Publications

Pre-print

1. 1. Genomic selection strategies for clonal propagated crops
      Werner, C.R., C.R. Gaynor, D.J. Sargent, A. Lillo, G. Gorjanc, J.M. Hickey
      bioRxiv

1. 1. A Two-Part Strategy using Genomic Selection in Hybrid Crop Breeding Programs
      Powell, M.O., C.R. Gaynor, G. Gorjanc, C.R. Werner, J.M. Hickey
      bioRxiv

1. 1. AlphaPart – R implementation of the method for partitioning genetic trends
      Obsteter, J., J. Holl, R., J.M. Hickey, G. Gorjanc
      bioRxiv

1. 1. Genetics of recombination rate variation in the pig
      Johnsson, M., A. Whalen, R. Ros-Freixedes, G.Gorjanc, C. Chen, W.O. Herring, D. de Konning, J.M. Hickey
      bioRxiv

1. 1. Using high-throughput phenotypes to enable genomic selection by inferring genotypes
      Whalen, A, R. C. Gaynor, J.M. Hickey
      bioRxiv

1. 1. Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations
      Gonen, S, Valentin Wimmer, R. C. Gaynor, Ed Byrne, G. Gorjanc, J.M. Hickey
      bioRxiv

1. 1. AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data
      Whalen, A, G. Gorjanc, J.M. Hickey
      bioRxiv

1. 1. Genomic data enables genetic evaluation using data recorded on LMIC smallholder dairy farms
      Powell, M. O., R. Mrode, R. C. Gaynor, M. Johnsson, G. Gorjanc, J.M. Hickey
      bioRxiv

1. 1. A family-based phasing algorithm for sequence data
      Battagin, M., S. Gonen, R. Ros-Freixedes, A. Whalen, G. Gorjanc, J.M. Hickey
      bioRxiv

1. 1. 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
      Batista, L., R.C. Gaynor, G.R.A. Margarido, T. Byrne, P. Amer, G. Gorjanc, J.M. Hickey
      bioRxiv

2020

1. 1. Extending long-range phasing and haplotype library imputation algorithms to very large and heterogeneous datasets
      Money, D.P, D. Wilson, J. Jenko, G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 52:38.

1. 1. Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling
      Ros-Freixedes, R., A. Whalen, A.J. Mileham, G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 52:18.

1. 1. Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations
      Ros-Freixedes, R., A. Whalen, C. Chen, G. Gorjanc, W.O. Herring, A.J. Mileham, J.M. Hickey
      Genetics Selection Evolution, 52:17.

1. 1. In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop
      Cowling W.A., R. C. Gaynor, R. Antolin, G. Gorjanc, S.M. Edwards, O. Powell, J.M. Hickey
      Scientific Reports, 10:4037.

2019

1. 1. Modelling spatial variation in agricultural field trials with INLA
      M. Lie Selle, I. Steinsland, J.M. Hickey, G. Gorjanc
      Theoretical and Applied Genetics, 132:3277-3293.

1. 1. Efficient use of genomic information for sustainable genetic improvement in small cattle populations
      J. Obšteter, J. Jenko, J.M. Hickey, G. Gorjanc
      Journal of Dairy Science, 102:9971-9982.

1. 1. Students’, colleagues’ and research partners’ experience about work and accomplishments from collaborating with Robin Thompson
      Hickey, J.M., W.G. Hill, A. Blasco, N. Cameron, B. Cullis, B. McGuirk, E. Mäntysaari, J. Ruane, G. Simm R. Veerkamp, P.M. Visscher, N.R. Wray
      Journal of Animal Breeding and Genetics, 136:301-309.

1. 1. The Fest Issue on Robin Thompson’s contributions to statistics, genetics and animal/plant genetic improvement schemes
      Hickey, J.M., G. Gorjanc, W.G. Hill
      Journal of Animal Breeding and Genetics, 136:229-229.

1. 1. Family-specific genotype arrays increase the accuracy of pedigree based imputation at very low marker densities
      Whalen, A., G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 51:33.

1. 1. The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition
      Dawson, I.K., W. Powell, P. Hendre, J. Bančič, J.M. Hickey, R. Kindt, S. Hoad, I. Hale, R. Jamnadass
      New Phytologist, 224:37-54.

1. 1. Removal of alleles by genome editing – RAGE against the deleterious load
      Johnsson, M., R.C. Gaynor, J. Jenko, G. Gorjanc, D.J. de Koning, J.M. Hickey
      Genetics Selection Evolution, 51:14.

