The University of Queensland

Role of the genomics-phenomics-agronomy paradigm in plant breeding

Chen, Chunpeng James, Rutkoski, Jessica, Schnable, James C., Murray, Seth C., Wang, Lizhi, Jin, Xiuliang, Stich, Benjamin, Crossa, Jose, Hayes, Ben J. and Zhang, Zhiwu (2023). Role of the genomics-phenomics-agronomy paradigm in plant breeding. Plant breeding reviews. (pp. 627-673) edited by Irwin Goldman. Hoboken, NJ United States: John Wiley and Sons. doi: 10.1002/9781119874157.ch10

“SpeedGS” to accelerate genetic gain in spring wheat

Voss-Fels, Kai P., Herzog, Eva, Dreisigacker, Susanne, Sukumaran, Sivakumar, Watson, Amy, Frisch, Matthias, Hayes, Ben and Hickey, Lee T. (2019). “SpeedGS” to accelerate genetic gain in spring wheat. Applications of genetic and genomic research in cereals. (pp. 303-327) edited by Thomas Miedaner and Viktor Korzun. Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-102163-7.00014-4

Overview of statistical methods for genome-wide association studies (GWAS)

Hayes, Ben (2013). Overview of statistical methods for genome-wide association studies (GWAS). Genome-wide association studies and genomic prediction. (pp. 149-169) New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-447-0_6

Genome-wide association studies and linkage disequilibrium in cattle

Goddard, M. E. and Hayes, B. J. (2012). Genome-wide association studies and linkage disequilibrium in cattle. Bovine genomics. (pp. 192-210) edited by James E. Womack. Oxford, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118301739.ch13

Genetics: cattle genomics

Hayes, B. J., Cocks, B. and Goddard, M. E. (2011). Genetics: cattle genomics. Encyclopedia of dairy sciences. (pp. 663-668) edited by John W. Fuquay. Kidlington, Oxford, United Kingdom: Elsevier. doi: 10.1016/B978-0-12-374407-4.00211-9

Modern biotechnology and aquaculture

Hayes, Ben and Andersen, Oivind (2005). Modern biotechnology and aquaculture. Selection and Breeding Programs in Aquaculture. (pp. 301-317) Springer Netherlands. doi: 10.1007/1-4020-3342-7_19

Population genetics

Andersen, Oivind and Hayes, Ben (2005). Population genetics. Selection and Breeding Programs in Aquaculture. (pp. 23-33) Berlin/Heidelberg: Springer Netherlands. doi: 10.1007/1-4020-3342-7_3

Genome scanning for quantitative trait loci

Hayes B.J., Kinghorn B.P. and Ruvinsky A. (2004). Genome scanning for quantitative trait loci. Mammalian Genomics. (pp. 507-539) CABI Publishing.

144 Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd

Engle, Bailey N, Moser, Gerhard, Villiers, Kira, Suarez, Mathias, Grey, Eliza, Hayes, Ben J and Kelly, Matthew (2023). 144 Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd. Journal of Animal Science, 101 (Supplement_3), 34-35. doi: 10.1093/jas/skad281.042

Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available

Hayes, Ben J., Copley, James, Dodd, Elsie, Ross, Elizabeth M., Speight, Shannon and Fordyce, Geoffry (2023). Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available. Genetics Selection Evolution, 55 (1) 71. doi: 10.1186/s12711-023-00847-6

Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations

Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Moore, Stephen S., Corbet, Nicholas J., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2023). Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations. Heredity, 131 (5-6), 350-360. doi: 10.1038/s41437-023-00651-4

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits

Chen, Chensong, Powell, Owen, Dinglasan, Eric, Ross, Elizabeth M., Yadav, Seema, Wei, Xianming, Atkin, Felicity, Deomano, Emily and Hayes, Ben J. (2023). Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits. The Plant Genome e20390. doi: 10.1002/tpg2.20390

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

Costilla, R., Zeng, J., Al Kalaldeh, M., Swaminathan, M., Gibson, J.P., Ducrocq, V. and Hayes, B.J. (2023). Developing flexible models for genetic evaluations in smallholder crossbred dairy farms. Journal of Dairy Science. doi: 10.3168/jds.2022-23135

Advancing artificial intelligence to help feed the world

Hayes, Ben J., Chen, Chensong, Powell, Owen, Dinglasan, Eric, Villiers, Kira, Kemper, Kathryn E. and Hickey, Lee T. (2023). Advancing artificial intelligence to help feed the world. Nature Biotechnology, 41 (9), 1-2. doi: 10.1038/s41587-023-01898-2

Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle

Lamb, H. J., Nguyen, L. T., Briody, T. E., Ambrose, R. K., Hayes, B. J., Mahony, T. J. and Ross, E. M. (2023). Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle. Animal Production Science, 63 (11), 1074-1085. doi: 10.1071/an22451

Predicting phenotypes of beef eating quality traits

Forutan, Mehrnush, Lynn, Andrew, Aliloo, Hassan, Clark, Samuel A., McGilchrist, Peter, Polkinghorne, Rod and Hayes, Ben J. (2023). Predicting phenotypes of beef eating quality traits. Frontiers in Genetics, 14 1089490. doi: 10.3389/fgene.2023.1089490

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants

Nguyen, Tuan V., Vander Jagt, Christy J., Wang, Jianghui, Daetwyler, Hans D., Xiang, Ruidong, Goddard, Michael E., Nguyen, Loan T., Ross, Elizabeth M, Hayes, Ben J., Chamberlain, Amanda J. and MacLeod, Iona M. (2023). In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genetics Selection Evolution, 55 (1) 9, 1-15. doi: 10.1186/s12711-023-00783-5

Multi-breed genomic predictions and functional variants for fertility of tropical bulls

Porto-Neto, Laercio R., Alexandre, Pamela A., Hudson, Nicholas J., Bertram, John, McWilliam, Sean M., Tan, Andre W. L., Fortes, Marina R. S., McGowan, Michael R., Hayes, Ben J. and Reverter, Antonio (2023). Multi-breed genomic predictions and functional variants for fertility of tropical bulls. PLoS One, 18 (1) e0279398, 1-19. doi: 10.1371/journal.pone.0279398

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Yadav, Seema, Ross, Elizabeth, Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2022). Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane.

Identification of genomic variants causing variation in quantitative traits: a review

Meuwissen, Theo, Hayes, Ben, MacLeod, Iona and Goddard, Michael (2022). Identification of genomic variants causing variation in quantitative traits: a review. Agriculture, 12 (10) 1713, 1-11. doi: 10.3390/agriculture12101713

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

Olasege, Babatunde S., Porto-Neto, Laercio R., Tahir, Muhammad S., Gouveia, Gabriela C., Cánovas, Angela, Hayes, Ben J. and Fortes, Marina R. S. (2022). Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits. BMC Genomics, 23 (1) 684, 1-20. doi: 10.1186/s12864-022-08898-7

Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms

Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E. and McNeill, David M. (2022). Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms. Journal of Dairy Science, 105 (10), 8454-8469. doi: 10.3168/jds.2021-21343

Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E. and McNeill, David M. (2022). Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam. Tropical Animal Health and Production, 54 (5) 313. doi: 10.1007/s11250-022-03303-7

Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: a review

Widyas, Nuzul, Widi, Tri Satya Mastuti, Prastowo, Sigit, Sumantri, Ika, Hayes, Ben J. and Burrow, Heather M. (2022). Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: a review. Agriculture, 12 (10) 1566. doi: 10.3390/agriculture12101566

genomicSimulation: fast R functions for stochastic simulation of breeding programs

Villiers, Kira, Dinglasan, Eric, Hayes, Ben J and Voss-Fels, Kai P (2022). genomicSimulation: fast R functions for stochastic simulation of breeding programs. G3 Genes|Genomes|Genetics, 12 (10) jkac216, 1-6. doi: 10.1093/g3journal/jkac216

Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes

Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry, Turni, Conny, Hayes, Ben J., Fordyce, Geoffry and Tabor, Ala E. (2022). Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes. Scientific reports, 12 (1) 15075, 1-12. doi: 10.1038/s41598-022-19022-w

Metagenomic predictions: a review 10 years on

Ross, Elizabeth M. and Hayes, Ben J. (2022). Metagenomic predictions: a review 10 years on. Frontiers in Genetics, 13 865765, 1-9. doi: 10.3389/fgene.2022.865765

Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Naseem, Muhammad Noman, Kamran, Muhammad, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2022). Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis. BMC Genomics, 23 (1) 454, 1-20. doi: 10.1186/s12864-022-08686-3

Genomics applied to livestock and aquaculture breeding

Yáñez, José M., Xu, Peng, Carvalheiro, Roberto and Hayes, Ben (2022). Genomics applied to livestock and aquaculture breeding. Evolutionary Applications, 15 (4), 517-522. doi: 10.1111/eva.13378

Evaluation of host depletion and extraction methods for shotgun metagenomic analysis of bovine vaginal samples

