Genetic and phenotypic traits in livestock

Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study

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.

Evaluating the efficiency and accuracy of a commercial test for estimating genetic risk of bovine congestive heart failure

The paper evaluates a commercial test for estimating genetic risk of bovine congestive heart failure, finding it efficient and accurate with reference DNA but less so with rapid extraction kit DNA.

Reintroducing genetic diversity in populations from cryopreserved material: The case of Abondance, a French local dairy cattle breed

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.

Single and Multi-trait Genomic Prediction for agronomic traits in Euterpe edulis

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.

Beyond Scenarios - Optimization of breeding program design (MoBPSopti)

This paper introduces a framework for numerically optimizing breeding programs by maximizing a target function that combines genetic gain and diversity conservation, using stochastic simulations and kernel regression.

MtDNA d-loop variation in Prespa dwarf cattle (Bos taurus) from Albania

The paper reports mtDNA d-loop diversity in Albanian Prespa dwarf cattle, identifying high diversity and haplogroups T3 and T1, suggesting a complex female genetic history.

Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce

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

Genomic selection strategies for clonally propagated crops

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.

Artificial selection footprints in domestic chicken genomes

This study identifies numerous selective sweeps and genes under artificial selection in indigenous and commercial chickens using re-sequencing and statistical analysis.

Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection

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

Impact of mixing between parallel year groups on genomic prediction in Atlantic salmon breeding programmes under random selection

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.

A single base pair duplication in SLC33A1 gene causes fetal losses and neonatal lethality in Manech Tete Rousse dairy sheep

The paper identifies a single base pair duplication in SLC33A1 causing fetal losses and neonatal lethality in MTR sheep through whole genome sequencing and breeding studies.

Multi-environment analysis enhances genomic prediction accuracy of agronomic traits in sesame

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%.

Homozygous haplotype deficiency in Manech Tete Rousse dairy sheep revealed a nonsense variant in MMUT gene affecting newborn lamb viability

The paper identifies recessive deleterious variants in Manech Tete Rousse dairy sheep using genome scans, finds a nonsense mutation in MMUT causing lamb mortality, and links other haplotypes to morphological traits.

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

The paper constructs a graph-based sheep pan-genome to identify structural variations and their association with tail phenotypes in domestic and wild sheep.

Using visual scores and categorical data for genomic prediction of complex traits in breeding programs

This study evaluates methods for genomic prediction using categorical data in breeding programs, finding that mixed models and Bayesian approaches perform well despite normality violations.

Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs

The paper analyzes the prevalence and clinical impact of Mendelian disease variants in over a million dogs using genotype and electronic medical record data.

Extending the breeder's equation to take aim at the Target Population of Environments

The paper discusses the importance of the MET-TPE relationship in genomic prediction for improving breeding outcomes in target populations of environments.

Advanced marker-assisted selection versus genomic selection in breeding programs

This study compares advanced marker-assisted selection and genomic selection in tree breeding, finding genomic selection outperforms MAS in most scenarios except when using large unrelated populations for GWAS.

SNP profile for quantitative trait nucleotide in populations with small effective size and its impact on mapping and genomic predictions

The paper investigates SNP profiles around QTN in small Ne populations and shows how these profiles affect genomic prediction accuracy and QTN detection.

FarmGTEx TWAS-server: an interactive web server for customized TWAS analysis in both human and farm animals

The paper introduces a web server for multi-species transcriptome-wide association study (TWAS) analysis, enabling gene expression prediction and trait association in humans and farm animals.

Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

The paper constructs a duck pan-genome and identifies transposon-derived structural variations linked to bodyweight and white plumage traits in ducks.

Exponential increase in QTL detection with increased sample size.

The paper simulates GWAS in rats to show that larger sample sizes lead to an exponential increase in the number of significant loci detected.

Accuracy of direct genomic values and methylation profile through genotype-by-LowPass sequencing using Nanopore technology

This study evaluates genotype-by-LowPass Nanopore sequencing for estimating direct genomic values and methylation marks in dairy cattle, showing high reliability with recent chemistry.

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

This study uses mitochondrial DNA analysis to investigate the genetic diversity and evolutionary origins of Philippine native pigs, revealing their ancestry from three Sus scrofa lineages and no domestication from endemic wild pigs.

Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into genetic variants in candidate genes for disease resistance

The paper reports the first whole genome sequence of Red Chittagong Cattle and identifies genetic variants in disease resistance candidate genes.

Predicting Phenotypes From Novel Genomic Markers Using Deep Learning

This paper develops a deep learning model to predict phenotypes using structural variations and transposable elements, showing higher accuracy than SNPs and conventional models.

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture in long-term genetic gains in wheat

The paper uses multi-trait genomic prediction models and simulations to show that complex trait genetic architecture improves long-term genetic gains in wheat breeding.

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

The paper compares mate-allocation strategies in sugarcane breeding that use additive and non-additive genetic effects to maximize clonal performance and reduce inbreeding.

The application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study

The paper estimates the functional effects of KEGG pathways on bovine stature using SNP summary statistics from GWAS and mixed linear models.