Ben Hayes

Summary

Country: Australia

Publications

  1. pmc Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    Ben J Hayes
    Victorian Institute of Animal Science, Department of Natural Resources and Environment, Attwood, Victoria, 3049, Australia
    Genome Res 13:635-43. 2003
  2. pmc Design of a bovine low-density SNP array optimized for imputation
    Didier Boichard
    UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research INRA, Jouy en Josas, France
    PLoS ONE 7:e34130. 2012
  3. pmc Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation
    Hans D Daetwyler
    Biosciences Research Division, Department of Primary Industries, Bundoora, Victoria 3083, Australia
    Genet Sel Evol 44:33. 2012
  4. pmc Genes of the RNASE5 pathway contain SNP associated with milk production traits in dairy cattle
    Lesley Ann Raven
    Biosciences Research Division, Department of Primary Industries Victoria, 5 Ring Rd, Bundoora 3086, Australia
    Genet Sel Evol 45:25. 2013
  5. pmc Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle
    Mehar S Khatkar
    Reprogen Animal Bioscience, Faculty of Veterinary Science, University of Sydney, 425 Werombi Road, Camden, NSW 2570, Australia
    BMC Genomics 13:538. 2012
  6. pmc Genome position specific priors for genomic prediction
    Rasmus Froberg Brøndum
    Centre for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Tjele, 8830, Denmark
    BMC Genomics 13:543. 2012
  7. pmc High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing
    Elizabeth M Ross
    Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia
    BMC Genet 13:53. 2012
  8. doi request reprint The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation
    Ben J Hayes
    Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia
    Trends Genet 29:206-14. 2013
  9. doi request reprint Accuracy of genotype imputation in sheep breeds
    B J Hayes
    Biosciences Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria 3083, Australia
    Anim Genet 43:72-80. 2012
  10. pmc Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers
    Gerhard Moser
    Dairy Futures Cooperative Research Centre, Australia
    Genet Sel Evol 42:37. 2010