1. 1. The effects of training population design on genomic prediction accuracy in wheat
      McKinnon Edwards, S., J.B. Buntjer, R. Jackson, A.R. Bentley, J. Lage, E. Byrne, C. Burt, P. Jack, S. Berry, E. Flatman, B. Poupard, S. Smith, C. Hayes, R.C. Gaynor, G. Gorjanc, P. Howell, E. Ober, I.J. Mackay, J.M. Hickey
      Theoretical and Applied Genetics, 132:1943-1952.

1. 1. Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle
      Jenko, J., M.C. McClure, D. Matthews, J. McClure, M. Johnsson, G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 51:9.

1. 1. A Large-Scale Pedigree Resource of Wheat Reveals Evidence for Adaptation and Selection by Breeders
      N. Fradgley , K.A. Gardner, J. Cockram, J. Elderfield, J.M. Hickey, P. Howell, R. Jackson, I.J. Mackay
      PLOS Biology, 17(2):e3000071.

2018

1. 1. A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs
      Gottardo, P., G. Gorjanc, M. Battagin, C.R. Gaynor, J. Jenko, R. Ros-Freixedes, C.B.A. Whitelaw, A. Mileham, W. Herring, J.M. Hickey
      G3 – Genes, Genomes, Genetics, 9:203-215.

1. 1. Sequence variability, constraint and selection in the CD163 gene in pigs
      Johnsson, M., R. Ros-Freixedes, G. Gorjanc, M.A. Campbell, S. Naswa, K. Kelly, J. Lightner, S. Rounsley, J.M. Hickey
      Genetics Selection Evolution, 50:69.

1. 1. Hybrid peeling for fast and accurate calling, phasing and imputation with sequence data of any coverage in pedigrees
      Whalen, A., R. Ros-Freixedes, D. L. Wilson, G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 50:67.

1. 1. Parentage assignment with low density array data and low coverage sequence data
      Whalen, A., G. Gorjanc, J.M. Hickey
      Journal of Animal Breeding and Genetics, 136:102-112.

1. 1. Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
      Ros-Freixedes, R., M. Battagin, M. Johnsson, G. Gorjanc, DA.J. Mileham, S.D. Rounsley, J.M. Hickey
      Genetics Selection Evolution, 50:64.

1. 1. Assessment of the performance of hidden Markov models for imputation in animal breeding
      Whalen, A., G. Gorjanc, R. Ros-Freixedes, J.M. Hickey
      Genetics Selection Evolution, 50:44.

1. 1. A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-lateral plant populations
      Gonen, S., V. Wimmer, R.C. Gaynor, E. Byrne, G. Gorjanc, J.M. Hickey
      Theoretical Applied Genetics, 131:2345-2357.

1. 1. Accuracy of genotype imputation in Labrador Retrievers
      Friedrich, J., R. Antolin, S. M. Edwards, E. Sánchez-Molano, M. J. Haskell, J.M. Hickey, P. Wiener
      Animal Genetics, 49:303-311.

1. 1. Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection
      Gorjanc, G., R. C. Gaynor, J.M. Hickey
      Theoretical and Applied Genetics, 131:1953-1966.

1. 1. AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs
      Gorjanc, G., J.M. Hickey
      Bioinformatics, 19:3408-3411.

1. 1. Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers
      Edwards, S.M., J.A. Woolliams, J.M. Hickey, S.C. Blott, D.N. Clements, E. Sánchez-Molano, R.J. Todhunter, P. Wiener
      Frontiers Genetics, 9:101.

2017

1. 1. A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
      Ros-Freixedes, R., S. Gonen, G. Gorjanc, J.M. Hickey
      Genetics Selection Evolution, 49:78

1. 1. Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery
      Hickey, J.M., T. Chiurugwi, I. Mackay, W. Powell, and Implementing Genomic Selection in CGIAR Breeding Programs Workshop Participants.
      Nature Genetics, 49:1297-1303.

1. 1. The potential of shifting recombination hotspots to increase genetic gain in livestock breeding
      Gonen, S., M. Battagin, S.E. Johnston, G. Gorjanc and J. M. Hickey.
      Genetics Selection Evolution, 49:55.

1. 1. A two-part strategy for using genomic selection to develop inbred lines
      Gaynor, R.C., G. Gorjanc, A. R. Bentley, E. S. Ober, P. Howell, R. Jackson, I. J. Mackay, J. M. Hickey.
      Crop Science, 57:2372-2386.

1. 1. A method for the allocation of sequencing resources in genotyped livestock populations
      Gonen,S., R. Ros-Freixedes, M. Battagin, G. Gorjanc and J.M. Hickey.
      Genetics Selection Evolution, 49:47.