Ong, Chian Teng, Boe-Hansen, Gry, Ross, Elizabeth M., Blackall, Patrick J., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Evaluation of host depletion and extraction methods for shotgun metagenomic analysis of bovine vaginal samples. Microbiology Spectrum, 10 (2), e0041221. doi: 10.1128/spectrum.00412-21

Environmental variation effects fertility in tropical beef cattle

Copley, James P., Engle, Bailey N., Ross, Elizabeth M., Speight, Shannon, Fordyce, Geoffry, Wood, Benjamin J., Voss-Fels, Kai P. and Hayes, Benjamin J. (2022). Environmental variation effects fertility in tropical beef cattle. Translational Animal Science, 6 (2) txac035, 1-10. doi: 10.1093/tas/txac035

Author correction: a chickpea genetic variation map based on the sequencing of 3,366 genomes

Varshney, Rajeev K., Roorkiwal, Manish, Sun, Shuai, Bajaj, Prasad, Chitikineni, Annapurna, Thudi, Mahendar, Singh, Narendra P., Du, Xiao, Upadhyaya, Hari D., Khan, Aamir W., Wang, Yue, Garg, Vanika, Fan, Guangyi, Cowling, Wallace A., Crossa, José, Gentzbittel, Laurent, Voss-Fels, Kai Peter, Valluri, Vinod Kumar, Sinha, Pallavi, Singh, Vikas K., Ben, Cécile, Rathore, Abhishek, Punna, Ramu, Singh, Muneendra K., Tar’an, Bunyamin, Bharadwaj, Chellapilla, Yasin, Mohammad, Pithia, Motisagar S., Singh, Servejeet ... Liu, Xin (2022). Author correction: a chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 604 (7905), E12-E12. doi: 10.1038/s41586-022-04660-x

Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle

Ross, Elizabeth M., Sanjana, Hari, Nguyen, Loan T., Cheng, YuanYuan, Moore, Stephen S. and Hayes, Ben J. (2022). Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle. Frontiers in Genetics, 13 784663, 784663. doi: 10.3389/fgene.2022.784663

Genetic variation in PLAG1 is associated with early fertility in Australian Brahman cattle

Engle, Bailey N and Hayes, Ben J (2022). Genetic variation in PLAG1 is associated with early fertility in Australian Brahman cattle. Journal of Animal Science, 100 (4) skac084. doi: 10.1093/jas/skac084

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing

Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry B., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. Journal of Animal Science, 100 (1) skab344. doi: 10.1093/jas/skab344

Genomic prediction using low-coverage portable Nanopore sequencing

Lamb, Harrison J., Hayes, Ben J., Randhawa, Imtiaz A. S., Nguyen, Loan T. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage portable Nanopore sequencing. PLoS One, 16 (12) e0261274, e0261274. doi: 10.1371/journal.pone.0261274

An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology

Hayes, Ben J., Nguyen, Loan T., Forutan, Mehrnush, Engle, Bailey N., Lamb, Harrison J., Copley, James P., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology. Frontiers in Genetics, 12 760450, 760450. doi: 10.3389/fgene.2021.760450

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Varshney, Rajeev K., Roorkiwal, Manish, Sun, Shuai, Bajaj, Prasad, Chitikineni, Annapurna, Thudi, Mahendar, Singh, Narendra P., Du, Xiao, Upadhyaya, Hari D., Khan, Aamir W., Wang, Yue, Garg, Vanika, Fan, Guangyi, Cowling, Wallace A., Crossa, José, Gentzbittel, Laurent, Voss-Fels, Kai Peter, Valluri, Vinod Kumar, Sinha, Pallavi, Singh, Vikas K., Ben, Cécile, Rathore, Abhishek, Punna, Ramu, Singh, Muneendra K., Tar’an, Bunyamin, Bharadwaj, Chellapilla, Yasin, Mohammad, Pithia, Motisagar S., Singh, Servejeet ... Liu, Xin (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599 (7886), 622-627. doi: 10.1038/s41586-021-04066-1

Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers

Burrow, Heather M., Mrode, Raphael, Mwai, Ally Okeyo, Coffey, Mike P. and Hayes, Ben J. (2021). Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers. Agriculture, 11 (11) 1172. doi: 10.3390/AGRICULTURE11111172

A linkage disequilibrium-based approach to position unmapped SNPs in crop species

Yadav, Seema, Ross, Elizabeth M., Aitken, Karen S., Hickey, Lee T., Powell, Owen, Wei, Xianming, Voss-Fels, Kai P. and Hayes, Ben J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics, 22 (1) 773, 773. doi: 10.1186/s12864-021-08116-w

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

Bang, Nguyen N., Hayes, Ben J., Lyons, Russell E., Randhawa, Imtiaz A. S., Gaughan, John B. and McNeill, David M. (2021). Genomic diversity and breed composition of Vietnamese smallholder dairy cows. Journal of Animal Breeding and Genetics, 139 (2), 1-16. doi: 10.1111/jbg.12651

Prowler: a novel trimming algorithm for Oxford Nanopore sequence data

Lee, Simon, Nguyen, Loan T., Hayes, Ben J. and Ross, Elizabeth (2021). Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics, 37 (21), 3936-3937. doi: 10.1093/bioinformatics/btab630

Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle

Olasege, Babatunde S., Tahir, Muhammad S., Gouveia, Gabriela C., Kour, Jagish, Porto-Neto, Laercio R., Hayes, Ben J. and Fortes, Marina R. S. (2021). Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle. Animal Production Science, 61 (18), 1863-1872. doi: 10.1071/an21097

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

Forutan, Mehrnush, Ross, Elizabeth, Chamberlain, Amanda J., Nguyen, Loan, Mason, Brett, Moore, Stephen, Garner, Josie B., Xiang, Ruidong and Hayes, Ben J. (2021). Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Communications Biology, 4 (1) 829, 1-14. doi: 10.1038/s42003-021-02340-6

Multiple country and breed genomic prediction of tick resistance in beef cattle

Cardoso, Fernando Flores, Matika, Oswald, Djikeng, Appolinaire, Mapholi, Ntanganedzeni, Burrow, Heather M., Yokoo, Marcos Jun Iti, Campos, Gabriel Soares, Gulias-Gomes, Claudia Cristina, Riggio, Valentina, Pong-Wong, Ricardo, Engle, Bailey, Porto-Neto, Laercio, Maiwashe, Azwihangwisi and Hayes, Ben J. (2021). Multiple country and breed genomic prediction of tick resistance in beef cattle. Frontiers in Immunology, 12 620847, 1-11. doi: 10.3389/fimmu.2021.620847

Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

Ong, Chian Teng, Turni, Conny, Blackall, Patrick J., Boe-Hansen, Gry, Hayes, Ben J. and Tabor, Ala E. (2021). Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review. Animal Microbiome, 3 (1) 41, 41. doi: 10.1186/s42523-021-00106-3

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

O’Connor, Katie M., Hayes, Ben J., Hardner, Craig M., Alam, Mobashwer, Henry, Robert J. and Topp, Bruce L. (2021). Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics, 22 (1) 370, 1-12. doi: 10.1186/s12864-021-07694-z

Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae

Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M., Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A., Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique ... Capitan, Aurélien (2021). Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae. Molecular Biology and Evolution, 38 (6), 2260-2272. doi: 10.1093/molbev/msab021

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Trigo, Beatriz B., Utsunomiya, Adam T. H., Fortunato, Alvaro A. A. D., Milanesi, Marco, Torrecilha, Rafaela B. P., Lamb, Harrison, Nguyen, Loan, Ross, Elizabeth M., Hayes, Ben, Padula, Romulo C. M., Sussai, Thayla S., Zavarez, Ludmilla B., Cipriano, Rafael S., Caminhas, Maria M. T., Lopes, Flavia L., Pelle, Cassiano, Leeb, Tosso, Bannasch, Danika, Bickhart, Derek, Smith, Timothy P. L., Sonstegard, Tad S., Garcia, Jose F. and Utsunomiya, Yuri T. (2021). Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution, 53 (1) 40, 40. doi: 10.1186/s12711-021-00633-2

Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects

Yadav, Seema, Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Sun, Yue, Nguyen, Loan T., Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S., Hayes, Ben J. and Voss-Fels, Kai P. (2021). Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. Theoretical and Applied Genetics, 134 (7), 2235-2252. doi: 10.1007/s00122-021-03822-1

Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds

Randhawa, Imtiaz A. S., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J. and Lyons, Russell E. (2021). Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds. Animals, 11 (3) 870, 1-21. doi: 10.3390/ani11030870

Imputation accuracy to whole-genome sequence in Nellore cattle

Fernandes Junior, Gerardo A., Carvalheiro, Roberto, de Oliveira, Henrique N., Sargolzaei, Mehdi, Costilla, Roy, Ventura, Ricardo V., Fonseca, Larissa F. S., Neves, Haroldo H. R., Hayes, Ben J. and de Albuquerque, Lucia G. (2021). Imputation accuracy to whole-genome sequence in Nellore cattle. Genetics Selection Evolution, 53 (1) 27. doi: 10.1186/s12711-021-00622-5

Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 729, 1-25. doi: 10.3390/ani11030729

Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 674, 1-22. doi: 10.3390/ani11030674

Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle

Chen, Long, Pryce, Jennie E., Hayes, Ben J. and Daetwyler, Hans D. (2021). Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle. Animals, 11 (2) 541, 1-16. doi: 10.3390/ani11020541

Accuracy of genomic prediction of complex traits in sugarcane

Hayes, Ben J., Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Yue, Jenny, Nguyen, Loan, Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S. and Voss-Fels, Kai P. (2021). Accuracy of genomic prediction of complex traits in sugarcane. Theoretical and Applied Genetics, 134 (5), 1455-1462. doi: 10.1007/s00122-021-03782-6

Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding

Voss-Fels, Kai P., Wei, Xianming, Ross, Elizabeth M., Frisch, Matthias, Aitken, Karen S., Cooper, Mark and Hayes, Ben J. (2021). Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. Theoretical and Applied Genetics, 134 (5), 1493-1511. doi: 10.1007/s00122-021-03785-3

Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate—a preliminary study

Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N. and McNeill, David M. (2021). Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate—a preliminary study. Animals, 11 (2) 351, 1-21. doi: 10.3390/ani11020351

Breed-adjusted genomic relationship matrices as a method to account for population stratification in multibreed populations of tropically adapted beef heifers

Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Corbet, Nicholas J., Allen, Jack M., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2021). Breed-adjusted genomic relationship matrices as a method to account for population stratification in multibreed populations of tropically adapted beef heifers. Animal Production Science, 61 (18), 1788-1795. doi: 10.1071/an21057

Feed preference response of weaner bull calves to Bacillus amyloliquefaciens H57 probiotic and associated volatile organic compounds in high concentrate feed pellets

Ngo, Thi Thuy, Bang, Nguyen N., Dart, Peter, Callaghan, Matthew, Klieve, Athol, Hayes, Ben and McNeill, David (2020). Feed preference response of weaner bull calves to Bacillus amyloliquefaciens H57 probiotic and associated volatile organic compounds in high concentrate feed pellets. Animals, 11 (1) 51, 51-15. doi: 10.3390/ani11010051

Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo

Garner, J. B., Chamberlain, A. J., Vander Jagt, C., Nguyen, T. T.T., Mason, B. A., Marett, L. C., Leury, B. J., Wales, W. J. and Hayes, B. J. (2020). Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo. Scientific Reports, 10 (1) 19181, 19181. doi: 10.1038/s41598-020-75438-2

The future of livestock management: a review of real-time portable sequencing applied to livestock

Lamb, Harrison J., Hayes, Ben J., Nguyen, Loan T. and Ross, Elizabeth M. (2020). The future of livestock management: a review of real-time portable sequencing applied to livestock. Genes, 11 (12) 1478, 1-27. doi: 10.3390/genes11121478

Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries)

Ross, Elizabeth M., Hayes, Ben J., Tucker, David, Bond, Jude, Denman, Stuart E. and Oddy, Victor Hutton (2020). Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries). Journal of Animal Science, 98 (10) skaa262. doi: 10.1093/jas/skaa262

Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock

Raymond, Biaty, Yengo, Loic, Costilla, Roy, Schrooten, Chris, Bouwman, Aniek C., Hayes, Ben J., Veerkamp, Roel F. and Visscher, Peter M. (2020). Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock. PLoS Genetics , 16 (9) e1008780, 1-20. doi: 10.1371/journal.pgen.1008780

Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament

Costilla, Roy, Kemper, Kathryn E., Byrne, Enda M., Porto-Neto, Laercio R., Carvalheiro, Roberto, Purfield, Deirdre C., Doyle, Jennifer L., Berry, Donagh P., Moore, Stephen S., Wray, Naomi R. and Hayes, Ben J. (2020). Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament. Genetics Selection Evolution, 52 (1) 51, 51. doi: 10.1186/s12711-020-00569-z

X chromosome variants are associated with male fertility traits in two bovine populations

Fortes, Marina R. S., Porto-Neto, Laercio R., Satake, Nana, Nguyen, Loan T., Freitas, Ana Claudia, Melo, Thaise P., Scalez, Daiane Cristina Becker, Hayes, Ben, Raidan, Fernanda S. S., Reverter, Antonio and Boe-Hansen, Gry B. (2020). X chromosome variants are associated with male fertility traits in two bovine populations. Genetics Selection Evolution, 52 (1) 46, 46. doi: 10.1186/s12711-020-00563-5

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Naval-Sánchez, Marina, Porto-Neto, Laercio R., Cardoso, Diercles F., Hayes, Ben J., Daetwyler, Hans D., Kijas, James and Reverter, Antonio (2020). Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genetics Selection Evolution, 52 (1) 27, 27. doi: 10.1186/s12711-020-00546-6

Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers

Warburton, Christie L., Engle, Bailey N., Ross, Elizabeth M., Costilla, Roy, Moore, Stephen S., Corbet, Nicholas J., Allen, Jack M., Laing, Alan R., Fordyce, Geoffry, Lyons, Russell E., McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2020). Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers. Genetics Selection Evolution, 52 (1) 28, 28. doi: 10.1186/s12711-020-00547-5

Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing

Lamb, Harrison J., Ross, Elizabeth M., Nguyen, Loan T., Lyons, Russell E., Moore, Stephen S. and Hayes, Ben J. (2020). Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing. Journal of Animal Science, 98 (5) skaa127, skaa127. doi: 10.1093/jas/skaa127

Accelerating genetic gain in sugarcane breeding using genomic selection

Yadav, Seema, Jackson, Phillip, Wei, Xianming, Ross, Elizabeth M., Aitken, Karen, Deomano, Emily, Atkin, Felicity, Hayes, Ben J. and Voss-Fels, Kai P. (2020). Accelerating genetic gain in sugarcane breeding using genomic selection. Agronomy, 10 (4) 585, 585. doi: 10.3390/agronomy10040585

Genome-wide association studies for yield component traits in a macadamia breeding population

O’Connor, Katie, Hayes, Ben, Hardner, Craig, Nock, Catherine, Baten, Abdul, Alam, Mobashwer, Henry, Robert and Topp, Bruce (2020). Genome-wide association studies for yield component traits in a macadamia breeding population. BMC Genomics, 21 (1) 199, 199. doi: 10.1186/s12864-020-6575-3

Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships

Hunt, Colleen H., Hayes, Ben J., van Eeuwijk, Fred A., Mace, Emma S. and Jordan, David R. (2020). Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships. Theoretical and Applied Genetics, 133 (3), 1009-1018. doi: 10.1007/s00122-019-03526-7

Optimized genetic testing for polledness in multiple breeds of cattle

Randhawa, Imtiaz A. S., Burns, Brian M., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J., Ferretti, Ryan, Schutt, Karen M. and Lyons, Russell E. (2019). Optimized genetic testing for polledness in multiple breeds of cattle. G3: Genes, Genomes, Genetics, 10 (2), g3.400866.2019-544. doi: 10.1534/g3.119.400866

Boosting genetic gain in allogamous crops via speed breeding and genomic selection

Jighly, Abdulqader, Lin, Zibei, Pembleton, Luke W., Cogan, Noel O. I., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2019). Boosting genetic gain in allogamous crops via speed breeding and genomic selection. Frontiers in Plant Science, 10 1364, 1364. doi: 10.3389/fpls.2019.01364

The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance

Mulder, Herman A., Lee, Sang Hong, Clark, Sam, Hayes, Ben J. and van der Werf, Julius H. J. (2019). The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance. Genetics, 213 (2), 361-378. doi: 10.1534/genetics.119.302336

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

Xiang, Ruidong, Van Den Berg, Irene, MacLeod, Iona M., Hayes, Benjamin J., Prowse-Wilkins, Claire P., Wang, Min, Bolormaa, Sunduimijid, Liu, Zhiqian, Rochfort, Simone J., Reich, Coralie M., Mason, Brett A., Vander Jagt, Christy J., Daetwyler, Hans D., Lund, Mogens S., Chamberlain, Amanda J. and Goddard, Michael E. (2019). Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. Proceedings of the National Academy of Sciences of the United States of America, 116 (39), 19398-19408. doi: 10.1073/pnas.1904159116

Multivariate genomic selection and potential of rapid indirect selection with speed breeding in spring wheat

Watson, Amy, Hickey, Lee T., Christopher, Jack, Rutkoski, Jessica, Poland, Jesse and Hayes, Ben J. (2019). Multivariate genomic selection and potential of rapid indirect selection with speed breeding in spring wheat. Crop Science, 59 (5), 1945-1959. doi: 10.2135/cropsci2018.12.0757

Across‐breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

Melo, Thaise Pinto, Salinas Fortes, Marina Rufino, Hayes, Ben, Albuquerque, Lucia Galvão and Carvalheiro, Roberto (2019). Across‐breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle. Journal of Animal Breeding and Genetics, 137 (2) jbg.12429, 139-154. doi: 10.1111/jbg.12429

