of sheep breeds to infer phylogenetic relationships and identify genetic lineages.

PHARP: A pig haplotype reference panel for genotype imputation

PHARP provides a high-quality pig haplotype reference panel for genotype imputation, enabling improved GWAS and genomic prediction.

A joint learning approach for genomic prediction in polyploid grasses

This paper develops a joint learning approach to improve genomic prediction in polyploid grasses, achieving over 50% accuracy improvements over traditional methods.

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

The paper develops a high-density 665 K SNP array for rainbow trout and demonstrates its utility in detecting linkage disequilibrium at shorter genomic distances.

Interpreting single-step genomic evaluations as mixed effects neural networks of three layers: pedigree, genotypes, and phenotypes

The paper introduces a neural network framework for genomic evaluations that integrates pedigree, genotypes, and phenotypes, showing improved prediction performance over traditional methods.

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

This study evaluates genomic selection for improving growth traits in European flat oysters using low-density SNP panels and finds that similar prediction accuracies can be achieved with fewer markers.

Assessing the response to genomic selection by simulation

This paper uses simulation to address two key questions in plant breeding: the number of entries needed to select the best one with a defined probability and the probability of selecting the top entries when some are chosen.

Predicting Dog Phenotypes from Genotypes

This paper predicts dog phenotypes (breed, height, weight) from genotypes using linear and non-linear methods, showing that linear methods outperform non-linear for breed classification but not for height and weight regression.

Using polygenic risk score about complex traits to predict production performance in crossbreeding of yeast

The paper uses polygenic risk scores to predict production performance in yeast crossbreeding, finding significant correlations between PRS and growth traits in F1 hybrids and their parents.

Complex Traits and Candidate Genes: Estimation of Genetic Variance Components Across Modes of Inheritance

This paper demonstrates that average semivariance can estimate genetic variance components across different modes of inheritance in complex traits.

A novel hyper-parameter can increase the prediction accuracy in a single-step genetic evaluation

This paper introduces a new hyper-parameter, the scale factor, to improve the prediction accuracy of the HBLUP method in genetic evaluation using simulated and real cattle data.

Clonal breeding strategies to harness heterosis: insights from stochastic simulation

This study compares clonal breeding strategies using stochastic simulation to determine their genetic gain per unit cost, finding that reciprocal recurrent selection (RRS) is optimal in diploids with high genomic selection intensity but not in autopolyploids.

Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats

This study genotypes over 11,000 domestic cats to analyze genetic variants related to blood type, disease, and traits, revealing breed-specific distributions and diversity.

Mate selection: a useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding

This paper compares mate selection strategies with conventional methods in oil palm breeding to reduce inbreeding and increase genetic progress using genomic selection simulations.

Comparing Heritability Estimators under Alternative Structures of Linkage Disequilibrium

This study compares heritability estimators under different LD structures and relatedness, finding no significant performance differences between fixed and random SNP-effect methods.

Rare and population-specific functional variation across pig lines

The paper identifies rare and population-specific functional variants in commercial pig lines and assesses their impact on production traits and genomic prediction.

Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes

The paper identifies a genetic variant in the LEPR gene associated with body fat reserves in sheep through genome-wide association studies.

An attempt of using public ambient temperature data in swine genetic evaluation for litter size traits at birth in Japan

This study evaluates the use of public ambient temperature data in swine genetic evaluation for litter size traits in Japan, finding that incorporating temperature improves phenotypic variability explanation without harming genetic evaluation performance.