Collaborators

Detail Information

Publications45

  1. pmc Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    Ben J Hayes
    Victorian Institute of Animal Science, Department of Natural Resources and Environment, Attwood, Victoria, 3049, Australia
    Genome Res 13:635-43. 2003
    ..Results indicated an exponentially increasing N in humans and a declining N in dairy cattle. CSH is a valuable statistic for inferring population histories from haplotype data, and has implications for mapping of disease loci...
  2. pmc Design of a bovine low-density SNP array optimized for imputation
    Didier Boichard
    UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research INRA, Jouy en Josas, France
    PLoS ONE 7:e34130. 2012
    ..The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle...
  3. pmc Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation
    Hans D Daetwyler
    Biosciences Research Division, Department of Primary Industries, Bundoora, Victoria 3083, Australia
    Genet Sel Evol 44:33. 2012
    ..Carcass and novel meat quality traits were predicted in a multi-breed sheep population that included Merino, Border Leicester, Polled Dorset and White Suffolk sheep and their crosses...
  4. pmc Genes of the RNASE5 pathway contain SNP associated with milk production traits in dairy cattle
    Lesley Ann Raven
    Biosciences Research Division, Department of Primary Industries Victoria, 5 Ring Rd, Bundoora 3086, Australia
    Genet Sel Evol 45:25. 2013
    ..We then tested SNP in close proximity to the genes of this pathway for association with milk production traits in a large dairy cattle dataset...
  5. pmc Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle
    Mehar S Khatkar
    Reprogen Animal Bioscience, Faculty of Veterinary Science, University of Sydney, 425 Werombi Road, Camden, NSW 2570, Australia
    BMC Genomics 13:538. 2012
    ..For the accuracy of genomic selection, a comparison of direct genetic values (DGV) was made by dividing the data into training and validation sets under a range of imputation scenarios...
  6. pmc Genome position specific priors for genomic prediction
    Rasmus Froberg Brøndum
    Centre for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Tjele, 8830, Denmark
    BMC Genomics 13:543. 2012
    ..The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed...
  7. pmc High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing
    Elizabeth M Ross
    Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia
    BMC Genet 13:53. 2012
    ..Given faecal samples are much easier to obtain than rumen fluid samples; we also investigated whether rumen metagenome profiles were predictive of faecal metagenome profiles...
  8. doi request reprint The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation
    Ben J Hayes
    Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia
    Trends Genet 29:206-14. 2013
    ..Here, we review these gains. We also discuss how the use of whole-genome sequence data should both accelerate the rate of gain and enable rapid discovery and elimination of genetic defects from livestock populations...
  9. doi request reprint Accuracy of genotype imputation in sheep breeds
    B J Hayes
    Biosciences Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria 3083, Australia
    Anim Genet 43:72-80. 2012
    ..This is promising, suggesting that in silico genome re-sequencing is possible in sheep if a suitable pool of key ancestors is sequenced for each breed...
  10. pmc Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers
    Gerhard Moser
    Dairy Futures Cooperative Research Centre, Australia
    Genet Sel Evol 42:37. 2010
    ..The objective of this study was to evaluate the use of low-density assays to predict direct genomic value (DGV) on five milk production traits, an overall conformation trait, a survival index, and two profit index traits (APR, ASI)...
  11. pmc Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms
    Arne B Gjuvsland
    Centre for Integrative Genetics CIGENE, Norwegian University of Life Sciences, As, Norway
    BMC Syst Biol 1:32. 2007
    ..Here we explore to which degree the phenotypic manifestation of local and distant polymorphisms is a dynamic feature of regulatory design...
  12. pmc A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns
    Sigbjørn Lien
    Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N 1432, As, Norway
    BMC Genomics 12:615. 2011
    ..The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species...
  13. pmc Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle
    Saber Qanbari
    Animal Breeding and Genetics Group, Department of Animal Sciences, Georg August University, 37075 Gottingen, Germany
    BMC Genomics 12:318. 2011
    ....
  14. pmc Recent and historical recombination in the admixed Norwegian Red cattle breed
    Marte Sodeland
    Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, N 1432 Aas, Norway
    BMC Genomics 12:33. 2011
    ..While measures of LD is also crucial for determining the number of markers required for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies...
  15. pmc Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle
    Marte Sodeland
    Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N 1432 Aas, Norway
    BMC Genet 12:70. 2011
    ..Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population...
  16. pmc Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle
    Hanne Gro Olsen
    BoviBank Ltd, Aas, Norway
    BMC Genet 8:32. 2007
    ....
  17. pmc Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits
    Ben J Hayes
    Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia
    PLoS Genet 6:e1001139. 2010
    ....
  18. doi request reprint Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species
    B J Hayes
    Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora 3083, Australia
    Genet Res (Camb) 91:367-71. 2009
    ..Here, we demonstrate the value of selective genotyping strategies which balance the contribution of families across high and low phenotypes to greatly reduce rates of false discovery with a minimal effect on power...
  19. doi request reprint Genome-wide association and genomic selection in animal breeding
    Ben Hayes
    Biosciences Research Division, Department of Primary Industries Victoria, 1 Park Drive, Bundoora 3083, Australia
    Genome 53:876-83. 2010
    ..Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships...
  20. pmc Accuracy of genomic breeding values in multi-breed dairy cattle populations
    Ben J Hayes
    Biosciences Research Division, Department of Primary Industries Victoria, Bundoora, Australia
    Genet Sel Evol 41:51. 2009
    ..The accuracies were obtained both as a function of elements of the inverse coefficient matrix and from the realised accuracies of GEBV...
  21. pmc A validated genome wide association study to breed cattle adapted to an environment altered by climate change
    Ben J Hayes
    Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia
    PLoS ONE 4:e6676. 2009
    ..The validated marker panels we have reported here will aid selection for high milk production under anticipated climate change scenarios, for example selection of sires whose daughters will be most productive at low levels of feeding...
  22. doi request reprint Technical note: prediction of breeding values using marker-derived relationship matrices
    B J Hayes
    Department of Primary Industries Victoria, Attwood, Victoria 3049, Australia
    J Anim Sci 86:2089-92. 2008
    ..The approach is demonstrated for an Angus data set with 9,323 SNP markers genotyped...
  23. doi request reprint Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle
    B J Hayes
    Cooperative Research Centre for Beef Genetic Technologies, CJ Hawkins Homestead, University of New England, Armidale, Australia
    Genet Res 89:215-20. 2007
    ..A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes...
  24. doi request reprint Increased accuracy of artificial selection by using the realized relationship matrix
    B J Hayes
    Biosciences Research Division, Department of Primary Industries Victoria, 1 Park Drive, Bundoora 3083, Australia
    Genet Res (Camb) 91:47-60. 2009
    ..3, and N(e)=100, approximately 12474 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0.7 [corrected]...
  25. doi request reprint Invited review: Genomic selection in dairy cattle: progress and challenges
    B J Hayes
    Department of Primary Industries Victoria, Biosciences Research Division, Bundoora, Australia
    J Dairy Sci 92:433-43. 2009
    ..Many challenges with genomic selection and its implementation remain, including increasing the accuracy of GEBV, integrating genomic information into national and international genetic evaluations, and managing long-term genetic gain...
  26. doi request reprint A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle
    B J Hayes
    Cooperative Research Centre for Beef Genetic Technologies, CJ Hawkins Homestead, University of New England, Armidale, NSW 2351, Australia
    Anim Genet 40:176-84. 2009
    ..Finally, for the chromosome tested, the location of selection signatures between dairy and beef cattle was correlated with the location of selection signatures within dairy cattle...
  27. pmc Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination
    Ben Hayes
    Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N 1432 As, Norway
    Genetics 174:455-64. 2006
    ..Further, there was evidence for a site of preferential recombination between CSN2 and CSN1S2. The value of the haplotypes for haplotype-assisted selection (HAS) is discussed...
  28. doi request reprint The origin of selection signatures on bovine chromosome 6
    B J Hayes
    Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, VIC 3049, Australia
    Anim Genet 39:105-11. 2008
    ....
  29. ncbi request reprint SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
    Ben J Hayes
    Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, Victoria, Australia 3049
    Bioinformatics 23:1692-3. 2007
    ..In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates...
  30. pmc An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic ca
    Sean MacEachern
    Primary Industries Research Victoria, Animal Genetics and Genomics, Attwood, Vic, Australia
    BMC Genomics 10:181. 2009
    ..We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP) in beef (Angus) and dairy (Holstein) cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in Domestic cattle...
  31. pmc Casein haplotypes and their association with milk production traits in Norwegian Red cattle
    Heidi Nilsen
    Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
    Genet Sel Evol 41:24. 2009
    ..Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding...
  32. doi request reprint Overview of Statistical Methods for Genome-Wide Association Studies (GWAS)
