Genetic and phenotypic traits in livestock

Modeling breeding programs considering social behavior in large groups of farmed fish

This study evaluates how social interactions affect fish breeding programs through stochastic simulations, showing increased phenotypic variability and altered genetic gains under different selection strategies.

Comparison of localGEBV and Optimal Haplotype Stacking Fitness Functions using a Novel R Package: HapSelect

The paper compares localGEBV and OHS fitness functions for parent selection in inbred crops using a novel R package, finding similar long-term genetic gains with dosage-based localGEBV offering simpler workflows.

An endogenous retrovirus insertion disrupting bovine ALKBH8 causes a failure-to-thrive syndrome with immunodeficiency associated with juvenile mortality in Brown Swiss cattle

Joint modeling of social genetic effects in mono- and pluri-specific groups: case study in intercrops

The paper develops a quantitative genetic model to analyze direct and social genetic effects in mono- and intercropped species, providing software for implementation and demonstrating its effectiveness through simulations.

Two-tower models for genomic prediction of reproductive outcomes and sex-specific fertility liabilities: simulation insights

This study evaluates two-tower machine learning models for predicting reproductive outcomes and sex-specific fertility liabilities using simulated genomic data.

Genome-wide meQTL mapping in cattle blood reveals cis and trans regulation of DNA methylation

This study maps cis and trans meQTLs in cattle blood DNA methylation using EpiChip data, identifying regulatory genes and hotspots associated with methylation patterns.

Enhancing predictive accuracy of yield traits in cassava through multi-trait genomic prediction

This study compares single-trait and multi-trait genomic prediction models for cassava yield traits, showing that multi-trait models improve predictive accuracy and reduce phenotyping burden.

A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits

This study creates a cattle transcriptome BodyMap across 52 tissues and 3 developmental stages, identifying lncRNAs and RNA editing sites linked to beef production traits.

Dissecting genetic variance structure and evaluating genomic prediction models for single-cross hybrids derived from Stiff Stalk and Non-Stiff Stalk maize heterotic groups

This study evaluates genomic prediction models for maize hybrids using GBLUP-based multi-kernel models to estimate genetic variance components and predict hybrid performance.

Mapping the Landscape of Allele-Specific Expression In Porcine Genomes

This study profiles allele-specific expression across 42 tissues and 34 pig breeds using an open-source pipeline, revealing widespread and tissue-specific allelic imbalance.

A cis-regulatory variant in ASIP causes gray coat color in the donkey

The paper identifies a cis-regulatory variant in the ASIP gene associated with gray coat color in donkeys through genome-wide analysis and functional validation.

Evidence of inbreeding depression on stature in Brown Swiss cattle

This study identifies inbreeding depression on stature in Brown Swiss cattle and discovers a recessive QTL linked to a splice donor variant in ABCC6.

Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array

This study develops a 72k SNP array to assess BKD resistance in Arctic charr and finds genomic prediction is feasible with moderate accuracy.

Genomic Dimensionality Bounds Mixed-Model Association Power, Fine-Mapping Resolution, and Genomic Prediction Reliability

This paper develops a framework explaining differences in GWAS results between livestock and humans by linking them to effective genomic dimensionality and population genetics parameters.

A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits

The paper presents a reusable TWAS workflow for cattle to identify gene-trait associations using GWAS and transcriptomic data, improving variant calling and detecting novel associations.

Insights from farming Macrocystis pyrifera offshore: phenotypic analysis, genome-wide association studies, genomic selection

The paper analyzes phenotypic data and performs genome-wide association studies and genomic selection for giant kelp to improve breeding programs.

Widespread genetic testing control inherited polycystic kidney disease in cats

This study examines the impact of PKD1 genetic testing on feline populations, finding a significant decrease in the PKD1 variant frequency and no changes in genetic structure or inbreeding.

Monitor individual health and improve breeding success in Crested ibis (Nipponia nippon)

The paper uses quantitative genetic tools to analyze growth traits in Crested ibis to improve breeding success and monitor individual health.

Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle

The paper identifies and validates copy number variation in dairy cattle using linked-read and short-read sequencing, finding 7218 high-confidence CNV regions with strong inheritance evidence.

Imputed graph-genotyped structural variants identify regulatory haplotypes associated with gene expression in Atlantic salmon

Genomic Inbreeding and Selection Signatures analyses in the Doberman Pinscher breed

This study analyzes genomic inbreeding and selection signatures in Doberman Pinschers using multiple methods, identifying loci associated with neurodevelopmental pathways.

Cross Potential Selection for Multiple Traits Considering the Progeny Distribution of Future Inbred Lines in Plant Breeding Programs

This paper introduces CPS-MT, a breeding strategy that improves a target trait while maintaining essential traits within ranges by evaluating cross-pairs based on predicted progeny distributions.

Genomic Prediction Enables Same-Season Selection for Reduced Glycosidic Nitrile in Eastern U.S. Winter Barley

This study demonstrates that genomic selection can predict glycosidic nitrile content in winter barley during the same growing season, enabling earlier breeding decisions.

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

The paper uses long-read RNA-seq to uncover isoform-level and context-specific regulatory effects in cattle, improving the resolution of molecular atlases and GWAS loci.

An interpretable machine learning framework for dog breed inference and ancestry decomposition

This paper introduces an interpretable machine learning framework to infer dog breeds from genomic data, achieving high accuracy and identifying key genetic variants.

PEC: a robust algorithm to reconcile pedigree and SNP-chip data on the basis of LD block, haplotype information, and Mendelian conflicts

PEC corrects pedigree errors in livestock by using LD blocks, haplotype information, and Mendelian conflict checks, improving genomic evaluation accuracy.

Daily feeding rhythms may play a role in the genetic variability of feed efficiency in growing pigs

This study investigates how daily feeding rhythms and genetic polymorphisms influence feed efficiency in pigs, finding heritable feeding behaviors and genetic correlations with RFI.

Genomic Informational Field Theory (GIFT) to identify genetic associations of a complex trait using a small sample size

This paper introduces GIFT, a method that enables accurate genetic association analysis in small datasets, identifying loci linked to height at withers in ponies and validating a hypothesis about insulin physiology.

High quality genome assemblies of African cattle breeds using PacBio HiFi sequencing

The paper presents high-quality genome assemblies for five African cattle breeds using PacBio HiFi sequencing, achieving high contiguity and completeness.

Genomic selection for seed yield enhances flax breeding efficiency

This study demonstrates that genomic selection improves flax breeding efficiency by reducing field testing costs and enhancing prediction accuracy for seed yield.