Genetic and phenotypic traits in livestock

This study compares seven genomic cross selection criteria to improve genetic gain and diversity in inbred plant breeding by evaluating their impact on progeny performance and genetic variance.

The paper quantifies how gene expression and splicing QTL explain heritability in cattle traits using Bayesian methods across 16 tissues.

The paper develops optimized matrix-vector multiplication methods for genomic prediction, improving computational efficiency on GPUs and CPUs for large datasets.

This study analyzes the genetic diversity and phylogeography of Sri Lankan cattle breeds, finding strong relationships with South Indian Hallikar cattle and significant taurine admixture in two breeds.

This study evaluates the use of low-density SNP panels with imputation for genomic selection in rainbow trout to improve resistance to Flavobacterium columnare, finding comparable accuracy to high-density panels at lower cost.

This paper evaluates a multiplexed plant-animal SNP array for diverse applications, showing high SNP performance across species and cost savings through pooling.

This study investigates the genetic structure and genome-wide associations of Kazakh horses, identifying SNPs linked to traits like size and weight.

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.

This study evaluates the impact of using whole-genome sequence data for genomic predictions in pig lines, finding modest improvements in accuracy for maternal lines but mixed results for terminal lines.

This study simulates GWA and variant selection to determine optimal sample sizes and variant inclusion strategies based on genomic dimensionality and effective population size.

The paper introduces a flexible empirical Bayes method for multivariate multiple regression to improve prediction of multi-tissue gene expression from genotypes.

The paper identifies a selective sweep near the fibromelanosis locus in Kadaknath chickens, showing hitchhiking of the BPIL gene due to linkage with the Fm locus.

This study identifies the genetic architecture of acute hyperthermia resistance in rainbow trout and shows it is polygenic with no major genetic correlations to production traits.

The paper estimates variance components, characterizes phenotypes, and evaluates genetic factors associated with bovine congestive heart failure in commercial feeder cattle.

This paper estimates the heritability of protein efficiency in pigs under a protein-restricted diet and its genetic correlations with performance and meat quality traits.

This study generates a chromosome-level genome of Chinese crested ducks, identifies genetic compensation mechanisms, and reveals the genetic basis of crest formation.

The paper reports whole genome sequencing and de novo assemblies of four Bos indicus breeds, identifying phenotypic and biological process-related genes compared to B. taurus.

The paper improves prediction of binary traits by combining genomic and phenotypic data using a two-step statistical method that prioritizes phenotypic variables.

This study evaluates how genomic selection (GS) can improve genetic gain in clone breeding programs, showing that GS strategies outperform phenotypic selection and recommend specific implementation stages for potato breeding.

This study evaluates how haplotype reference panel size and composition affect variant calling accuracy from low-pass sequencing in cattle, finding that breed-specific panels improve imputation accuracy.

This study simulates the long-term effects of genomic selection on genetic mean and variance in layer chicken breeding programs, finding that optimal contribution selection balances genetic gain and variance loss best.

This study shows that using cryopreserved semen from an old bull helped restore genetic diversity in a cattle breed without increasing inbreeding and improved reproductive performance.

This study applies genomic prediction for Euterpe edulis to improve breeding programs, finding that single-trait models provide greater selection gains than multi-trait models.

This study shows that preselecting QTL markers improves genomic selection accuracy for oligogenic traits in Norway spruce, but not for polygenic traits.

This study compares genomic selection strategies in clonal plant breeding, finding that selecting parents based on genomic predicted cross performance leads to faster genetic gain and reduced inbreeding.

The paper introduces StageWise, an R package for genomic selection in multi-environment, multi-trait plant breeding, showing improved model fit and selection indices.

This study simulates Atlantic salmon breeding programs to show that mixing between parallel year groups improves genomic prediction accuracy by reducing genetic distance and increasing genetic variation.

This study compares single- and multi-environment genomic prediction models for agronomic traits in sesame, finding that multi-environment analysis improves prediction accuracy by 15%-58%.