1. 1. Potential of Low-Coverage Genotyping-by-Sequencing and Imputation for Cost-Effective Genomic Selection in Biparental Segregating Populations
      Gorjanc, G., J.F. Dumasy, S. Gonen, R. C. Gaynor, R. Antolin, J. M. Hickey.
      Crop Science, 57:1–17.

1. 1. Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon
      Tsai, H.Y., O. Matika, S. M. Edwards, R. Antolín-Sánchez, A. Hamilton, D. R. Guy, A. E. Tinch, K. Gharbi, M. J. Stear, J. B. Taggart, J. E. Bron, J. M. Hickey, R. D. Houston.
      G3 (Bethesda). 117.040717.

1. 1. A hybrid method for the imputation of genomic data in livestock population
      Antolin R., C. Nettelblad, G. Gorjanc, D. Money, J.M. Hickey.
      Genetics Selection Evolution, 49:30.

1. 1. Prospects for Cost-Effective Genomic Selection via Accurate Within-Family Imputation
      Gorjanc, G., M. Battagin, J.F. Dumasy, R. Antolin, R. C. Gaynor, J. M. Hickey.
      Crop Science, 57:216–228.

1. 1. Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs
      Gonen, S, J. Jenko, G. Gorjanc, A.J. Mileham, C.B.A. Whitelaw, J.M. Hickey.
      Genetics Selection Evolution, 49:3.

2016

1. 1. Genome-Enabled Prediction Models for Yield Related Traits in Chickpea
      Roorkiwal, M., A. Rathore, R. R. Das, M. K. Singh, A. Jain, S. Samineni, P. M. Gaur, B. Chellapilla, S. Tripathi, Y. Li, J. M. Hickey, A. Lorenz, T. Sutton, J. Crossa, J. L. Jannink, R. K. Varshney.
      Frontiers in Plant Science, vol.7 no.1666

1. 1. Maximizing the potential of multi-parental crop populations
      Olufunmilayo, L., J. Elderfield, K. A. Gardner, R. C. Gaynor, J. M. Hickey, J. M. Hibberd, I. J. Mackay, A. R. Bentley.
      Applied & Translational Genomics, 11 (2016) 9–17.

1. 1. AlphaSim: Software for Breeding Program Simulation
      Faux A. M., G. Gorjanc, R. C. Gaynor , M. Battagin, S. M. Edwards, D. L. Wilson, Sarah J. Hearne, S. Gonen, and J. M. Hickey.
      The Plant Genome, vol. 9, no.3

1. 1. Effect of manipulating recombination rates on response to selection in livestock breeding programs
      Battagin, M., G. Gorjanc, A. M. Faux, S. E. Johnston and J. M. Hickey.
      Genetics Selection Evolution, 48:44.

1. 1. Implementation of Genomic Selection in The Poultry Industry
      Wolc, A., A. Kranis, J. Arango, P. Settar, J. E. Fulton, N. P. O’Sullivan, A. Avendano, K. A. Watson, J. M. Hickey, G. de los Campos, R.L. Fernando, D. J. Garrick, J. C. M. Dekkers.
      Animal Frontiers, 6: 1.

1. 1. Promotion of Alleles by Genome Editing in Livestock Breeding Programmes.
      Hickey, J. M. , C. Bruce, A. Whitelaw and G. Gorjanc.
      Journal of Animal Breeding and Genetics, 133(2):83-4.

1. 1. Initiating Maize Pre-Breeding Programs Using Genomic Selection to Harness Polygenic Variation from Landrace Populations.
      Gorjanc, G., J. Jenko, S. J. Hearne and J. M. Hickey.
      BMC Genomics, 17(1):30.

2015

1. 1. Analytical and Decision Support Tools for Genomics-Assisted Breeding.
      Varshney, R. K., V. K. Singh, J. M. Hickey, X. Xun, D. F. Marshall, J. Wang, D. Edwards and J. M. Ribaut.
      Trends in Plant Science, 21(4): 354–363.

1. 1. Gpluse: Beyond Genomic Selection.
      Mackay, I. J., E. S. Ober and J. M. Hickey.
      Food and Energy Security, 4(1):25-35.

1. 1. Potential of Promotion of Alleles by Genome Editing to Improve Quantitative Traits in Livestock Breeding Programs.
      Jenko, J., G. Gorjanc, M. A. Cleveland, R. K. Varshney, C. B. Whitelaw, J. A. Woolliams and J. M. Hickey.
      Genetics Selection Evolution, 47:55.

