Genetic and phenotypic traits in livestock

This paper introduces localGEBV, a haplotype-based method that improves QTL discovery and phenotypic prediction compared to traditional GWAS approaches in barley.

This study identifies and analyzes copy number variations in four South American camelid species using whole-genome data, revealing species-specific patterns and functional associations.

This study compares morpho-biometric traits of two Mozambican goat breeds, identifying phenotypic differences that support breed characterization and conservation strategies.

The paper analyzes transcriptomics and metabolomics data from coarse and fine cashmere goats to identify genes and metabolites associated with fiber diameter differences.

This study genotypes Red Steppe cattle to assess genetic diversity, inbreeding, and population structure using SNP data, identifying three ancestral components and candidates for breeding.

This study identifies three genomic regions and 12 candidate genes associated with age at first service in Chinese Holstein heifers using GWAS and colocalization analysis, highlighting ANAPC4 as a putative causal gene.

This paper evaluates how hyperparameters affect prediction stability and performance in genomic prediction for wheat breeding using Gradient Boosting Machines.

This paper evaluates deep learning's ability to predict genetic values in crossbred populations by capturing heterosis, finding it improves performance when heterosis is present.

This study uses whole-genome sequencing and genomic prediction to accelerate heartwood formation in oak trees by identifying genetic markers linked to heartwood traits.

WISER improves breeding value estimation by addressing population structure and genotype-environment confounding through spectral whitening, outperforming LS-means and BLUP across multiple species and traits.

The paper identifies SNPs and structural polymorphisms associated with growth traits in silver birch and evaluates their predictive power for growth rates across different environments.

This study assesses genetic diversity and conservation strategies for alpacas and llamas in Southern Peru using mitochondrial DNA analysis and evaluates the effectiveness of an ex situ germplasm bank.

This paper improves genomic prediction accuracy by using synthetic traits derived from hyperspectral data, showing higher accuracy than single-trait models for leaf traits in sorghum.

The paper constructs a cattle cell-type-specific regulatory variant atlas by integrating bulk and single-cell RNA-seq data, identifying eQTL and linking them to GWAS loci for breeding insights.

This study identifies mutual gene flow between Island Southeast Asian and Southern African goats through European maritime activities using genome-wide SNP analysis.

This study estimates heritability and breeding values for flowering and maturity time in almond using historical data and Bayesian models to improve breeding strategies.

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.

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

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

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

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

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.

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

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.

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

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

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

The paper analyzes trait persistence in laying hens from 70 to 92 weeks, identifying traits with stable genetic variance and those requiring alternative selection strategies.