John M. Hickey

Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population

The paper develops an algorithm to accurately assign breed origin to alleles in crossbred dairy cattle, achieving high accuracy in simulated breeding programs.

Using large-scale whole-genome sequence data for single-step genomic predictions in maternal and terminal pig lines

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.

Genomic selection strategies for clonally propagated crops

This study compares genomic selection strategies in clonal plant breeding, finding that selecting parents based on genomic predicted cross performance leads to faster genetic gain and reduced inbreeding.

Genomic prediction with whole-genome sequence data in intensely selected pig 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.

Rare and population-specific functional variation across pig lines

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

Performance of genetic imputation across commercial crop species

The paper demonstrates accurate genetic imputation in maize, sugar beet, and wheat without pedigrees, outperforming Beagle 5.1 in most scenarios.

Genetics of recombination rate variation in the pig

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.

Plant breeders should be determining economic weights for a selection index instead of using independent culling for choosing parents in breeding programs with genomic selection

The paper compares index selection and independent culling in genomic selection for multi-trait breeding programs, showing index selection is more efficient when economic weights are known.

AlphaPart - R implementation of the method for partitioning genetic trends

AlphaPart partitions genetic trends to identify sources of genetic gain in breeding programs using a simulated pig example.

Modelling illustrates that genomic selection provides new opportunities for intercrop breeding

This paper shows genomic selection in intercrop breeding programs leads to greater genetic gain than phenotypic selection, regardless of genetic correlation with monocrop yield.

AlphaSimR: An R-package for Breeding Program Simulations

AlphaSimR is an R package for simulating plant and animal breeding programs, offering flexibility in modeling complex breeding strategies.

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations

The paper introduces a method to phase and impute genotypes of missing parents in bi-parental plant populations, achieving high accuracy for both parents and their descendants.

Spatial modelling improves genetic evaluation in smallholder breeding programs

This study shows spatial modelling improves genetic evaluation in smallholder dairy cattle systems by better separating genetic and environmental effects.

AlphaImpute2: Fast and accurate pedigree and population based imputation for hundreds of thousands of individuals in livestock populations

AlphaImpute2 improves imputation accuracy and speed for large livestock populations, outperforming existing methods in both metrics.

AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data

AlphaFamImpute improves genotype imputation in full-sib families using low-coverage GBS data by leveraging shared haplotype segments between siblings.

Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling

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.

Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations

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.

Using high-throughput phenotypes to enable genomic selection by inferring genotypes

This paper develops a method to infer genotypes from high-throughput phenotypes to enable genomic selection in plant breeding programs, showing increased genetic gain in simulations.

Modelling spatial variation in agricultural field trials with INLA

This paper compares spatial models for agricultural field trials using INLA, showing AR1⊗AR1 and SPDE models provide best predictive performance with or without genomic data.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations

This paper simulates genomic selection strategies in a small dairy population to evaluate their impact on genetic gain, variation, and sustainability.

Removal of alleles by genome editing -- RAGE against the deleterious load

This study simulates genome editing and selection strategies to reduce deleterious load in animal breeding, finding that editing multiple recessive variants is more effective than selection against carriers.

The effects of training population design on genomic prediction accuracy in wheat

This study evaluates how training population design affects genomic prediction accuracy in wheat, finding that larger training sets and related crosses improve prediction accuracy.

Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle

The paper identifies three haplotypes with putatively recessive lethal alleles in Irish beef cattle and shows their pleiotropic effects on economically important traits.

A family-based phasing algorithm for sequence data

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

A strategy to exploit surrogate sire technology in livestock breeding programs

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.

Parentage assignment with genotyping-by-sequencing data

This paper evaluates using genotype-by-sequencing data for parentage assignment, showing high-coverage data performs similarly to array data and low-coverage data can be effective with sufficient markers.

Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

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

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

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.

Sequence variability, constraint and selection in the CD163 gene in pigs

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.

Assessment of the performance of different hidden Markov models for imputation in animal breeding

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.