1. 1. Imputation of Single Nucleotide Polymorphism Genotypes in Biparental, Backcross, and Topcross Populations with a Hidden Markov Model.
      Hickey, J. M., G. Gorjanc, R. K. Varshney and C. Nettelblad.
      Crop Science, 55(5):1934.

1. 1. Potential of Genotyping-by-Sequencing for Genomic Selection in Livestock Populations.
      Gorjanc, G., M. A. Cleveland, R. D. Houston and J. M. Hickey.
      Genetics Selection Evolution, 47:12.

1. 1. Reliability of Pedigree-Based and Genomic Evaluations in Selected Populations.
      Gorjanc, G., P. Bijma and J. M. Hickey.
      Genetics Selection Evolution, 47:65.

2014

1. 1. Alphampsim: Flexible Simulation of Multi-Parent Crosses.
      Hickey, J. M., G. Gorjanc, S. Hearne and B. E. Huang.
      Bioinformatics, 30(18):2686-8.

1. 1. Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation.
      Hickey, J. M., S. Dreisigacker, J. Crossa, S. Hearne, R. Babu, B. M. Prasanna, M. Grondona, A. Zambelli, V. S. Windhausen, K. Mathews and G. Gorjanc.
      Crop Science, 54(4):1476.

1. 1. Evaluation of Measures of Correctness of Genotype Imputation in the Context of Genomic Prediction: A Review of Livestock Applications.
      Calus, M. P., A. C. Bouwman, J. M. Hickey, R. F. Veerkamp and H. A. Mulder.
      Animal, 8(11):1743-53.

1. 1. Imputation of Non-Genotyped Individuals Based on Genotyped Relatives: Assessing the Imputation Accuracy of a Real Case Scenario in Dairy Cattle.
      Bouwman, A. C., J. M. Hickey, M. P. Calus and R. F. Veerkamp.
      Genetics Selection Evolution, 46:6.

2013

1. 1. Extending Long-Range Phasing and Haplotype Library Imputation Methods to Impute Genotypes on Sex Chromosomes.
      Hickey, J. M. and A. Kranis.
      Genetics Selection Evolution, 45:10.

1. 1. Genomic Evaluations Using Similarity between Haplotypes.
      Hickey, J. M., B. P. Kinghorn, B. Tier, S. A. Clark, J. H. van der Werf and G. Gorjanc.
      Journal of Animal Breeding and Genetics, 130(4):259-69

1. 1. Genotype Imputation to Increase Sample Size in Pedigreed Populations.
      Hickey, J. M., M. A. Cleveland, C. Maltecca, G. Gorjanc, B. Gredler and A. Kranis.
      Methods in Molecular Biology, 1019:395-410.

1. 1. Sequencing Millions of Animals for Genomic Selection 2.0.
      Hickey, J. M.
      Journal of Animal Breeding and Genetics, 130(5):331-2

1. 1. Genotype Phasing in Populations of Closely Related Individuals.
      Hickey, J. M.
      Methods in Molecular Biology, 1019:381-94.

1. 1. Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding.
      De Los Campos, G., J. M. Hickey, R. Pong-Wong, H. D. Daetwyler and M. P. Calus.
      Genetics, 193(2):327-45.

1. 1. Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking.
      Daetwyler, H. D., M. P. Calus, R. Pong-Wong, G. de Los Campos and J. M. Hickey.
      Genetics, 193(2):347-65.

1. 1. Genomic Prediction in CIMMYT Maize and Wheat Breeding Programs.
      Crossa, J., P. Pérez, J. Hickey, J. Burgueño, L. Ornella, J. Cerón-Rojas, X. Zhang, S. Dreisigacker, R. Babu, Y. Li, D. Bonnett and K. Mathews.
      Heredity, 112(1):48-60.

1. 1. Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing.
      G. Crossa, J., Y. Beyene, S. Kassa, P. Perez, J. M. Hickey, C. Chen, G. de los Campos, J. Burgueno, V. S. Windhausen, E. Buckler, J. L. Jannink, M. A. Lopez Cruz and R. Babu.
      G3 (Bethesda), 3(11):1903-26.

1. 1. Practical Implementation of Cost-Effective Genomic Selection in Commercial Pig Breeding Using Imputation.
      Cleveland, M. A. and J. M. Hickey.
      Journal of Animal Science, 91(8):3583-92.

1. 1. The Effect of Genomic Information on Optimal Contribution Selection in Livestock Breeding Programs.
      Clark, S. A., B. P. Kinghorn, J. M. Hickey and J. H. van der Werf.
      Genetics Selection Evolution, 45:44.

1. 1. Genetic Prediction of Complex Traits: Integrating Infinitesimal and Marked Genetic Effects.
      Carre, C., F. Gamboa, D. Cros, J. M. Hickey, G. Gorjanc and E. Manfredi.
      Genetica, 141(4-6):239-46.

2012

1. 1. Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments.
      Windhausen, V. S., G. N. Atlin, J. M. Hickey, J. Crossa, J. L. Jannink, M. E. Sorrells, B. Raman, J. E. Cairns, A. Tarekegne, K. Semagn, Y. Beyene, P. Grudloyma, F. Technow, C. Riedelsheimer and A. E. Melchinger.
      G3 (Bethesda), 2(11):1427-36.

1. 1. Assessment of Alternative Genotyping Strategies to Maximize Imputation Accuracy at Minimal Cost.
      Huang, Y., J. M. Hickey, M. A. Cleveland and C. Maltecca.
      Genetics Selection Evolution, 44:25.

1. 1. A Phasing and Imputation Method for Pedigreed Populations That Results in a Single-Stage Genomic Evaluation.
      Hickey, J. M., B. P. Kinghorn, B. Tier, J. H. van der Werf and M. A. Cleveland.
      Genetics Selection Evolution, 44:9.

1. 1. Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods.
      Hickey, J. M. and G. Gorjanc.
      G3 (Bethesda), 2(4):425-7.

1. 1. Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs.
      Hickey, J. M., J. Crossa, R. Babu and G. de los Campos.
      Crop Science, 52(2):654.

1. 1. A Common Dataset for Genomic Analysis of Livestock Populations.
      Cleveland, M. A., J. M. Hickey and S. Forni.
      G3 (Bethesda), 2(4):429-35.

1. 1. The Importance of Information on Relatives for the Prediction of Genomic Breeding Values and the Implications for the Makeup of Reference Data Sets in Livestock Breeding Schemes.
      Clark, S. A., J. M. Hickey, H. D. Daetwyler and J. H. van der Werf.
      Genetics Selection Evolution, 44:4.

2011

1. 1. A Combined Long-Range Phasing and Long Haplotype Imputation Method to Impute Phase for SNP Genotypes.
      Hickey, J. M., B. P. Kinghorn, B. Tier, J. F. Wilson, N. Dunstan and J. H. van der Werf.
      Genetics Selection Evolution, 43:12.

1. 1. Genotype Imputation for the Prediction of Genomic Breeding Values in Non-Genotyped and Low-Density Genotyped Individuals.
      Cleveland, M. A., J. M. Hickey and B. P. Kinghorn.
      BMC Proceedings, Volume 5 Supplement 3:S6.

1. 1. Different Models of Genetic Variation and Their Effect on Genomic Evaluation.
      Clark, S. A., J. M. Hickey and J. H. van der Werf.
      Genetics Selection Evolution, 43:18.

2010

1. 1. Accuracy of Estimated Genomic Breeding Values for Wool and Meat Traits in a Multi-Breed Sheep Population.
      Daetwyler, H. D., J. M. Hickey, J. M. Henshall, S. Dominik, B. Gredler, J. H. J. van der Werf and B. J. Hayes.
      Animal Production Science, 50(12):1004.

2009

1. 1. Estimation of Prediction Error Variances Via Monte Carlo Sampling Methods Using Different Formulations of the Prediction Error Variance.
      Hickey, J. M., R. F. Veerkamp, M. P. Calus, H. A. Mulder and R. Thompson.
      Genetics Selection Evolution, 41:23.

2008

1. 1. Estimation of Accuracy and Bias in Genetic Evaluations with Genetic Groups Using Sampling.
      Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie, H. A. Mulder and R. F. Veerkamp.
      Journal of Animal Science, 86(5):1047-56.

2007

1. 1. Genetic Parameters for EUROP Carcass Traits within Different Groups of Cattle in Ireland.
      Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie and R. F. Veerkamp.
      Journal of Animal Science, 85(2):314-21.

1. 1. Heterogeneity of Genetic Parameters for Calving Difficulty in Holstein Heifers in Ireland.
      Hickey, J. M., M. G. Keane, D. A. Kenny, A. R. Cromie, P. R. Amer and R. F. Veerkamp.
      Journal of Dairy Science, 90(8):3900-8.

2006

1. 1. Genetic Aspects of Growth of Holstein-Friesian Dairy Cows from Birth to Maturity.
      Coffey, M. P., J. M. Hickey and S. Brotherstone.
      Journal of Dairy Science, 89(1):322-9.