    Ben Hayes
    Biosciences Research Division, Department of Primary Industries, Bundoora, Vic, Australia
    Methods Mol Biol 1019:149-69. 2013
    ..Methodology for more complex models for GWAS, including haplotype-based approaches, accounting for identical by descent versus identical by state, and fitting all markers simultaneously are described and illustrated with examples...
  33. ncbi request reprint Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records
    B J Hayes
    Victorian Institute of Animal Science, Department of Natural Resources and Environment, Attwood, Victoria, 3049, Australia
    J Dairy Sci 86:3736-44. 2003
    ..90 between protein yield at the 5th and 95th percentile of THI. The use of response to environment estimated breeding values to improve the accuracy of international sire evaluations is discussed...
  34. pmc Reliability of genomic predictions across multiple populations
    A P W de Roos
    Biosciences Research Division, Department of Primary Industries Victoria, University of Melbourne, Bundoora 3083, Australia
    Genetics 183:1545-53. 2009
    ..Our results suggest that the most accurate genomic predictions are achieved when phenotypes from all populations are combined in one training set, while for more diverged populations a higher marker density is required...
  35. doi request reprint Deterministic models of breeding scheme designs that incorporate genomic selection
    J E Pryce
    Biosciences Research Division, Department of Primary Industries Victoria, Bundoora, Australia
    J Dairy Sci 93:5455-66. 2010
    ..It is likely that breeding companies will move rapidly to alter their breeding schemes to make use of genomic selection because benefits to the breeding companies and to the industry are considerable...
  36. ncbi request reprint Genomic selection
    M E Goddard
    University of Melbourne, Attwood, Australia
    J Anim Breed Genet 124:323-30. 2007
    ..Implementation of genomic selection is likely to have major implications for genetic evaluation systems and for genetic improvement programmes generally and these are discussed...
  37. doi request reprint A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes
    J E Pryce
    Biosciences Research Division, Department of Primary Industries Victoria, Bundoora 3083, Australia
    J Dairy Sci 93:3331-45. 2010
    ..Promising candidate genes have been identified in several of the validated regions...
  38. doi request reprint Gene by environment interactions for production traits in Australian dairy cattle
    M Lillehammer
    Norwegian University of Life Sciences, Department of Animal and Aquacultural Sciences, 1432 As, Norway
    J Dairy Sci 92:4008-17. 2009
    ..Potential gene candidates and application of the markers is discussed. About one-third of the significant markers affect intercept and slope in opposite directions, and some of these facilitate marker-assisted selection for robustness...
  39. doi request reprint Genetic markers for lactation persistency in primiparous Australian dairy cows
    J E Pryce
    Department of Primary Industries, 1 Park Drive, Bundoora, Victoria 3083, Australia
    J Dairy Sci 93:2202-14. 2010
    ..Persistency is a good candidate for genomic selection because the trait is expressed late in lactation...
  40. ncbi request reprint Multivariate analysis of a genome-wide association study in dairy cattle
    S Bolormaa
    Biosciences Research Division, Department of Primary Industries Victoria, 1 Park Drive, Bundoora 3083, Australia
    J Dairy Sci 93:3818-33. 2010
    ..The multivariate analysis did not appear to increase the precision with which putative QTL were mapped...
  41. ncbi request reprint Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10
    Monica Aa Opsal
    Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N 1432 Aas, Norway
    Gene 384:45-50. 2006
    ..The differences in expression are in accordance with the evolutionary history of this gene cluster, where TLR10 diverged from the common ancestral gene before the duplication event that created TLR1 and TLR6...
  42. doi request reprint Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms
    I M MacLeod
    Cooperative Research Centre for Beef Genetic Technologies, Armidale, NSW, Australia
    J Anim Breed Genet 127:133-42. 2010
    ..Selective genotyping also resulted in a significant increase in false positives, even when pedigree structure was accounted for...
  43. ncbi request reprint A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle
    H G Olsen
    Centre for Integrative Genetics, Norwegian University of Life Sciences, Box 5003, N 1432 Aas, Norway
    Anim Genet 41:273-80. 2010
    ..e. SPP1, IBSP and MEPE) are of particular interest and we suggest that these genes are screened in candidate gene studies for dystocia and stillbirth in cattle as well as other species...
  44. pmc Statistical epistasis is a generic feature of gene regulatory networks
    Arne B Gjuvsland
    Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N 1432 Aas, Norway
    Genetics 175:411-20. 2007
    ..This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation...
  45. pmc Recent human effective population size estimated from linkage disequilibrium
    Albert Tenesa
    Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK
    Genome Res 17:520-6. 2007
    ..The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago...