Genetic and phenotypic traits in livestock

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

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

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.

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

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.

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

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.

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

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.

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.

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

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

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.

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

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

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.

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

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

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

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

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 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.

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

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.

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.

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.

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.

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.

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