Unraveling genetic sensitivity of beef cattle to environmental variation under tropical conditions

Carvalheiro, Roberto, Costilla, Roy, Neves, Haroldo H. R., Albuquerque, Lucia G., Moore, Stephen and Hayes, Ben J. (2019). Unraveling genetic sensitivity of beef cattle to environmental variation under tropical conditions. Genetics Selection Evolution, 51 (1) 29, 29. doi: 10.1186/s12711-019-0470-x

Breeding crops to feed 10 billion

Hickey, Lee T., N. Hafeez, Amber, Robinson, Hannah, Jackson, Scott A., Leal-Bertioli, Soraya C. M., Tester, Mark, Gao, Caixia, Godwin, Ian D., Hayes, Ben J. and Wulff, Brande B. H. (2019). Breeding crops to feed 10 billion. Nature Biotechnology, 37 (7), 744-754. doi: 10.1038/s41587-019-0152-9

Breeding improves wheat productivity under contrasting agrochemical input levels

Voss-Fels, Kai P., Stahl, Andreas, Wittkop, Benjamin, Lichthardt, Carolin, Nagler, Sabrina, Rose, Till, Chen, Tsu-Wei, Zetzsche, Holger, Seddig, Sylvia, Majid Baig, Mirza, Ballvora, Agim, Frisch, Matthias, Ross, Elizabeth, Hayes, Ben J., Hayden, Matthew J., Ordon, Frank, Leon, Jens, Kage, Henning, Friedt, Wolfgang, Stützel, Hartmut and Snowdon, Rod J. (2019). Breeding improves wheat productivity under contrasting agrochemical input levels. Nature Plants, 5 (7), 706-714. doi: 10.1038/s41477-019-0445-5

Publisher correction: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, Keeble-Gagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L., Davies, John P., Webb, Steve R., Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew and Akhunov, Eduard (2019). Publisher correction: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51 (7), 1194-1194. doi: 10.1038/s41588-019-0463-2

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, Keeble-Gagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L., Davies, John P., Webb, Steve R., Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew and Akhunov, Eduard (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51 (5), 896-904. doi: 10.1038/s41588-019-0382-2

Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle

Van Den Berg, I., Hayes, B. J., Chamberlain, A. J. and Goddard, M. E. (2019). Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle. BMC Genomics, 20 (1) 291, 291. doi: 10.1186/s12864-019-5656-7

Complex trait prediction from genome data: contrasting EBV in livestock to PRS in humans: genomic prediction

Wray, Naomi R., Kemper, Kathryn E., Hayes, Benjamin J., Goddard, Michael E. and Visscher, Peter M. (2019). Complex trait prediction from genome data: contrasting EBV in livestock to PRS in humans: genomic prediction. Genetics, 211 (4), 1131-1141. doi: 10.1534/genetics.119.301859

Population structure, genetic diversity and linkage disequilibrium in a macadamia breeding population using SNP and silicoDArT markers

O’Connor, Katie, Kilian, Andrzej, Hayes, Ben, Hardner, Craig, Nock, Catherine, Baten, Abdul, Alam, Mobashwer and Topp, Bruce (2019). Population structure, genetic diversity and linkage disequilibrium in a macadamia breeding population using SNP and silicoDArT markers. Tree Genetics & Genomes, 15 (2) 24, 24. doi: 10.1007/s11295-019-1331-z

Selecting for nut characteristics in macadamia using a genome-wide association study

O’Connor, Katie, Hayes, Ben, Hardner, Craig, Alam, Mobashwer and Topp, Bruce (2019). Selecting for nut characteristics in macadamia using a genome-wide association study. HortScience, 54 (4), 629-632. doi: 10.21273/hortsci13297-18

1000 Bull Genomes Project to map simple and complex genetic traits in cattle: applications and outcomes

Hayes, Ben J. and Daetwyler, Hans D. (2019). 1000 Bull Genomes Project to map simple and complex genetic traits in cattle: applications and outcomes. Annual Review of Animal Biosciences, 7 (1), 89-102. doi: 10.1146/annurev-animal-020518-115024

Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk

Liu, Zhiqian, Wang, Tingting, Pryce, Jennie E., MacLeod, Iona M., Hayes, Ben J., Chamberlain, Amanda J., Jagt, Christy Vander, Reich, Coralie M., Mason, Brett A., Rochfort, Simone and Cocks, Benjamin G. (2019). Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk. Scientific Reports, 9 (1) 2137, 2137. doi: 10.1038/s41598-019-38488-9

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Giuffra, Elisabetta, Tuggle, Christopher K., and the FAANG Consortium, Archibald, Alan L., Acloque, Herve, Chamberlain, Amanda J., Cochrane, Guy, Daetwyler, Hans D., Djebali, Sarah, Eory, Lel, Foissac, Sylvain, Goddard, Michael E., Groenen, Martien A. M., Halstead, Michelle, Harrison, Peter W., Hayes, Benjamin J., Kern, Colin, Khatib, Hasan, Kuo, Richard I., MacHugh, David E., Macleod, Iona M., Madsen, Ole, Reecy, James M., Ross, Pablo J., Watson, Mick, Wells, Jerry M. and Zhou, Huaijun (2019). Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annual Review of Animal Biosciences, Vol 7, 7 (1), 65-88. doi: 10.1146/annurev-animal-020518-114913

Multivariate genomic predictions for age at puberty in tropically adapted beef heifers

Engle, Bailey N., Corbet, Nicholas J., Allen, Jamie M., Laing, Alan R., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M., Burns, Brian M. and Hayes, Ben J. (2019). Multivariate genomic predictions for age at puberty in tropically adapted beef heifers. Journal of Animal Science, 97 (1), 90-100. doi: 10.1093/jas/sky428

Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

Hardner, Craig M., Hayes, Ben J., Kumar, Satish, Vanderzande, Stijn, Cai, Lichun, Piaskowski, Julia, Quero-Garcia, José, Campoy, José Antonio, Barreneche, Teresa, Giovannini, Daniela, Liverani, Alessandro, Charlot, Gérard, Villamil-Castro, Miguel, Oraguzie, Nnadozie and Peace, Cameron P. (2019). Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array. Horticulture Research, 6 (1) 6, 6. doi: 10.1038/s41438-018-0081-7

Towards a new phenotype for tick resistance in beef and dairy cattle: a review

Burrow, Heather M., Mans, Ben J., Cardoso, Fernando F., Birkett, Michael A., Kotze, Andrew C., Hayes, Ben J., Mapholi, Ntanganedzeni, Dzama, Kennedy, Marufu, Munyaradzi C., Githaka, Naftaly W. and Djikeng, Appolinaire (2019). Towards a new phenotype for tick resistance in beef and dairy cattle: a review. Animal Production Science, 59 (8), 1401-1427. doi: 10.1071/AN18487

Towards multi-breed genomic evaluations for female fertility of tropical beef cattle

Hayes, Ben J., Corbet, Nicholas J., Allen, Jack M., Laing, Alan R., Fordyce, Geoffry, Lyons, Russel, McGowan, Michael R. and Burns, Brian M. (2019). Towards multi-breed genomic evaluations for female fertility of tropical beef cattle. Journal of Animal Science, 97 (1), 55-62. doi: 10.1093/jas/sky417

Accelerating crop genetic gains with genomic selection

Voss-Fels, Kai Peter, Cooper, Mark and Hayes, Ben John (2018). Accelerating crop genetic gains with genomic selection. Theoretical and Applied Genetics, 132 (3), 669-686. doi: 10.1007/s00122-018-3270-8

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Koufariotis, L., Hayes, B. J., Kelly, M., Burns, B. M., Lyons, R., Stothard, P., Chamberlain, A. J. and Moore, S. (2018). Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled. Scientific Reports, 8 (1) 17761, 17761. doi: 10.1038/s41598-018-35698-5

Harnessing genomic information for livestock improvement

Georges, Michel, Charlier, Carole and Hayes, Ben (2018). Harnessing genomic information for livestock improvement. Nature Reviews Genetics, 20 (3), 135-156. doi: 10.1038/s41576-018-0082-2

Candidate mutations used to aid the prediction of genetic merit for female reproductive traits in tropical beef cattle

Fortes, Marina Rufino Salinas, Enculescu, Charmaine, Porto Neto, Laercio R., Lehnert, Sigrid A., McCulloch, Russell and Hayes, Ben (2018). Candidate mutations used to aid the prediction of genetic merit for female reproductive traits in tropical beef cattle. Revista Brasileira de Zootecnia, 47 e20170226. doi: 10.1590/rbz4720170226

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Xiang, Ruidong, Hayes, Ben J., Vander Jagt, Christy J., MacLeod, Iona M., Khansefid, Majid, Bowman, Phil J., Yuan, Zehu, Prowse-Wilkins, Claire P., Reich, Coralie M., Mason, Brett A., Garner, Josie B., Marett, Leah C., Chen, Yizhou, Bolormaa, Sunduimijid, Daetwyler, Hans D., Chamberlain, Amanda J. and Goddard, Michael E. (2018). Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues. BMC Genomics, 19 (1) 521, 521. doi: 10.1186/s12864-018-4902-8

