Genetic and phenotypic traits in livestock

Predicting phenotypes with one step genetic decision trees

The paper uses computer vision and machine learning to predict growth traits in snapper, finding that models capture 18-40% of genetic variation but face challenges from population structure.

Early life exploration behavior and life-history loci are co-localized in an adaptive genomic hotspot in Atlantic salmon.

This study identifies a genomic region linked to both exploration behavior and age at maturity in Atlantic salmon, suggesting a co-adapted trait complex.

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep

The paper evaluates regional heritability mapping methods to identify QTLs in Soay sheep, finding that some methods detect new trait-associated regions not found by GWAS.

Large effect life-history genomic regions are associated with functional morphological traits in Atlantic salmon

The paper investigates the association between life-history loci and morphological traits in Atlantic salmon, finding complex relationships that may result from pleiotropy or linkage.

How partial phenotyping to reduce generation intervals can help to increase annual genetic gain in selected honeybee populations

This study shows that reducing the generation interval in honeybee breeding by focusing on early traits can increase genetic gain, though it requires strategies to manage inbreeding.

TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs

TypeSINE identifies SINE retrotransposon polymorphisms in pigs, revealing body size-associated variants and population history.

Clinical, Biological and Pathological Investigation of Bovine Lymphocyte Intestinal Retention Deficit (BLIRD): a new genetic disorder affecting life expectancy and immunity in Holstein dairy cattle

This paper investigates a new genetic disorder in Holstein cattle caused by an ITGB7 mutation, showing reduced lifespan, poor growth, and immune-related symptoms in homozygous carriers.

PCAGP, a parallel convolutional attention network-based method for crop genomic prediction

PCAGP improves crop genomic prediction accuracy by using a parallel convolutional attention network, outperforming existing methods across multiple datasets.

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

This study evaluates factors affecting genomic prediction accuracy in switchgrass, finding that exome capture and multi-allelic variants improve predictions for complex traits.

Incorporating gene expression and environment improves genomic prediction of wheat traits

This study improves genomic prediction of wheat traits by integrating gene expression and environmental data, showing that combining transcriptome and environment data enhances prediction accuracy.

Prioritization of Deleterious Mutations Improves Genomic Prediction and Increases the Rate of Genetic Gain in Common Bean (Phaseolus vulgaris L.), a Simulation Study

This study shows that prioritizing deleterious mutations improves genomic prediction accuracy for yield in common bean and increases genetic gain through optimized breeding strategies.

Advances in multi-trait genomic prediction approaches: Classification, comparative analysis, and perspectives

This paper classifies and compares multi-trait genomic prediction models using an Oryza sativa diversity panel to identify strengths and limitations of existing approaches.

Genetic estimates and genome-wide association studies of antibody response in Tanzanian dairy cattle

The paper identifies genetic variants associated with antibody responses to infectious diseases in Tanzanian dairy cattle using genome-wide association studies.

Transcriptomic Prediction of Breeding Values in Loblolly Pine

This study uses transcriptomic data to predict breeding values in loblolly pine by analyzing gene expression patterns and their relationship to genetic variation.

A mechanistic model in sheep incorporating energy allocation trade-offs between the ewe and her lambs

This paper presents a mechanistic energy allocation model in sheep that incorporates trade-offs between the ewe and her lambs, simulating lifetime responses to feeding and management.

Back to the Future: Environmental genomic selection to take advantage of polygenic local adaptation

This paper applies environmental genomic selection to barley landraces to identify key parents for breeding adapted to specific environments.

Optimizing Cost-Effective Gene Expression Phenotyping Approaches in Cattle Using 3' mRNA Sequencing

This paper optimizes 3' mRNA sequencing for cost-effective gene expression phenotyping in cattle using whole blood samples, identifying the best library prep kit and sequencing depth.

Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes

The paper constructs a bovine pangenome using long-read sequencing and identifies structural variants associated with key phenotypes in French cattle breeds.

Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing

This study constructs a draft pangenome for Indian desi cattle using short-read sequencing, identifying novel sequences that improve genetic variant discovery and mapping accuracy.

Identification of Bone Morphogenic Protein (BMP15) gene at exons 1 and 2 in Indigenous, Mozaffornagri, and Dorper ram breeds of Bangladesh and its phylogenetic relationship with other breeds

The paper identifies the BMP15 gene in three Bangladeshi sheep breeds and finds no polymorphisms, but reports strong genetic links between local and international breeds.

Research on crop phenotype prediction using SNP context and whole-genome feature embedding

This paper introduces SNP-context and whole-genome feature embeddings using DNABERT-2 for crop phenotype prediction, showing improved accuracy over traditional methods for traits with varying heritability.

Estimation of heritabilities and genetic correlations by time slices using predictivity in large genomic models

The paper develops formulas to estimate heritabilities and genetic correlations in large genomic models using predictivity, validated with real and simulated data.

Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

The paper identifies a structural variant upstream of KIT associated with facial depigmentation in white-headed cattle using pangenome analysis and long-read sequencing.

Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)

This study generates the first banteng reference genome and analyzes 78 resequenced samples to explore its domestication history and genetic structure.

High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing

The paper imputes SNVs and SVs from low-coverage WGS data in Atlantic salmon, showing improved accuracy with SV genotype likelihoods.

Genome-wide association studies reveal novel loci associated with carcass and body measures in goats (Capra hircus)

This study identifies novel genetic loci associated with growth and carcass traits in Chongqing local goats using whole-genome resequencing.

LCORL and STC2 variants increase body size and growth rate in cattle and other animals

The paper identifies LCORL and STC2 variants associated with increased body size and growth rate in cattle and other domesticated animals through genetic analysis and mouse models.

Trajectories of genetic correlations in populations under selection: from theory to a case-study

The paper investigates how multi-trait selection affects genetic correlations in populations, using theory and a case study on dairy cattle data.

A similarity matrix for preserving haplotype diversity among parents in genomic selection

The paper introduces a similarity matrix to preserve haplotype diversity in genomic selection by quantifying parent similarity based on gamete covariance, showing improved genetic variability and gain.

Improved Genomic Prediction Performance with Ensembles of Diverse Models

The paper shows that combining multiple genomic prediction models improves accuracy and reduces errors in predicting crop traits, supporting the Diversity Prediction Theorem.