Genetic and phenotypic traits in livestock

The paper describes a method for high-resolution genotype imputation in outbred intercrosses using low-coverage whole-genome sequencing and evaluates it in a chicken F2 pedigree.

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

The paper develops methods to assign parentage using low-depth sequencing data by combining relatedness estimates and excess mismatch rate metrics, showing consistency with microsatellite results.

The paper introduces a best prediction approach for additive genomic variance in random-effects models, incorporating linkage disequilibrium and improving upon existing methods.

The paper develops an ARMS-PCR diagnostic test for beta-casein A1/A2 SNP genotyping in Holstein Friesian cattle and surveys its prevalence in Pakistani populations.

This paper introduces two new algorithms for faster REML estimation in linear mixed-effects models used in GWAS, showing they are faster and more accurate than existing methods.

This study characterizes epistatic genetic architecture in cowpea using a MAGIC population and evaluates genomic selection models, finding that epistasis significantly impacts traits and improves prediction accuracy.

This study predicts genetic correlations in plant breeding crosses to improve multiple traits, finding that cross selection based on predicted correlations increases multi-trait genetic gain.

The paper creates a gene expression atlas for goats, identifying transcriptional differences in immune signatures compared to sheep.

This study identifies eQTL in Thoroughbred skeletal muscle, revealing heritable variation in genes related to cofactor metabolism and potential impacts on athletic performance.

This study identifies genomic regions associated with resistance to IPNV in rainbow trout using GWAS and finds candidate genes related to viral replication and immune response.

This study identifies a novel gene region associated with feline disproportionate dwarfism, suggesting a potential model for human undiagnosed dwarfism cases.

This study identifies genetic markers associated with resistance to PMCV in Atlantic salmon using a genome-wide association approach.

The paper uses genomic selection analyses to show that blight tolerance in chestnut hybrids is polygenic, not controlled by major genes, and that higher American chestnut genome inheritance correlates with lower blight tolerance.

The paper reports the first reference genome assembly of the Black Bengal goat using de novo assembly and structural annotations.

This study shows that family-specific low-density genotype arrays improve pedigree-based imputation accuracy, especially at very low marker densities.

This study quantifies how variation in recombination rates affects variance in realised relationship across genomes, showing complex patterns depending on genomic architecture.

This study identifies novel and known selection signals for fat deposition in African and Eurasian sheep breeds using SNP data and statistical methods.

This study evaluates genomic selection for predicting resistance to koi herpesvirus disease in carp using RAD-seq data, showing improved accuracy over pedigree-based methods.

This study performs GWAS and evaluates genomic selection for growth and fillet yield in Nile tilapia using imputed SNP panels, finding imputation improves genomic prediction accuracy.

This paper uses random regression models to improve genetic inference of longitudinal traits in rice by identifying both persistent and time-specific quantitative trait loci.

This paper estimates linkage disequilibrium and effective population size in coho salmon using ddRAD markers, suggesting 75,000 SNPs for association studies and an effective population size of 100 ten generations ago.

The paper examines the relationship between inbreeding depression and fecundity in Golden Retrievers using genomic data from the Golden Retriever Lifetime Study.

This paper develops a statistical model to detect buffering loci in genome-wide association studies and identifies loci with significant epistatic effects but no additive effects in bovine data.

The paper annotates transcriptomes and chromatin structures in liver and T cells from four livestock species using RNA-seq, ATAC-seq, and Hi-C, revealing conserved regulatory elements and genome organization patterns.

This study compares graph-based and linear reference-based methods for variant genotyping in cattle, finding Graphtyper more accurate and sensitive than GATK and SAMtools.

The paper introduces Sci-LMM, a framework for analyzing population-scale family trees, and estimates heritability of longevity and reproductive fitness in a large historical pedigree.

This study improves genomic prediction for drought tolerance in rice by using trait-specific markers and multi-environment models, achieving higher predictive ability than traditional methods.

This study uses RAD-sequencing to estimate GRM-based heritability in a wild roe deer population, showing robustness to genotyping errors and the impact of quality filters on heritability estimates.

This study uses metagenomic data and machine learning to predict growth and carcass traits in pigs, finding that microbiome data from later stages improves prediction accuracy.