Genetic and phenotypic traits in livestock

Ensemble-based genomic prediction for maize flowering-time improves prediction accuracy and reveals novel insights into trait genetic variation

This paper improves genomic prediction accuracy for maize flowering-time traits using an ensemble approach, revealing novel insights into trait genetic variation.

Haplotype-resolved genome assemblies for Norwegian Red cattle

The paper develops haplotype-resolved genome assemblies for Norwegian Red cattle to improve variant detection and genomic predictions.

Genomic Prediction Enables Provenance-Aware Selection in 1 Sessile Oak (Quercus petraea) using Foliar Physiological Traits

This study uses genomic prediction to select resilient sessile oak genotypes based on foliar physiological traits, showing high heritability and across-provenance predictability.

Bayesian marker-based principal component ridgeregression - a flexible multipurpose framework forquantitative genetics in wild study systems

This paper introduces a Bayesian marker-based principal component ridge regression framework for estimating quantitative genetic parameters in wild study systems, showing efficient estimation of additive genetic variance and accurate breeding value prediction.

Unlocking the potential of Capsicum Germplasm Collections for Climate Resilience and Fruit Quality

This paper develops a framework combining genomic prediction and a large language model to select climate-resilient pepper cultivars from germplasm collections.

Genetic prediction with ARG-powered linear algebra

The paper develops a method to estimate variance components and predict genetic values using ancestral recombination graphs (ARGs) and linear mixed models on large datasets.

Optimization of reference population for imputation of low-density SNPs panel for genomic prediction in Atlantic salmon.

This study evaluates how different reference populations affect SNP imputation and genomic prediction accuracy in Atlantic salmon using low-density SNP panels.

Multi-trait Multi-environment Genomic Prediction Strategies for Miscanthus sacchariflorus Populations

This study evaluates MTME genomic prediction models for Miscanthus sacchariflorus, finding they improve prediction for some traits but not all, depending on the cross-validation scenario.

The enhanced multi-tissue atlas of regulatory effects in cattle

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

Weather Characterization for Optimizing Genomic Prediction in Miscanthus sacchariflorus

This study optimizes genomic prediction in Miscanthus sacchariflorus by incorporating weather data to improve model performance across different locations.

ENHANCING GENOMIC PREDICTION MODELS IN MISCANTHUS POPULATIONS BY INCORPORATING THE GENOTYPE-BY-ENVIRONMENT INTERACTION

The paper evaluates cross-validation schemes for genomic selection in perennial Miscanthus species, showing improved predictive ability by incorporating genotype-by-environment interactions.

BioWorldModel: A Multi-Kingdom Trajectory Architecture for Genomic Prediction with Evolutionary Curriculum Learning

BioWorldModel predicts multi-trait phenotypic distributions across fungi, plants, and animals using a unified architecture, outperforming species-specific baselines.

Bayes factor for linear mixed model in genetic association studies

The paper introduces a method to compute Bayes factors for linear mixed models in genetic association studies using Bayesian regression and demonstrates its equivalence to BLUP predictions.

Use of a Sire MGS model to disentangle paternal and maternal origins of genetic variance in lifetime productivity of tropical dairy cattle.

The paper applies a Sire MGS model to partition genetic variance into paternal and maternal components for lifetime productivity in tropical dairy cattle, finding significant maternal contributions.

Across-breed analyses of genome-wide association studies for stature and mammary gland morphology in cattle reveal pleiotropic effects of the Friesian POLLED haplotype

The paper performs genome-wide association studies in cattle to identify QTL for stature and mammary gland morphology, finding pleiotropic effects of the Friesian POLLED haplotype on mammary traits.

A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus

This paper presents a high-quality chromosome-level genome assembly of the Kolbroek pig, providing a genetic resource for studying genetic variation and improving breeding programs.

Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

The paper constructs a cattle pangenome to identify novel non-reference unique insertions (NRUIs) and links them to economically important traits.

iGS: A Zero-Code Dual-Engine Graphical Software for Polygenic Trait Prediction

The paper introduces a zero-code graphical tool for polygenic trait prediction in breeding, showing linear models are robust for additive traits while machine learning and deep learning excel in complex traits.

Integration of Proxy Intermediate Omics traits into a Nonlinear Two-Step model for accurate phenotypic prediction

The paper proposes a nonlinear two-step model integrating proxy intermediate omics traits to improve phenotypic prediction in soybean, showing better accuracy than linear models.

Modeling missing parents in single-step test-day SNP-BLUP evaluation of dairy cattle

This study compares methods for handling missing parental information in genomic breeding value predictions for dairy cattle, finding that grouping missing parents as genetic groups is more robust for ungenotyped individuals in incomplete pedigrees.

Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

The paper identifies stage-specific regulatory variants in pig skeletal muscle by analyzing chromatin accessibility, molecular QTLs, and GWAS data across prenatal and postnatal stages.

Integrating Longitudinal Metabolite Profiles Improves Trait Prediction in Pigs in a Trait- and Timepoint-Dependent Manner

This study integrates longitudinal metabolite profiles into genomic prediction models for pig traits, showing improved prediction accuracy depending on the trait and timepoint of metabolite sampling.

Genomic diversity, population structure and admixture in native cattle breeds of Benin

This study analyzes genetic diversity and admixture in Benin's cattle breeds, finding significant differentiation between taurine and zebu breeds and gene flow from zebu to taurine due to adaptive factors.

BayesR3AD: Joint analysis of additive and dominance in Bayesian mixture models

BayesR3AD extends Bayesian mixture models to jointly estimate additive and dominance genetic effects, improving prediction accuracy for fertility and longevity in Holstein cattle.

Sparse testcrossing for early-stage genomic prediction of general combining ability to increase genetic gain in maize hybrid breeding programs

The paper proposes sparse testcrossing with 3-5 testers to improve genetic gain in maize hybrid breeding by balancing simplicity, resource efficiency, and GCA prediction accuracy.

Genome-Wide Linkage Disequilibrium, Haplotype Block Structure, and Population Diversity in Nili-Ravi Buffalo (Bubalus bubalis)

The paper characterizes linkage disequilibrium, haplotype blocks, and population diversity in Nili-Ravi buffalo using SNP data to identify a haplotype associated with bTB resistance.

MultiGS: A comprehensive and user-friendly genomic prediction platform Integrating statistical, machine learning, and deep learning models for breeders

MultiGS is a genomic prediction platform that integrates various models for breeders, showing improved accuracy and efficiency in different prediction scenarios.

Epigenome-informed prioritization of bivalent chromatin SNPs enhances genomic prediction robustness: a proof-of-concept study in Pacific white shrimp (Litopenaeus vannamei)

This study uses epigenetic annotations to prioritize SNPs in shrimp, improving genomic prediction accuracy and reducing costs.

PyMSQ: a python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection

PyMSQ provides a fast Python package for computing Mendelian sampling variance, covariance, and haplotype-based similarity in genomic selection, enhancing haplotype diversity management.

A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating

This paper develops a quantitative genetic model to analyze how indirect genetic effects and genomic imprinting influence genetic variance under random and assortative mating.