Genetic and phenotypic traits in livestock

Improved Genomic Prediction Performance with Ensembles of Diverse Models

The paper shows that combining multiple genomic prediction models improves accuracy and reduces errors in predicting crop traits, supporting the Diversity Prediction Theorem.

Integrating Phenomic Selection Using Single-Kernel Near-Infrared Spectroscopy and Genomic Selection for Corn Breeding Improvement

This study combines genomic and phenomic selection in corn breeding using single-kernel NIRS to improve predictive accuracy and reduce genotyping costs.

Genomic insights into post-domestication expansion and selection of body size in ponies

The paper analyzes the genomic data of 385 horses from 49 breeds to explore the demographic history and genetic factors influencing body size in ponies, identifying cis-regulatory elements and genetic affinities.

Unravelling the genetic architecture of persistence in production, quality, and efficiency traits in laying hens at late production stages

The paper analyzes trait persistence in laying hens from 70 to 92 weeks, identifying traits with stable genetic variance and those requiring alternative selection strategies.

Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly

The paper selects for large body size in black soldier flies and finds repeatable phenotypic but not genetic responses, highlighting high genetic redundancy in polygenic traits.

The impact of epistasis on the genomic prediction of non-assessed and non-overlapping single crosses in multi-environment trials

This study evaluates how epistasis affects genomic prediction of untested single crosses in multi-environment trials, finding that epistasis significantly impacts prediction accuracy and coincidence index.

Managing the genetic diversity of animal populations using cryobanks: optimizing the constitution of ex situ collection?

This study optimizes the constitution of cryopreserved collections for managing genetic diversity in animal populations by simulating breeding scenarios and evaluating the impact of collection size, age, and sampling strategies.

Genomic and Phenomic Prediction for Soybean Seed Yield, Protein, and Oil

This paper compares genomic and phenomic prediction for soybean seed yield, protein, and oil content, finding phenomic prediction outperforms genomic for yield while genomic is better for protein and oil.

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain

This study evaluates cross-selection methods with genomic selection in potato breeding to improve long-term genetic gain while maintaining diversity.

Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models

This study improves genomic selection in hexaploid wheat by incorporating additive and epistatic effects, leading to a 3% increase in prediction accuracy for grain yield.

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

The paper performs a multi-breed meta-GWAS in pigs to identify genomic regions associated with complex traits and integrates with PigGTEx to prioritize variant-gene-tissue-trait circuits.

Comparing statistical learning methods for complex trait prediction from gene expression

The paper compares statistical learning methods for predicting complex traits from gene expression in Drosophila, finding method-specific accuracy differences and improved performance with functional annotations.

WISER: an innovative and efficient method for correcting population structure in omics-based selection and association studies

WISER improves phenotype estimation in omics studies by correcting population structure, outperforming LS and BLUP across multiple species and datasets.

Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

This paper optimizes a ddRAD GBS pipeline for non-model species using mock reference genomes and demonstrates its effectiveness in bovine and European whitefish data.

Unraveling the inbreeding depression patterns in a self-pollinated eucalyptus population

This study examines inbreeding depression in a self-pollinated eucalyptus population by analyzing genomic and phenotypic data to estimate inbreeding depression and genetic parameters.

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

PIGOME is a multi-omics database for pig functional genomics that integrates various sequencing datasets and provides tools for exploring genomic variants, gene expression, and epigenetic signals.

Principal Component Analysis of Major Biometric Traits and Indices of Indigenous Sheep Ewe Populations, and Relationships with their Body Weights

The paper uses PCA to analyze biometric traits and indices of three indigenous sheep populations in Ethiopia, finding correlations with body weights and suggesting their suitability for different production purposes.

Evaluation of genomic and phenomic prediction for application in apple breeding

This study evaluates genomic and phenomic prediction methods for apple breeding, showing that expanding training sets improves predictive ability but leave-one-family-out validation reduces it, while phenomic data are less effective.

Evaluating genotyping strategies for a small managed population with simulation

This paper evaluates genotyping strategies for a service dog population using simulation, finding that low-pass sequencing outperforms SNP arrays in imputation accuracy and cost-effectiveness.

Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost

The paper proposes an iterative feedback method combining pooled genotyping and imputation to improve SNP genotype accuracy at reduced cost.

Exploring Genomic Signatures of Selection in Guineafowl and Chicken Populations Across Diverse Climatic Zones: A Comparative Analysis of Africa, Asia, and Europe Research Article

This study identifies genomic signatures of selection in guineafowl and chicken populations across Africa, Asia, and Europe, revealing genes and pathways involved in stress response and environmental adaptation.

Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations

This study proposes a method to select optimal cross pairs in inter-population crosses by considering genetic effects across populations, showing increased genetic gains in multiple traits.

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities

The paper identifies the Id locus in Black Bone Chickens, locates it to a 1.6 Mb region, and suggests it may function as a polygenic supergene cluster influencing dermal pigmentation.

Trait genetic architecture and population structure determine model selection for genomic prediction in natural Arabidopsis Thaliana populations

The paper evaluates genomic prediction models for 36 traits in Arabidopsis thaliana, finding regression models generally most accurate, with random forest better for biochemical traits.

Optimization of a maize rapid cycle breeding scheme using the Modular Breeding Program Simulator (MoBPS)

The paper uses stochastic simulations to optimize a maize breeding scheme by balancing genetic gains and diversity through additional phenotyping and external genetic material.

Don't Benchmark Phenomic Prediction Against Genomic Prediction Accuracy

The paper argues that benchmarking phenomic prediction against genomic prediction using cross-validation is inappropriate because accuracy differences do not reliably reflect breeder's equation parameters and other factors influence selection outcomes.

Strategies to improve selection compared to selection based on estimated breeding values

The paper compares selection strategies to improve genetic gain and reduce inbreeding over multiple generations using simulation software.

Genomic prediction of individual inbreeding levels for the management of genetic diversity in populations with small effective size

The paper evaluates methods for predicting inbreeding levels using genomic data in small populations, finding that model-based and rule-based approaches perform well under various conditions.

A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection

This study constructs a water buffalo pangenome using graph genomics, revealing extensive structural variation and population-specific selection signatures in 711 global samples.

hibayes: An R Package to Fit Individual-Level, Summary-Level and Single-Step Bayesian Regression Models for Genomic Prediction and Genome-Wide Association Studies

hibayes provides an R package for fitting Bayesian regression models in genomic prediction and GWAS, supporting individual-level, summary-level, and single-step approaches.