Genetic and phenotypic traits in livestock

Integrating temporal genomic and transcriptomic analyses to decipher genetic basis of feed intake in dairy cattle

This study integrates genomic and transcriptomic analyses across lactation stages in dairy cattle to identify temporal genetic variants and molecular mechanisms associated with feed intake.

Assessment of segregation variance estimates from derivation, simulations, and empirical data in autotetraploid species exemplified in potato

The paper derives algebraic methods to predict segregation variance in autotetraploid species, compares them with simulations and empirical data, and finds they correlate well with simulations but not with empirical data due to small family sizes.

European taurine vs Indian indicine cattle: a comparative genomic study reveals regions of differentiation during evolution and selection during crossbreeding

The paper compares European taurine and Indian indicine cattle genomes to identify genes involved in heat tolerance and immune response, and examines their inheritance in crossbreeds.

Seven Millennia of Human Exploitation drove genomic Changes in Iberian Sheep

This study analyzes ancient Iberian sheep genomes to show how human activities shaped their genetic diversity over 7,000 years, including maritime introduction, Steppe ancestry influx, and Roman-era expansion.

Farm animal evolution demonstrates hidden molecular basis of human traits

The paper investigates missing regulation by comparing trait-associated variants in cattle and pigs to human genetics, finding increased regulatory variant ascertainment in livestock.

Comparative analysis of genomic prediction approaches for multiple time-resolved traits in maize

This study compares genomic prediction methods for multiple time-resolved traits in maize, finding MegaLMM excels in snapshot accuracy while dynamicGP is better for longitudinal accuracy.

Beekeepers' preferences for honeybee breeding goals: a French case study

This study surveys French beekeepers to identify their preferences for honeybee breeding goals, finding strong support for multi-trait selection and specific traits like disease resistance and honey yield.

Co-occurring Amino Acid Substitutions Reveal Shared Evolutionary Links between Mammary Gland Location and Litter Size in Mammals

This study links mammary gland location and litter size in mammals through amino acid substitutions, natural selection, and protein networks.

Proteomics profiles of growth-related proteins of Red Sokoto and West African Dwarf goats

This study compares plasma proteomic profiles of Red Sokoto and West African Dwarf goats to identify growth-related differences in protein expression and functional pathways.

Genomic and pedigree-based approaches to predict parental breeding values for nut and kernel traits in almond (Prunus dulcis Mill. D. A. Webb)

This study uses genomic and pedigree-based methods to predict breeding values for nut and kernel traits in almond, finding that genomic methods provide slightly better predictions than pedigree-based methods.

Spatial modelling improves genomic evaluation in Tanzanian smallholder admixed dairy cattle

This paper improves genomic evaluation in Tanzanian smallholder dairy cattle by incorporating spatial modelling to better separate genetic and environmental effects.

Integrative Whole-Genome Analysis reveals Genomic Signatures of Innate Immunity in Indicine Cattle.

The paper identifies genomic signatures of innate immunity in indicine cattle breeds through whole-genome analysis, revealing immune-related variants and selection signals absent in taurine breeds.

Sex-linked dilution colour in the European domestic goose confirmed to be a 1-bp deletion in the Melan-A gene

The paper confirms a 1-bp deletion in the MLANA gene causes sex-linked dilution in European domestic geese, leading to autosexing traits.

Molecular QTL are enriched for structural variants in a cattle long-read cohort

The paper identifies molecular QTL enriched for structural variants in a cattle long-read sequencing cohort, showing SVs have a significant impact on gene expression and splicing.

MateR: a novel framework for computing the usefulness criterion and applying genomic mating

MateR computes a new usefulness criterion and diversity metric for genomic mating, improving accuracy in predicting family means and variances and tracking additive variation loss.

The use of cross-validation has overestimated the value of genomic selection in plant breeding

The paper argues that cross-validation overestimates genomic selection's effectiveness in plant breeding, especially when used for accuracy improvement rather than selection intensity.

Unraveling IGK Locus in Dog Breeds: IMGT(R) New Insights into Canine Immunogenetics.

This study curates the IGK locus in nine dog breeds, identifies genetic variations, and updates the IMGT(R) database with comprehensive data, enhancing understanding of canine immunogenetics.

Ensembles of Graph Attention Networks Supervised by Genotype-to-Phenotype Structures Improved Genomic Prediction Performance

This study evaluates graph attention networks (GAT) for genomic prediction in crops, finding that ensembles of GAT models outperform single models using gene network structures.

Optimisation of Weighted Ensembles of Genomic Prediction Models in Maize

This study evaluates three weight optimisation approaches for genomic prediction ensembles in maize, finding that weighted models improve prediction performance when weights differ from equal weights, but no single method clearly outperforms others.

Optimizing population simulations to accurately parallel empirical data for digital breeding

This paper improves simulation accuracy for digital breeding by integrating GWAS-derived genetic architecture into trait simulations, achieving high concordance with empirical data.

Genomic approaches to build de novo elite breeding gene pools from locally-adapted landraces

The paper develops genomic approaches to build elite gene pools from locally-adapted landraces, finding that QGI effectively identifies elite pairs while cis-elite crosses yield better genetic gain.

Optimizing progeny allocation strategies in breeding schemes while updating genomic prediction models

The paper develops a framework that optimizes breeding strategies by updating genomic prediction models during breeding schemes, showing improved performance under moderate to low selection intensities.

Equine Parentage Testing with SNPs and beyond: developing a platform independent panel

The paper develops a platform-independent SNP panel for equine parentage testing, demonstrating its robustness and utility for breed identification and disease assays.

Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction

The paper introduces Reciprocal BLUP, a multi-omics framework that improves plant phenotype prediction by analyzing cross-layer relationships between genome, metabolome, and microbiome data.

Allelic Variation in CYP3A4 and PLB1 Drives Feed Efficiency and Immunometabolic Resilience in Beef Cattle

The paper identifies genetic markers CYP3A4 and PLB1 associated with improved feed efficiency and immune resilience in beef cattle through genotyping and gene expression analysis.

When does accounting for gene-environment interactions improve complex trait prediction? A case study with Drosophila lifespan

This study investigates when gene-environment interactions improve complex trait prediction by analyzing Drosophila lifespan data across different cross-validation scenarios.

Genomic prediction in insects: a case study on wing morphology traits in the jewel wasp Nasonia vitripennis

This paper applies genomic prediction to wing morphology traits in Nasonia vitripennis using GBLUP and GBS data, finding higher accuracy in 5-fold cross-validation than across-generation validations.

Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

This study determines the optimal SNP density for maximizing genomic prediction accuracy and heritability estimates in three spruce species, finding plateaus between 4000 to 8000 SNPs.

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.

D-BLUP: a differentiable genomic BLUP model with learnable variance and marker weights

D-BLUP integrates genomic BLUP into gradient-based machine learning by making it differentiable, allowing direct learning of variance and marker weights from prediction error.