Genetic and phenotypic traits in livestock

A Near Telomere-to-Telomere Reference Genome for Drakensberger Cattle Achieved Through Trio-Binned Long-Read Sequencing

The paper presents a high-quality, haplotype-resolved genome assembly for Drakensberger cattle using long-read sequencing, achieving high accuracy and completeness.

Selection History Models in a Population under Ongoing Directional Selection

This study evaluates two models, BayesS and [G], for detecting selection history in animal breeding, showing their effectiveness varies with heritability and data characteristics.

Estimating haplotype values and mutation effects in the context of a local DNA tree

This paper introduces a TBLUP method using local DNA trees to estimate haplotype and mutation effects, showing improved accuracy and efficiency compared to traditional SNP-based approaches.

Genomic prediction for general combining ability in hybrid canola (Brassica napa L.)

The paper evaluates genomic prediction for general combining ability in canola hybrids using different cross-validation strategies and finds varying predictive abilities across traits.

End-to-end genomic prediction: direct prediction of images and text from genome-wide molecular markers

This paper introduces end-to-end genomic prediction to directly predict images and text from genetic markers, showing comparable accuracy to traditional numeric phenotype-based methods.

A multi-tissue atlas of genetic regulatory effects in sheep

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

Integrative analysis of gene networks associated with adipose and muscle traits in Hanwoo steers

This study identifies co-expression modules and hub genes associated with fat and muscle traits in Hanwoo steers using WGCNA, revealing tissue-specific gene regulation mechanisms.

Fine-mapping methods for complex traits: essential adaptations for samples of related individuals

This paper introduces Bayesian fine-mapping methods adapted for related individuals, showing improved accuracy in pig data compared to existing tools.

Back to the horns: a reconstruction of the ancestral horn state through distinct types of recombination events.

This study identifies de-novo generation of ancestral horned variants in cattle through distinct recombination events at the POLLED locus, highlighting genetic complexity in polledness.

Marker effect p-values for single-step SNP-BLUP genomic models

This paper calculates p-values for SNP effects in ssSNPBLUP models and compares them to GWAS in cattle populations, finding higher SNP reliability in larger reference populations.

Origins and diversity of Exmoor ponies: A mitogenome framework for assessing maternal lineage diversification in endangered pony breeds

The paper uses mitochondrial DNA sequences to assess maternal lineage diversity in Exmoor ponies and their relationships to other horse breeds.

Inferring domestic goat demographic history through ancient genome imputation

This paper uses genotype imputation to analyze low coverage ancient goat genomes, revealing demographic patterns and genetic consequences of domestication.

Genomic prediction of agronomic traits in perennial ryegrass (Lolium perenne L.) and genotype x environment interactions at the limit of the species distribution

The paper evaluates genomic prediction models for agronomic traits in perennial ryegrass under genotype x environment interactions, showing improved accuracy when accounting for these interactions.

Comparative assessment of genomic, phenomic, and metabolomic prediction models in biparental grapevine breeding populations

The paper benchmarks genomic, phenomic, and metabolomic prediction models for agronomic traits in grapevine breeding populations, finding genomic prediction most accurate and metabolomic intermediate.

DiffBreed: Automatic differentiation enables efficient gradient-based optimization of breeding strategies

DiffBreed uses automatic differentiation to optimize breeding strategies, achieving higher genetic gains than equal allocation through gradient-based optimization.

Genome landscape and genetic architecture of recombination in domestic goats (Capra Hircus)

This study builds sex-specific recombination maps and identifies genetic loci associated with recombination rates in two French goat breeds.

Ensemble AnalySis with Interpretable Genomic Prediction (EasiGP): Computational Tool for Interpreting Ensembles of Genomic Prediction Models

EasiGP is a tool that interprets genomic prediction models by visualizing marker effects on trait phenotypes, revealing both known and novel genetic regions in maize.

A tailored variant filtering procedure for multi-breed and multi-species unbalanced animal SNP collections

The paper develops a tailored variant filtering method for multi-breed and multi-species SNP datasets to reduce bias from standard approaches.

Genomic and regulatory basis of adaptation in Cameroonian Gudali and Simgud Cattle

The paper identifies genomic signatures of selection in Gudali and Simgud cattle, linking them to genes involved in immunity, thermotolerance, and forage detection.

How Accurate is Genomic Prediction Across Wild Populations?

This study evaluates genomic prediction accuracy across wild house sparrow populations and finds lower accuracy compared to within-population predictions.

Genome assemblies of Indian desi cattle reveals hotspots of rearrangements and immune-related genetic diversity

This study presents high-quality genome assemblies of five Indian desi cattle breeds, identifying immune-related genetic diversity and rearrangement hotspots.

Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning

This paper develops a deep learning framework to predict the regulatory impact of non-coding variants in farmed animals using chromatin data, improving genomic prediction for livestock and aquaculture.

The variability of goat microRNA genes is strongly shaped by functional constraints

The study identifies miRNA polymorphisms in goats, finding low variation in seed regions due to purifying selection and higher variation in regulatory regions of isolated populations.

Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

Harnessing genome prediction in Brassica napus through a nested association mapping population

This study evaluates genome prediction accuracy in Brassica napus using nested association mapping, finding that rrBLUP and RKHS models and SNaP markers improve prediction accuracy for agronomic traits.

Expanding the gain-variance Pareto via optimal recycling and genomic mating

This paper introduces an integrated genomic mating strategy that combines optimal recycling with genomic mating to enhance genetic diversity and gain efficiency in breeding programs.

Review: Assessing available genetic diversity estimates of rare breeds of livestock

This paper reviews genetic diversity estimates of rare UK livestock breeds, finding gaps in DNA-based measures and discrepancies between census and DNA-based Ne estimates.

An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array

The paper identifies high heterozygous call rates in purebred horses using the Axiom Equine 670K SNP array and shows that genotype concordance improves with quality filtering and batch effect correction.

Integrating three genetic dimensions relating to piglet birth weight: direct and maternal effects on the mean and genetic control of residual variance

This paper estimates direct and maternal genetic effects on piglet birth weight and its variability, finding maternal effects are crucial while direct effects are negligible.

Learning genetic values of individuals with incomplete pedigree, genomic and phenotypic data

The paper introduces Hy-BLUP, a Bayesian prediction method for handling incomplete pedigree, genomic, and phenotypic data in genome-enabled prediction.