Genetic and phenotypic traits in livestock

This study uses metabolomics and genomic approaches to improve prediction of healthful compounds in oat seeds by identifying latent factors associated with lipid metabolism.

The paper estimates heritability of body and antler traits in free-ranging white-tailed deer using genomic-relatedness matrices and finds moderate heritability for body traits but low and variable heritability for antler traits.

This study evaluates the impact of including the X chromosome in genomic predictions for reproductive and andrological traits in beef cattle, finding improved predictive accuracy for some traits.

The paper designs experiments for fine-mapping quantitative trait loci in livestock populations, showing that optimal sample size depends on heritability and the number of causative variants.

The paper identifies mitochondrial gene networks associated with feed efficiency in pigs through transcriptomic analysis and pathway enrichment.

The paper identifies a regulatory mutation in BMP15 on the X chromosome in sheep that increases litter size by 0.2 lambs per lambing at heterozygosity.

This study identifies ten genetic loci associated with milk yield, fat, and protein traits in Holstein cattle using GWAS and FarmCPU method.

This study uses genetic factor analytic modeling to explore the genetic relationships among cattle temperament measures, validating an objective movement-based method as an alternative to subjective scoring.

This study uses whole genome sequencing of 5 Tibetan sheep breeds to identify selective signatures related to high-altitude adaptability and physical traits.

This study sequenced the reindeer genome and analyzed its genetic makeup, identifying genes and domestication events linked to adaptation and evolution.

This study evaluates genomic prediction models with genotype by environment interaction for kernel zinc concentration in maize, finding that models incorporating G x E interactions improve prediction accuracy.

AlphaFamImpute improves genotype imputation in full-sib families using low-coverage GBS data by leveraging shared haplotype segments between siblings.

This study shows that a two-part hybrid crop breeding strategy with genomic selection and a maximum avoidance of inbreeding crossing scheme maximizes genetic gain and long-term genetic variance.

The paper identifies genetic regulators of mineral amount in Nelore cattle muscle using co-expression and regulatory impact factor analyses, finding extracellular matrix interactions as core regulators.

This study identifies introgression and selection events in goat domestication, linking them to immune and behavioral genes.

This paper introduces Origin Specific Genomic Selection (OSGS) to improve the introgression of beneficial exotic alleles in crop breeding by partitioning marker effects based on allele origin.

The paper develops regularized selection indices to improve breeding value prediction using hyper-spectral image data, showing higher accuracy for grain yield than traditional methods.

This study identifies genetic variants and metabolite interactions associated with feed efficiency in pigs using mGWAS and network analysis.

The paper proposes optimal cross selection strategies to broaden genetic diversity in breeding programs while maintaining short-term performance.

The paper estimates autozygosity in farmed coho salmon using runs of homozygosity (ROH) and compares genomic and pedigree-based inbreeding methods.

This study compares selection strategies for grain yield in winter wheat, finding that combining phenotypic selection with genomic selection improves genetic gains.

This study compares optimum contribution selection and mate selection in simulated aquaculture breeding programs, finding similar long-term genetic progress and inbreeding rates between the two strategies.

This study identifies genetic loci and gene expression patterns associated with Campylobacter resistance in broiler chickens, providing insights for breeding programs.

The paper discusses the interpretation of negative heritability estimates and suggests they may reflect real biological features rather than just statistical noise.

The paper sequenced six diverse horse breeds to identify and annotate SNPs, INDELs, CNVs, and SVs, revealing functional variants related to physiology and size.

This study evaluates sequencing strategies for whole-genome imputation using hybrid peeling, finding that 2% of the population sequenced at 2x coverage provides high accuracy.

This study demonstrates high accuracy of whole-genome sequence imputation in large livestock populations using hybrid peeling, with median individual-wise correlation of 0.97.

The paper simulates the effects of selfing in cassava genomic selection to purge deleterious alleles and finds that selfing reduces genomic prediction accuracy and limits long-term gains.

BWGS is an R package for genomic selection that enables GEBV computation and validation in wheat breeding, showing that training population size and marker selection are key for predictive ability.

MoBPS simulates breeding programs and compares their economic and genetic impacts using a modular, efficient framework with customizable modules.