Genetic and phenotypic traits in livestock

Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits

The paper assembles a complete horse genome, identifies variants linked to reproduction and temperamental traits, and improves upon previous assemblies.

Impact of genomic selection on genetic diversity in five local European cattle breeds

This study examines the impact of genomic selection on genetic diversity in five European cattle breeds, finding inconsistent changes in inbreeding rates and highlighting the role of breeding strategies over GS itself.

Genetic analysis of iris pigmentation in Swiss pig breeds identifies a missense KITLG variant as a potential causal factor for pale and heterochromatic irises

Multi-omics analysis reveals genetic regulatory mechanismsof muscle traits in wild and domesticated Bactrian camels

The paper integrates multi-omics data from Bactrian camels to identify regulatory mechanisms and genetic variants influencing muscle traits.

Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data

This study improves genomic prediction of stalk lodging resistance in maize by integrating multi-environment data, showing that multi-environment models significantly enhance prediction accuracy for most traits.

randPedPCA: Rapid approximation of principal components from large pedigrees

The paper introduces randPedPCA, an R package for rapid PCA of large pedigrees using sparse matrices and randomised linear algebra, demonstrating its efficiency on simulated and real datasets.

Local genomic estimates provide a powerful framework for haplotype discovery

This paper introduces localGEBV, a haplotype-based method that improves QTL discovery and phenotypic prediction compared to traditional GWAS approaches in barley.

Copy number variation in the genome of four South American camelid species

This study identifies and analyzes copy number variations in four South American camelid species using whole-genome data, revealing species-specific patterns and functional associations.

Pedigree-based genome-wide imputation using a low-density amplicon panel for the highly polymorphic Pacific oyster Crassostrea (Magallana) gigas

The paper demonstrates genome-wide imputation using a low-density amplicon panel in Pacific oysters to reduce genotyping costs and improve selective breeding.

Phenological characterization of Mozambican native caprine breeds assessed through morpho-biometric traits and zoometric indices

This study compares morpho-biometric traits of two Mozambican goat breeds, identifying phenotypic differences that support breed characterization and conservation strategies.

Genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Swiss Large White pigs

This study uses GWAS and RHM to identify genomic regions associated with protein efficiency and performance traits in pigs, highlighting candidate genes and noncoding RNAs.

Differential transcriptomics and metabolomics analyses of the skin of coarse and fine Liaoning cashmere goats

The paper analyzes transcriptomics and metabolomics data from coarse and fine cashmere goats to identify genes and metabolites associated with fiber diameter differences.

GPFN: Prior-Data Fitted Networks for Genomic Prediction

This paper introduces GPFN, a new genomic prediction method that outperforms linear models on multiple traits and matches their performance on a structured prediction task.

Genomic Diversity and Population Structure of Red Steppe Cattle Based on High-Density SNP Genotyping

This study genotypes Red Steppe cattle to assess genetic diversity, inbreeding, and population structure using SNP data, identifying three ancestral components and candidates for breeding.

Genomic Regions and Variant Analysis Reveal Candidate Genes Associated with Age at First Service in Chinese Holstein Heifers

This study identifies three genomic regions and 12 candidate genes associated with age at first service in Chinese Holstein heifers using GWAS and colocalization analysis, highlighting ANAPC4 as a putative causal gene.

Multi-objective Evaluation and Optimization of Stochastic Gradient Boosting Machines for Genomic Prediction and Selection in Wheat (Triticum aestivum) Breeding

This paper evaluates how hyperparameters affect prediction stability and performance in genomic prediction for wheat breeding using Gradient Boosting Machines.

Deep Learning for genomic prediction accounting for heterosis in crossbreeding systems

This paper evaluates deep learning's ability to predict genetic values in crossbred populations by capturing heterosis, finding it improves performance when heterosis is present.

Genomic selection for accelerated heartwood formation in Pedunculate oak (Quercus robur L.) using whole-genome sequencing

This study uses whole-genome sequencing and genomic prediction to accelerate heartwood formation in oak trees by identifying genetic markers linked to heartwood traits.

Family-based Selection: An Efficient Method for Increasing Phenotypic Variability

This paper introduces a Python-based model to study how family-based selection affects phenotypic variability in D. melanogaster, showing that it can increase variability more effectively than individual-based selection.

WISER: spectral whitening of fixed effects for improved breeding value estimation in structured, unbalanced, and genotype-environment-confounded populations

WISER improves breeding value estimation by addressing population structure and genotype-environment confounding through spectral whitening, outperforming LS-means and BLUP across multiple species and traits.

Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population

The paper develops an algorithm to accurately assign breed origin to alleles in crossbred dairy cattle, achieving high accuracy in simulated breeding programs.

Genetic basis of traits and performance in UK silver birch

The paper identifies SNPs and structural polymorphisms associated with growth traits in silver birch and evaluates their predictive power for growth rates across different environments.

Genetic score omics regression and multi-trait meta-analysis detect widespread cis-regulatory effects shaping bovine complex traits

GSOR and MTAO detect widespread cis-regulatory effects on bovine complex traits by linking gene expression with genetic scores and multi-trait associations.

Assessment of Ex Situ Conservation Strategies for the Preservation of Domestic South American Camels in Southern Peru: Insights from Mitochondrial DNA Analysis

This study assesses genetic diversity and conservation strategies for alpacas and llamas in Southern Peru using mitochondrial DNA analysis and evaluates the effectiveness of an ex situ germplasm bank.

Improving Multi-Trait Genomic Prediction Efficiency Through The Incorporation Of Synthetic Traits Selected Based on Co-heritability

This paper improves genomic prediction accuracy by using synthetic traits derived from hyperspectral data, showing higher accuracy than single-trait models for leaf traits in sorghum.

An atlas of cell type specific regulatory effects in cattle

The paper constructs a cattle cell-type-specific regulatory variant atlas by integrating bulk and single-cell RNA-seq data, identifying eQTL and linking them to GWAS loci for breeding insights.

Optimizing the use of cryopreserved genetic resources for the selection and conservation of animal populations

This study shows that using cryopreserved genetic resources can help manage genetic diversity in animal populations, either by slowing its loss or guiding selection, but requires careful management to avoid issues with old genetic material.

Genome-wide analysis reveals mutual gene flow between goats from Island Southeast Asia and from Southern Africa

This study identifies mutual gene flow between Island Southeast Asian and Southern African goats through European maritime activities using genome-wide SNP analysis.

Dissecting the genetic architecture of flowering and maturity time in almond (Prunus dulcis): heritability estimates and breeding value predictions from historical data

This study estimates heritability and breeding values for flowering and maturity time in almond using historical data and Bayesian models to improve breeding strategies.

An integrative approach to prioritize candidate causal genes for complex traits in cattle

The paper tests three methods to identify causal genes for milk lipid traits in cattle using GWAS, transcriptomics, and gene ontology analysis, finding significant overlaps but limited power.