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Wang, Min, Hancock, Timothy P., Chamberlain, Amanda J., Vander Jagt, Christy J., Pryce, Jennie E., Cocks, Benjamin G., Goddard, Mike E. and Hayes, Benjamin J. (2018). Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits. BMC Genomics, 19 (1) 395, 395. doi: 10.1186/s12864-018-4800-0

Benchmarking Bayesian genome enabled-prediction models for age at first calving in Nellore cows

Mota, Rodrigo Reis, Silva, Fabyano Fonseca e, Guimarães, Simone Eliza Facioni, Hayes, Ben, Fortes, Marina Rufino Salinas, Kelly, Matthew John, Guimarães, José Domingos, Penitente-Filho, Jurandy Mauro, Ventura, Henrique Torres and Moore, Stephen (2018). Benchmarking Bayesian genome enabled-prediction models for age at first calving in Nellore cows. Livestock Science, 211, 75-79. doi: 10.1016/j.livsci.2018.03.009

Insights into population genetics and evolution of polyploids and their ancestors

Jighly, Abdulqader, Lin, Zibei, Forster, John W., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2018). Insights into population genetics and evolution of polyploids and their ancestors. Molecular Ecology Resources, 18 (5), 1157-1172. doi: 10.1111/1755-0998.12896

The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds

Newton, J. E., Hayes, B. J. and Pryce, J. E. (2018). The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds. Journal of Dairy Science, 101 (7), 6159-6173. doi: 10.3168/jds.2017-13476

An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle

Fritz, Sébastien, Hoze, Chris, Rebours, Emmanuelle, Barbat, Anne, Bizard, Méline, Chamberlain, Amanda, Escouflaire, Clémentine, Vander Jagt, Christy, Boussaha, Mekki, Grohs, Cécile, Allais-Bonnet, Aurélie, Philippe, Maëlle, Vallée, Amélie, Amigues, Yves, Hayes, Benjamin J., Boichard, Didier and Capitan, Aurélien (2018). An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. Journal of Dairy Science, 101 (7), 6220-6231. doi: 10.3168/jds.2017-14119

Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Koufariotis, Lambros T., Chen, Yi-Ping Phoebe, Stothard, Paul and Hayes, Ben J. (2018). Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits. BMC Genomics, 19 (237) 237, 237. doi: 10.1186/s12864-018-4617-x

Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period

DiGiacomo, K., Norris, E., Dunshea, F. R., Hayes, B. J., Marett, L. C., Wales, W. J. and Leury, B. J. (2018). Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period. Journal of Dairy Science, 101 (7), 6474-6485. doi: 10.3168/jds.2017-12569

A multi-trait Bayesian method for mapping QTL and genomic prediction

Kemper, Kathryn E., Bowman, Philip J., Hayes, Benjamin J., Visscher, Peter M. and Goddard, Michael E. (2018). A multi-trait Bayesian method for mapping QTL and genomic prediction. Genetics Selection Evolution, 50 (1) 10, 10. doi: 10.1186/s12711-018-0377-y

Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection

Calus, M. P. L., Goddard, M. E., Wientjes, Y. C. J., Bowman, P. J. and Hayes, B. J. (2018). Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection. Journal of Dairy Science, 101 (5), 4279-4294. doi: 10.3168/jds.2017-13366

Development of genomic prediction in sorghum

Hunt, Colleen H., van Eeuwijk, Fred A., Mace, Emma S., Hayes, Ben J. and Jordan, David R. (2018). Development of genomic prediction in sorghum. Crop Science, 58 (2), 690-700. doi: 10.2135/cropsci2017.08.0469

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data

Nguyen, Quan H., Tellam, Ross L., Naval-Sanchez, Marina, Porto-Neto, Laercio R., Barendse, William, Reverter, Antonio, Hayes, Benjamin, Kijas, James and Dalrymple, Brian P. (2018). Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. Gigascience, 7 (3), 1-17. doi: 10.1093/gigascience/gix136

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Ponce, Carla Hurtado, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Mogens S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik ... Hayes, Ben J. (2018). Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nature Genetics, 50 (3), 362-367. doi: 10.1038/s41588-018-0056-5

Prospects for increasing yield in macadamia using component traits and genomics

O'Connor, Katie, Hayes, Ben and Topp, Bruce (2018). Prospects for increasing yield in macadamia using component traits and genomics. Tree Genetics & Genomes, 14 (1) 7. doi: 10.1007/s11295-017-1221-1

Rapid Discovery of de Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

Bourneuf, E., Otz, P., Pausch, H., Jagannathan, V., Michot, P., Grohs, C., Piton, G., Ammermüller, S., Deloche, M. C., Fritz, S., Leclerc, H., Péchoux, C., Boukadiri, A., Hozé, C., Saintilan, R., Créchet, F., Mosca, M., Segelke, D., Guillaume, F., Bouet, S., Baur, A., Vasilescu, A., Genestout, L., Thomas, A., Allais-Bonnet, A., Rocha, D., Colle, M. A., Klopp, C., Esquerré, D. ... Capitan, A. (2017). Rapid Discovery of de Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species. Scientific Reports, 7 (1) 11466, 11466. doi: 10.1038/s41598-017-11523-3

Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes

Hayes, B. J., Panozzo, J., Walker, C. K., Choy, A. L., Kant, S., Wong, D., Tibbits, J., Daetwyler, H. D., Rochfort, S., Hayden, M. J. and Spangenberg, G. C. (2017). Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes. Theoretical and Applied Genetics, 130 (12), 2505-2519. doi: 10.1007/s00122-017-2972-7

Breeding Differently—the Digital Revolution: High-Throughput Phenotyping and Genotyping

Slater, Anthony T., Cogan, Noel O. I., Rodoni, Brendan C., Daetwyler, Hans D., Hayes, Benjamin J., Caruana, Brittney, Badenhorst, Pieter E., Spangenberg, German C. and Forster, John W. (2017). Breeding Differently—the Digital Revolution: High-Throughput Phenotyping and Genotyping. Potato Research, 60 (3-4), 337-352. doi: 10.1007/s11540-018-9388-x

Genome-wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle

Mota, R. R., Guimarães, S. E. F., Fortes, M. R. S., Hayes, B., Silva, F. F., Verardo, L. L., Kelly, M. J., de Campos, C. F., Guimarães, J. D., Wenceslau, R. R., Penitente-Filho, J. M., Garcia, J. F. and Moore, S. (2017). Genome-wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle. Journal of Animal Breeding and Genetics, 134 (6), 484-492. doi: 10.1111/jbg.12299

Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts

Bouwman, Aniek C., Hayes, Ben J. and Calus, Mario P. L. (2017). Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts. Genetics, Selection, Evolution, 49 (1) 79, 79. doi: 10.1186/s12711-017-0355-9

Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect

Van Den Berg, Irene , Bowman, Phil J, MacLeod, Iona M., Hayes, Ben J., Wang, Tingting, Bolormaa, Sunduimijid and Goddard, Mike E. (2017). Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect. Genetics Selection Evolution, 49 (1) 70, 70. doi: 10.1186/s12711-017-0347-9

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

Qian, Lunwen, Hickey, Lee T., Stahl, Andreas, Werner, Christian R., Hayes, Ben, Snowdon, Rod J. and Voss-Fels, Kai P. (2017). Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops. Frontiers in Plant Science, 8 1534, 1534. doi: 10.3389/fpls.2017.01534

Short communication: implementation of a breeding value for heat tolerance in Australian dairy cattle

Nguyen, Thuy T. T., Bowman, Phil J., Haile-Mariam, Mekonnen, Nieuwhof, Gert J., Hayes, Benjamin J. and Pryce, Jennie E. (2017). Short communication: implementation of a breeding value for heat tolerance in Australian dairy cattle. Journal of Dairy Science, 100 (9), 7362-7367. doi: 10.3168/jds.2017-12898

Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping

Wang, Tingting, Chen, Yi-Ping Phoebe, MacLeod, Iona M., Pryce, Jennie E., Goddard, Michael E. and Hayes, Ben J. (2017). Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping. BMC Genomics, 18 (1) 618, 618. doi: 10.1186/s12864-017-4030-x

Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits

Wang, Min, Hancock, Timothy P., MacLeod, Iona M., Pryce, Jennie E., Cocks, Benjamin G. and Hayes, Benjamin J. (2017). Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. Genetics Selection Evolution, 49 (1) 56. doi: 10.1186/s12711-017-0331-4

Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Couldrey, C., Keehan, M., Johnson, T., Tiplady, K., Winkelman, A., Littlejohn, M. D., Scott, A., Kemper, K. E., Hayes, B., Davis, S. R. and Spelman, R. J. (2017). Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle. Journal of Dairy Science, 100 (7), 5472-5478. doi: 10.3168/jds.2016-12199

