M.P.L. Calus

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development

The paper integrates tissue-specific epigenetic annotations into genomic predictions of gene expression in three pig breeds, improving eQTL mapping interpretability but facing challenges in cross-breed predictions.

Selection History Models in a Population under Ongoing Directional Selection

This study evaluates two models, BayesS and [G], for detecting selection history in animal breeding, showing their effectiveness varies with heritability and data characteristics.

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.

The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations

This study examines how genomic selection affects allele frequencies and new mutations over fifty generations, finding that genomic selection leads to faster and larger changes in allele frequencies compared to pedigree selection.

Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence

This study evaluates genomic prediction models incorporating gene transcripts and finds that transcript-based models improve accuracy when phenotypes are measured close to transcript sampling, but combining transcript and SNP data does not consistently outperform single-omics models.

The long-term effects of genomic selection: Response to selection, additive genetic variance and genetic architecture

This study simulates the long-term effects of genomic selection on genetic architecture, showing that non-additive effects significantly impact genetic variance and allele frequency changes over generations.

Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice

This study compares linear models and gradient boosting machine for predicting complex traits in outbred mice, finding linear models generally outperform GBM, except for traits with epistatic effects.

Impact of genomic preselection on subsequent genetic evaluations with ssGBLUP - using real data from pigs

This study evaluates the impact of genomic preselection on accuracy and bias in ssGBLUP genetic evaluations using real pig data, finding minimal effects on accuracy and negligible bias.

Required marker properties for unbiased estimates of the genetic correlation between populations

The paper investigates how marker allele frequencies and linkage disequilibrium affect estimates of genetic correlation between populations, finding that marker allele frequencies should reflect causal loci frequencies for unbiased estimates.

Genomic prediction using individual-level data and summary statistics from multiple populations

This paper develops a method to integrate individual-level genomic data and summary statistics across populations to improve allele substitution effect estimates and genomic predictions.

Holstein Friesian mid-lactation Milk Polar Metabolite Composition in relation to Dietary Fat Composition and Diacylglycerol O-acyltransferase 1 Genotype

The paper examines how dietary fat and DGAT1 genotype influence polar metabolite composition in Holstein Friesian cow milk.

Properties Of Genomic Relationships For Estimating Current Genetic Variances Within And Genetic Correlations Between Populations

This paper defines a multi-population genomic relationship matrix to estimate current genetic variances within populations and genetic correlations between populations, and validates its properties through simulations.