Genetic and phenotypic traits in livestock

A large-effect locus on chromosome 4 underlies circadian feeding rhythmicity in pigs

This study identifies a QTL on chromosome 4 associated with circadian feeding rhythmicity in pigs, linking it to genes involved in feeding behavior and energy homeostasis.

An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis

The paper develops a low-cost genotyping panel for Yesso scallops to support breeding and disease resistance studies.

JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection

JanusX improves GWAS and genomic selection by reducing runtime and memory usage while maintaining accuracy across large datasets.

How to enviromically predict breeding genotypes as if they were commercial cultivars?

This paper develops a bivariate enviromic reaction-norm model to predict breeding genotypes as commercial cultivars by integrating genomic and environmental data, showing it can generate spatial recommendation maps for genotype deployment.

Context-dependent genetic regulation of gene expression in pigs

The paper identifies context-dependent genetic regulation of gene expression in pigs using quantile regression, revealing eQTLs that are conserved with humans and influence disease-relevant genes.

Optimizing genomic selection: A comparison of SNP selection strategies for reduced-density panels in beef cattle

This study compares SNP selection strategies for reduced-density panels in beef cattle to optimize computational efficiency while maintaining genomic prediction accuracy.

Genetic parameters and genotype-by-diet interactions forgrowth traits in Australian black soldier fly larvae: Implicationsfor selective breeding

This study estimates genetic parameters and genotype-by-diet interactions for growth traits in black soldier fly larvae, finding moderate heritability and significant dominance effects.

Bridging Morphology and Genomics: A rapid image-based assessment of genomic admixture in the endangered gayal (Bos frontalis)

This study develops an AI framework to predict genomic admixture from morphological images of gayal, achieving 87.87% accuracy in admixture estimation.

Multi-layered molecular regulation of complex traits in an advanced intercross line

The paper maps a multi-layered molecular QTL atlas in chicken to understand complex trait regulation across tissues and developmental stages.

Whole-genome resequencing-based comparative variant analysis identifies candidate genes associated with cross-beak phenotype in Huiyang Bearded chickens

The influence of parental and genotype effects on early survival and development in Atlantic salmon

This study investigates how parental and genotype effects influence early survival and development in Atlantic salmon offspring, finding that paternal vgll3 genotype affects survival while maternal effects are stronger for survival and hatching traits.

Structured Multimodal Deep Learning improves Genomic Prediction in Future Environments

The paper introduces SINN, a structured multimodal deep learning model that improves genomic prediction in new environments by combining statistical decomposition with deep learning, achieving higher accuracy than existing methods.

Genome-Wide Selection Signatures in Nili-Ravi Buffalo (Bubalus bubalis) Reveal a T-Cell Costimulatory and Cytokine-Signaling Gene Network Distinct from Classical Bovine Tuberculosis Candidate Genes

The paper identifies six novel immune-related genes in Nili-Ravi buffalo with selection signatures distinct from classical bovine tuberculosis candidate genes.

Transmission of an environmental modification in quails across three generations: changes in the contribution to phenotypic variability

The paper examines phenotypic variability across three generations of quails subjected to an initial environmental modification, finding increased epiline contribution to traits like body weight.

Extreme male reproductive skew limits effective population size in American Standardbred horses

This study examines how extreme male reproductive skew in American Standardbred horses reduces effective population size, leading to very low Ne/N ratios and genetic diversity loss.

Identifying crossovers in a cattle pangenome containing haplotype-resolved assemblies from half-siblings

The paper identifies crossover events in cattle using haplotype-resolved assemblies and methylation data from long-read sequencing, finding more events in half-siblings than in cousins.

Widely used GWAS methods can be poorly suited to SNP-level localization under diffuse polygenic architecture in livestock

This study shows that common GWAS methods can produce misleading associations in livestock with polygenic architecture, highlighting the need for methods that control long-range LD spillover.

The genetic basis of resistance to pathogens in rainbow trout: a meta-QTL analysis

This paper performs a meta-QTL analysis to identify genetic regions associated with pathogen resistance in rainbow trout, refining QTLs and identifying candidate genes involved in immune pathways.

Uncertainty-aware breeding decisions: MCMC-based optimum contribution selection increases breeding decision robustness

The paper introduces CVaR-OCS, a method that improves breeding decisions by incorporating uncertainty in genetic evaluations, leading to more robust selection outcomes.

Progeny-based genomic selection reveals untapped genetic potential in an underutilized medicinal plant, Perilla frutescens

This study applies genomic selection to improve medicinal compounds in red perilla, showing that GS-based crosses outperform phenotypic selection in target compound levels.

Genetic parameters and genome-wide association analysis of service sire effect on litter size and its relationship with boar semen quality in three terminal sire lines

This paper estimates genetic parameters and performs GWAS to analyze service sire effects on litter size and its relationship with semen quality in three terminal sire lines.

Variant intolerance scores in cattle

This paper estimates variant intolerance scores for cattle genes and predicts protein domains, finding similar patterns to other species and moderate correlation with human orthologs.

From long-term progeny trials to genomic selection: empirical prediction and simulation-guided redesign of Scots pine breeding in Germany

This paper evaluates genomic selection strategies for Scots pine breeding using long-term progeny trials and simulations, finding that genomic selection with phenotypic thinning provides the highest annual gains for certain traits.

Phenotyping replication is a major determinant of genomic predictive ability in sweet sorghum (Sorghum bicolor Moench)

The paper evaluates how phenotyping replication, training population size, and genomic relatedness affect genomic predictive ability in sweet sorghum breeding programs.

Long-term realized genetic gain and population dynamics under genomic selection in Brazilian cassava germplasm

The paper evaluates long-term genomic selection outcomes in Brazilian cassava breeding programs, showing genetic gains and changes in diversity across four selection cycles.

The genetic architecture of milk urea concentration in dairy cattle differs across the lactation cycle

This study identifies lactation-stage specific QTL for milk urea concentration in dairy cattle breeds, highlighting pleiotropic effects and candidate genes.

Genotypic and phenotypic consequences of domestication in dogs

This study uses runs of homozygosity to link genetic diversity with non-disease phenotypes in dogs, finding associations with traits like height, weight, and fur length.

Assessing the Role of Marker Density and Minor Allele Frequency on Machine Learning Driven Genomic Selection Accuracy in Grapevine

This study evaluates how marker density and minor allele frequency affect genomic selection accuracy in grapevine using machine learning models and conventional methods.

Parameterizing the genetic architecture under stabilizing selection

The paper derives an alternative to the beta-model for genetic architecture under stabilizing selection, linking evolutionary theory to mixed models for improved prediction.

Linking geography and mutation profiles across goat species

This study links geography and mutation profiles in goat species, finding strong correlations between specific mutations and geographic coordinates.