Exome sequence genotype imputation in globally diverse hexaploid wheat accessions

Shi, Fan, Tibbits, Josquin, Pasam, Raj K., Kay, Pippa, Wong, Debbie, Petkowski, Joanna, Forrest, Kerrie L., Hayes, Ben J., Akhunova, Alina, Davies, John, Webb, Steven, Spangenberg, German C., Akhunov, Eduard, Hayden, Matthew J. and Daetwyler, Hans D. (2017). Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theoretical and Applied Genetics, 130 (7), 1393-1404. doi: 10.1007/s00122-017-2895-3

Genomic prediction of reproduction traits for Merino sheep

Bolormaa, S., Brown, D. J., Swan, A. A., van der Werf, J. H. J., Hayes, B. J. and Daetwyler, H. D. (2017). Genomic prediction of reproduction traits for Merino sheep. Animal Genetics, 48 (3), 338-348. doi: 10.1111/age.12541

Evaluating the ability of a lifetime nutrient-partitioning model for simulating the performance of Australian Holstein dairy cows

Phuong, H. N., Friggens, N. C., Martin, O., Blavy, P., Hayes, B. J., Wales, W. J. and Pryce, J. E. (2017). Evaluating the ability of a lifetime nutrient-partitioning model for simulating the performance of Australian Holstein dairy cows. Animal Production Science, 57 (7), 1563-1568. doi: 10.1071/AN16452

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants

Lin, Zibei, Shi, Fan, Hayes, Ben J. and Daetwyler, Hans D. (2017). Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants. Theoretical and Applied Genetics, 130 (5), 969-980. doi: 10.1007/s00122-017-2863-y

Partitioning of energy and nitrogen in lactating primiparous and multiparous Holstein-Friesian cows with divergent residual feed intake

Marett, L. C., Williams, S. R. O., Hayes, B. J., Pryce, J. E. and Wales, W. J. (2017). Partitioning of energy and nitrogen in lactating primiparous and multiparous Holstein-Friesian cows with divergent residual feed intake. Animal Production Science, 57 (7), 1499-1506. doi: 10.1071/AN16476

Including nonadditive genetic effects in mating programs to maximize dairy farm profitability

Aliloo, H., Pryce, J. E., Gonzalez-Recio, O., Cocks, B. G., Goddard, M. E. and Hayes, B. J. (2017). Including nonadditive genetic effects in mating programs to maximize dairy farm profitability. Journal of Dairy Science, 100 (2), 1203-1222. doi: 10.3168/jds.2016-11261

Detection and validation of structural variations in bovine whole-genome sequence data

Chen, Long, Chamberlain, Amanda J., Reich, Coralie M., Daetwyler, Hans D. and Hayes, Ben J. (2017). Detection and validation of structural variations in bovine whole-genome sequence data. Genetics Selection Evolution, 49 (1) 13. doi: 10.1186/s12711-017-0286-5

Corrigendum: Genomic selection improves heat tolerance in dairy cattle

Garner, J. B., Douglas, M. L., Williams, S. R. O., Wales, W. J., Marett, L. C., Nguyen, T. T. T., Reich, C. M. and Hayes, B. J. (2017). Corrigendum: Genomic selection improves heat tolerance in dairy cattle. Scientific Reports, 7 (1) 39896, 39896. doi: 10.1038/srep39896

A practical future-scenarios selection tool to breed for heat tolerance in Australian dairy cattle

Nguyen, Thuy T. T., Hayes, Ben J. and Pryce, Jennie E. (2017). A practical future-scenarios selection tool to breed for heat tolerance in Australian dairy cattle. Animal Production Science, 57 (7), 1488-1493. doi: 10.1071/AN16449

Optimizing resource allocation in a genomic breeding program for perennial ryegrass to balance genetic gain, cost, and inbreeding

Lin, Zibei, Wang, Junping, Cogan, Noel O. I., Pembleton, Luke W., Badenhorst, Pieter, Forster, John W., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2017). Optimizing resource allocation in a genomic breeding program for perennial ryegrass to balance genetic gain, cost, and inbreeding. Crop Science, 57 (1), 243-252. doi: 10.2135/cropsci2016.07.0577

Responses of dairy cows to short-term heat stress in controlled-climate chambers

Garner, J. B., Douglas, M., Williams, S. R. O., Wales, W. J., Marett, L. C., DiGiacomo, K., Leury, B. J. and Hayes, B. J. (2017). Responses of dairy cows to short-term heat stress in controlled-climate chambers. Animal Production Science, 57 (7), 1233-1241. doi: 10.1071/AN16472

Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

Kemper, K. E., Littlejohn, M. D., Lopdell, T., Hayes, B. J., Bennett, L. E., Williams, R. P., Xu, X. Q., Visscher, P. M., Carrick, M. J. and Goddard, M. E. (2016). Leveraging genetically simple traits to identify small-effect variants for complex phenotypes. BMC Genomics, 17 (1) 858, 858. doi: 10.1186/s12864-016-3175-3

Improving genetic gain with genomic selection in autotetraploid potato

Slater, Anthony T., Cogan, Noel O. I., Forster, John W., Hayes, Benjamin J. and Daetwyler, Hans D. (2016). Improving genetic gain with genomic selection in autotetraploid potato. Plant Genome, 9 (3), plantgenome2016.02.0021-15. doi: 10.3835/plantgenome2016.02.0021

GO-FAANG meeting: a gathering on functional annotation of animal genomes

Tuggle, Christopher K., Giuffra, Elisabetta, White, Stephen N., Clarke, Laura, Zhou, Huaijun, Ross, Pablo J., Acloque, Herve, Reecy, James M., Archibald, Alan, Bellone, Rebecca R., Boichard, Michele, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard P. M. A., Delany, Mary E., Finno, Carrie J., Groenen, Martien A. M., Hayes, Ben, Lunney, Joan K., Petersen, Jessica L., Plastow, Graham S., Schmidt, Carl J., Song, Jiuzhou and Watson, Mick (2016). GO-FAANG meeting: a gathering on functional annotation of animal genomes. Animal Genetics, 47 (5), 528-533. doi: 10.1111/age.12466

Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle

Manzanilla-Pech, C. I. V., De Haas, Y., Hayes, B. J., Veerkamp, R. F., Khansefid, M., Donoghue, K. A., Arthur, P. F. and Pryce, J. E. (2016). Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle. Journal of Animal Science, 94 (10), 4151-4166. doi: 10.2527/jas.2016-0431

A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping

Wang, Tingting, Chen, Yi-Ping Phoebe, Bowman, Phil J., Goddard, Michael E. and Hayes, Ben J. (2016). A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping. BMC Genomics, 17 (1) 744, 744. doi: 10.1186/s12864-016-3082-7

Genomic selection improves heat tolerance in dairy cattle

Garner, J. B., Douglas, M. L., Williams, S. R. O., Wales, W. J., Marett, L. C., Nguyen, T. T. T., Reich, C. M. and Hayes, B. J. (2016). Genomic selection improves heat tolerance in dairy cattle. Scientific Reports, 6 (1) 34114, 34114. doi: 10.1038/srep34114

Models for genome x environment interaction: examples in livestock

Hayes, Ben J., Daetwyler, Hans D. and Goddard, Mike E. (2016). Models for genome x environment interaction: examples in livestock. Crop Science, 56 (5), 2251-2259. doi: 10.2135/cropsci2015.07.0451

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

Goddard, M. E., Kemper, K. E., MacLeod, I. M., Chamberlain, A. J. and Hayes, B. J. (2016). Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture. Proceedings of the Royal Society B: Biological Sciences, 283 (1835) 20160569, 20160569. doi: 10.1098/rspb.2016.0569

Genomic selection for tolerance to heat stress in Australian dairy cattle

Nguyen, Thuy T. T., Bowman, Phil J., Haile-Mariam, Mekonnen, Pryce, Jennie E. and Hayes, Benjamin J. (2016). Genomic selection for tolerance to heat stress in Australian dairy cattle. Journal of Dairy Science, 99 (4), 2849-2862. doi: 10.3168/jds.2015-9685

Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2

Greyvenstein, O. F. C., Reich, C. M., van Marle-Koster, E., Riley, D. G. and Hayes, B. J. (2016). Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2. Animal Genetics, 47 (2), 263-266. doi: 10.1111/age.12411

Detailed phenotyping identifies genes with pleiotropic effects on body composition

Bolormaa, Sunduimijid, Hayes, Ben J., van der Werf, Julius H. J., Pethick, David, Goddard, Michael E. and Daetwyler, Hans D. (2016). Detailed phenotyping identifies genes with pleiotropic effects on body composition. BMC Genomics, 17 (224) 224, 1-21. doi: 10.1186/s12864-016-2538-0

Genetic gain and inbreeding from genomic selection in a simulated commercial breeding program for perennial ryegrass

