Roger Ros‐Freixedes

This study examines the association between mitochondrial DNA copy number and production traits in pigs, finding correlations with backfat thickness and carcase lean percentage.

The paper presents a high-quality long-read de novo genome assembly for the red-legged partridge, providing insights into its genetic dynamics and management.

The paper presents a nearly chromosome-level genome assembly and annotation of Alectoris rufa, revealing evolutionary relationships with quail and chicken.

This study evaluates the impact of using whole-genome sequence data for genomic predictions in pig lines, finding modest improvements in accuracy for maternal lines but mixed results for terminal lines.

This study evaluates the benefits of using whole-genome sequence data for genomic prediction in pigs, finding small improvements over marker arrays in some scenarios.

The paper identifies rare and population-specific functional variants in commercial pig lines and assesses their impact on production traits and genomic prediction.

This study estimates recombination rate variation in pigs using multiocus iterative peeling across 150,000 pigs, identifies heritability, and finds three genomic regions associated with recombination.

This study evaluates sequencing strategies for whole-genome imputation using hybrid peeling, finding that 2% of the population sequenced at 2x coverage provides high accuracy.

This study demonstrates high accuracy of whole-genome sequence imputation in large livestock populations using hybrid peeling, with median individual-wise correlation of 0.97.

AlphaFamSeq is a family-based phasing algorithm that minimizes errors and maximizes allele phasing, achieving high accuracy in simulated data.

This study simulates strategies for using surrogate sire technology to enhance genetic merit in livestock breeding, finding a three-stage approach most effective for maximizing genetic gain.

This paper introduces hybrid peeling, a method for efficiently calling, phasing, and imputing sequence data in pedigrees, showing improved accuracy and coverage.

The paper shows that index hopping and reference allele bias have minimal impact on genotype calls from low-coverage sequencing, but pruning low-support haplotypes introduces a significant reference allele bias.

The paper analyzes sequence variation, constraint, and selection in the CD163 gene in pigs, finding no knock-out variants and evidence of positive selection but no recent selective sweeps.

This study compares hidden Markov model-based imputation methods in animal breeding, finding that pre-phasing with Eagle2 or HAPI-UR and haploid imputation with minimac3 or IMPUTE2 is faster and more accurate than diploid imputation.

This paper introduces AlphaSeqOpt, a method that allocates low-coverage sequencing resources by targeting haplotypes to improve phasing and imputation accuracy.