Lin, Zibei, Cogan, Noel O. I., Pembleton, Luke W., Spangenberg, German C., Forster, John W., Hayes, Ben J. and Daetwyler, Hans D. (2016). Genetic gain and inbreeding from genomic selection in a simulated commercial breeding program for perennial ryegrass. Plant Genome, 9 (1), 876-883. doi: 10.3835/plantgenome2015.06.0046

Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle

Hayes, B. J., Donoghue, K. A., Reich, C. M., Mason, B. A., Bird-Gardiner, T., Herd, R. M. and Arthur, P. F. (2016). Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle. Journal of Animal Science, 94 (3), 902-908. doi: 10.2527/jas2015-0078

Technical note: equivalent genomic models with a residual polygenic effect

Liu, Z., Goddard, M. E., Hayes, B. J., Reinhardt, F. and Reents, R. (2016). Technical note: equivalent genomic models with a residual polygenic effect. Journal of Dairy Science, 99 (3), 2016-2025. doi: 10.3168/jds.2015-10394

Accounting for dominance to improve genomic evaluations of dairy cows for fertility and milk production traits

Aliloo, Hassan, Pryce, Jennie E., Gonzalez-Recio, Oscar, Cocks, Benjamin G. and Hayes, Ben J. (2016). Accounting for dominance to improve genomic evaluations of dairy cows for fertility and milk production traits. Genetics Selection Evolution, 48 (1) 186, 8.1-8.11. doi: 10.1186/s12711-016-0186-0

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

MacLeod, I. M., Bowman, P. J., Vander Jagt, C. J., Haile-Mariam, M., Kemper, K. E., Chamberlain, A. J., Schrooten, C., Hayes, B. J. and Goddard, M. E. (2016). Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits. BMC Genomics, 17 (1) 144. doi: 10.1186/s12864-016-2443-6

Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle

Raven, Lesley-Ann, Cocks, Benjamin G., Kemper, Kathryn E., Chamberlain, Amanda J., Vander Jagt, Christy J., Goddard, Michael E. and Hayes, Ben J. (2016). Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle. Mammalian Genome, 27 (1-2), 81-97. doi: 10.1007/s00335-015-9613-8

Accuracy and computational efficiency of genomic selection with high-density SNP and whole-genome sequence data

Wang, Tingting, Chen, Yi-Ping Phoebe and Hayes, Ben (2016). Accuracy and computational efficiency of genomic selection with high-density SNP and whole-genome sequence data. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 11 (034) 034, 1-18. doi: 10.1079/PAVSNNR201611034

Differentially expressed genes in endometrium and corpus luteum of holstein cows selected for high and low fertility are enriched for sequence variants associated with fertility

Moore, Stephen G., Pryce, Jennie E., Hayes, Ben J., Chamberlain, Amanda J., Kemper, Kathryn E., Berry, Donagh P., McCabe, Matt, Cormican, Paul, Lonergan, Pat, Fair, Trudee and Butler, Stephen T. (2016). Differentially expressed genes in endometrium and corpus luteum of holstein cows selected for high and low fertility are enriched for sequence variants associated with fertility. Biology of Reproduction, 94 (1) 19. doi: 10.1095/biolreprod.115.132951

Genomic selection: a paradigm shift in animal breeding

Meuwissen, Theo, Hayes, Ben and Goddard, Mike (2016). Genomic selection: a paradigm shift in animal breeding. Animal Frontiers, 6 (1), 6-14. doi: 10.2527/af.2016-0002

Reducing the carbon footprint of Australian milk production by mitigation of enteric methane emissions

Moate, Peter J., Deighton, Matthew H., Williams, S. Richard O., Pryce, Jennie E., Hayes, Ben J., Jacobs, Joe L., Eckard, Richard J., Hannah, Murray C. and Wales, William J. (2016). Reducing the carbon footprint of Australian milk production by mitigation of enteric methane emissions. Animal Production Science, 56 (7), 1017-1034. doi: 10.1071/AN15222

Accuracy of genotype imputation based on random and selected reference sets in purebred and crossbred sheep populations and its effect on accuracy of genomic prediction

Moghaddar, Nasir, Gore, Klint P., Daetwyler, Hans D., Hayes, Ben J. and van der Werf, Julius H. J. (2015). Accuracy of genotype imputation based on random and selected reference sets in purebred and crossbred sheep populations and its effect on accuracy of genomic prediction. Genetics Selection Evolution, 47 (1) 175. doi: 10.1186/s12711-015-0175-8

Rare variants in transcript and potential regulatory regions explain a small percentage of the missing heritability of complex traits in cattle

Gonzalez-Recio, Oscar, Daetwyler, Hans D., MacLeod, Iona M., Pryce, Jennie E., Bowman, Phil J., Hayes, Ben J. and Goddard, Michael E. (2015). Rare variants in transcript and potential regulatory regions explain a small percentage of the missing heritability of complex traits in cattle. PLoS One, 10 (12) e0143945, e0143945. doi: 10.1371/journal.pone.0143945

Extensive variation between tissues in allele specific expression in an outbred mammal

Chamberlain, Amanda J., Vander Jagt, Christy J., Hayes, Benjamin J., Khansefid, Majid, Marett, Leah C., Millen, Catriona A., Nguyen, Thuy T. T. and Goddard, Michael E. (2015). Extensive variation between tissues in allele specific expression in an outbred mammal. BMC Genomics, 16 (1) 993. doi: 10.1186/s12864-015-2174-0

Two-variance-component model improves genetic prediction in family datasets

Tucker, George, Loh, Po-Ru, MacLeod, Iona M., Hayes, Ben J., Goddard, Michael E., Berger, Bonnie and Price, Alkes L. (2015). Two-variance-component model improves genetic prediction in family datasets. American Journal of Human Genetics, 97 (5), 677-690. doi: 10.1016/j.ajhg.2015.10.002

A catalogue of novel bovine long noncoding RNA across 18 tissues

Koufariotis, Lambros T., Chen, Yi-Ping Phoebe, Chamberlain, Amanda, Jagt, Christy Vander and Hayes, Ben J. (2015). A catalogue of novel bovine long noncoding RNA across 18 tissues. PLoS One, 10 (10) e0141225, e0141225. doi: 10.1371/journal.pone.0141225

Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy

Bolormaa, S., Gore, K., van der Werf, J. H. J., Hayes, B. J. and Daetwyler, H. D. (2015). Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy. Animal Genetics, 46 (5), 544-556. doi: 10.1111/age.12340

Hot topic: Definition and implementation of a breeding value for feed efficiency in dairy cows

Pryce, J. E., Gonzalez-Recio, O., Nieuwhof, G., Wales, W. J., Coffey, M. P., Hayes, B. J. and Goddard, M. E. (2015). Hot topic: Definition and implementation of a breeding value for feed efficiency in dairy cows. Journal of Dairy Science, 98 (10) 73864, 7340-7350. doi: 10.3168/jds.2015-9621

Selection on optimal haploid value increases genetic gain and preserves more genetic diversity relative to genomic selection

Daetwyler, Hans D., Hayden, Matthew J., Spangenberg, German C. and Hayes, Ben J. (2015). Selection on optimal haploid value increases genetic gain and preserves more genetic diversity relative to genomic selection. Genetics, 200 (4), 1341-1348. doi: 10.1534/genetics.115.178038

Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows

Aliloo, Hassan, Pryce, Jennie E., Gonzalez-Recio, Oscar, Cocks, Benjamin G. and Hayes, Ben J. (2015). Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows. BMC Genetics, 16 (1) 89. doi: 10.1186/s12863-015-0241-9

Animal board invited review: Genetic possibilities to reduce enteric methane emissions from ruminants

Pickering, N. K., Oddy, V. H., Basarab, J., Cammack, K., Hayes, B., Hegarty, R. S., Lassen, J., McEwan, J. C., Miller, S., Pinares-Patino, C. S. and de Haas, Y. (2015). Animal board invited review: Genetic possibilities to reduce enteric methane emissions from ruminants. Animal, 9 (9), 1431-1440. doi: 10.1017/S1751731115000968

Impact of QTL properties on the accuracy of multi-breed genomic prediction

Wientjes, Yvonne C. J., Calus, Mario P. L., Goddard, Michael E. and Hayes, Ben J. (2015). Impact of QTL properties on the accuracy of multi-breed genomic prediction. Genetics Selection Evolution, 47 (42) 42, 1-16. doi: 10.1186/s12711-015-0124-6

Including overseas performance information in genomic evaluations of Australian dairy cattle

Haile-Mariam, M., Pryce, J. E., Schrooten, C. and Hayes, B. J. (2015). Including overseas performance information in genomic evaluations of Australian dairy cattle. Journal of Dairy Science, 98 (5), 3443-3459. doi: 10.3168/jds.2014-8785

A computationally efficient algorithm for genomic prediction using a Bayesian model

Wang, Tingting, Chen, Yi-Ping Phoebe, Goddard, Michael E., Meuwissen, Theo H. E., Kemper, Kathryn E. and Hayes, Ben J. (2015). A computationally efficient algorithm for genomic prediction using a Bayesian model. Genetics Selection Evolution, 47 (1) 82. doi: 10.1186/s12711-014-0082-4

Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

Kemper, Kathryn E., Reich, Coralie M., Bowman, Philip J., vander Jagt, Christy J., Chamberlain, Amanda J., Mason, Brett A., Hayes, Benjamin J. and Goddard, Michael E. (2015). Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions. Genetics Selection Evolution, 47 (1) 29. doi: 10.1186/s12711-014-0074-4

Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model

Moser, Gerhard, Lee, Sang Hong, Hayes, Ben J., Goddard, Michael E., Wray, Naomi R. and Visscher, Peter M. (2015). Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model. PLoS Genetics, 11 (4) e1004969, 1-22. doi: 10.1371/journal.pgen.1004969

Non-additive genetic variation in growth, carcass and fertility traits of beef cattle

Bolormaa, Sunduimijid, Pryce, Jennie E., Zhang, Yuandan, Reverter, Antonio, Barendse, William, Hayes, Ben J. and Goddard, Michael E. (2015). Non-additive genetic variation in growth, carcass and fertility traits of beef cattle. Genetics Selection Evolution, 47 (1) 26. doi: 10.1186/s12711-015-0114-8

How old are quantitative trait loci and how widely do they segregate?

Kemper, K. E., Hayes, B. J., Daetwyler, H. D. and Goddard, M. E. (2015). How old are quantitative trait loci and how widely do they segregate?. Journal of Animal Breeding and Genetics, 132 (2), 121-134. doi: 10.1111/jbg.12152

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

Andersson, Leif, Archibald, Alan L., Bottema, Cynthia D., Brauning, Rudiger, Burgess, Shane C., Burt, Dave W., Casas, Eduardo, Cheng, Hans H., Clarke, Laura, Couldrey, Christine, Dalrymple, Brian P., Elsik, Christine G., Foissac, Sylvain, Giuffra, Elisabetta, Groenen, Martien A., Hayes, Ben J., Huang, LuSheng S., Khatib, Hassan, Kijas, James W., Kim, Heebal, Lunney, Joan K., McCarthy, Fiona M., McEwan, John C., Nanduri, Bindu, Notredame, Cedric, Palti, Yniv, Plastow, Graham S., Reecy, James M., Rohrer, Gary A. ... Fortes, Marina (2015). Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology, 16 (1) 57, 1-6. doi: 10.1186/s13059-015-0622-4

Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations

Howard, Jeremy T., Maltecca, Christian, Haile-Mariam, Mekonnen, Hayes, Ben J. and Pryce, Jennie E. (2015). Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations. BMC Genomics, 16 (1) 187. doi: 10.1186/s12864-015-1352-4

Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth

Bolormaa, S., Hayes, B. J., Hawken, R. J., Zhang, Y., Reverter, A. and Goddard, M. E. (2014). Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth. Journal of Animal Science, 89 (7), 2050-2060. doi: 10.2527/jas.2010-3363

Genome-wide association studies for feedlot and growth traits in cattle

Bolormaa, S., Hayes, B. J., Savin, K., Hawken, R., Barendse, W., Arthur, P. F., Herd, R. M. and Goddard, M. E. (2014). Genome-wide association studies for feedlot and growth traits in cattle. Journal of Animal Science, 89 (6), 1684-1697. doi: 10.2527/jas.2010-3079

The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data

MacLeod, Iona M., Hayes, Ben J. and Goddard, Michael E. (2014). The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics, 198 (4), 1671-1684. doi: 10.1534/genetics.114.168344

Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

Pryce, Jennie E., Haile-Mariam, Mekonnen, Goddard, Michael E. and Hayes, Ben J. (2014). Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle. Genetics Selection Evolution, 46 (1) 71. doi: 10.1186/s12711-014-0071-7

Improving breeding efficiency in potato using molecular and quantitative genetics

Slater, Anthony T., Cogan, Noel O. I., Hayes, Benjamin J., Schultz, Lee, Dale, M. Finlay B., Bryan, Glenn J. and Forster, John W. (2014). Improving breeding efficiency in potato using molecular and quantitative genetics. Theoretical and Applied Genetics, 127 (11), 2279-2292. doi: 10.1007/s00122-014-2386-8

Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip

Kijas, James W., Porto-Neto, Laercio, Dominik, Sonja, Reverter, Antonio, Bunch, Rowan, McCulloch, Russell, Hayes, Ben J., Brauning, Rudiger and McEwan, John (2014). Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip. Animal Genetics, 45 (5), 754-757. doi: 10.1111/age.12197

Selection signatures in worldwide sheep populations

Fariello, Maria-Ines, Servin, Bertrand, Tosser-Klopp, Gwenola, Rupp, Rachel, Moreno, Carole, San Cristobal, Magali, Boitard, Simon, International Sheep Genomics Consortium and Hayes, Ben (2014). Selection signatures in worldwide sheep populations. PLoS One, 9 (8) e103813, e103813. doi: 10.1371/journal.pone.0103813

Genomic prediction for rust resistance in diverse wheat landraces

Daetwyler, Hans D., Bansal, Urmil K., Bariana, Harbans S., Hayden, Matthew J. and Hayes, Ben J. (2014). Genomic prediction for rust resistance in diverse wheat landraces. Theoretical and Applied Genetics, 127 (8), 1795-1803. doi: 10.1007/s00122-014-2341-8

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

Daetwyler, Hans D., Capitan, Aurelien, Pausch, Hubert, Stothard, Paul, Van Binsbergen, Rianne, Brondum, Rasmus F., Liao, Xiaoping, Djari, Anis, Rodriguez, Sabrina C., Grohs, Cecile, Esquerre, Diane, Bouchez, Olivier, Rossignol, Marie-Noelle, Klopp, Christophe, Rocha, Dominique, Fritz, Sebastien, Eggen, Andre, Bowman, Phil J., Coote, David, Chamberlain, Amanda J., Anderson, Charlotte, VanTassell, Curt P., Hulsegge, Ina, Goddard, Mike E., Guldbrandtsen, Bernt, Lund, Mogens S., Veerkamp, Roel F., Boichard, Didier A., Fries, Ruedi and Hayes, Ben J. (2014). Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46 (8), 858-865. doi: 10.1038/ng.3034

Whole-tract dry matter and nitrogen digestibility of lactating dairy cows selected for phenotypic divergence in residual feed intake

Thornhill, J. B., Marett, L. C., Auldist, M. J., Greenwood, J. S., Pryce, J. E., Hayes, B. J. and Wales, W. J. (2014). Whole-tract dry matter and nitrogen digestibility of lactating dairy cows selected for phenotypic divergence in residual feed intake. Animal Production Science, 54 (9), 1460-1464. doi: 10.1071/AN14200

Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle

van Binsbergen, Rianne, Bink, Marco C. A. M., Calus, Mario P. L., van Eeuwijk, Fred A., Hayes, Ben J., Hulsegge, Ina and Veerkamp, Roel F. (2014). Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle. Genetics Selection Evolution, 46 (1) 41, 1-13. doi: 10.1186/1297-9686-46-41

Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle

Koufariotis, Lambros, Chen, Yi-Ping Phoebe, Bolormaa, Sunduimijid and Hayes, Ben J. (2014). Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics, 15 (1) 436. doi: 10.1186/1471-2164-15-436

Incorporating heifer feed efficiency in the Australian selection index using genomic selection

Gonzalez-Recio, O., Pryce, J. E., Haile-Mariam, M. and Hayes, B. J. (2014). Incorporating heifer feed efficiency in the Australian selection index using genomic selection. Journal of Dairy Science, 97 (6), 3883-3893. doi: 10.3168/jds.2013-7515

Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition

Raven, Lesley-Ann, Cocks, Benjamin G., Goddard, Michael E., Pryce, Jennie E. and Hayes, Ben J. (2014). Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition. Genetics Selection Evolution, 46 (1) 29. doi: 10.1186/1297-9686-46-29

Improving the analysis of low heritability complex traits for enhanced genetic gain in potato

Slater, Anthony T., Wilson, Graeme M., Cogan, Noel O. I., Forster, John W. and Hayes, Benjamin J. (2014). Improving the analysis of low heritability complex traits for enhanced genetic gain in potato. Theoretical and Applied Genetics, 127 (4), 809-820. doi: 10.1007/s00122-013-2258-7

Selection for complex traits leaves little or no classic signatures of selection

Kemper, Kathryn E., Saxton, Sarah J., Bolormaa, Sunduimijid, Hayes, Benjamin J. and Goddard, Michael E. (2014). Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics, 15 (1) 246. doi: 10.1186/1471-2164-15-246

A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle

Bolormaa, Sunduimijid, Pryce, Jennie E., Reverter, Antonio, Zhang, Yuandan, Barendse, William, Kemper, Kathryn, Tier, Bruce, Savin, Keith, Hayes, Ben J. and Goddard, Michael E. (2014). A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genetics, 10 (3) e1004198, e1004198. doi: 10.1371/journal.pgen.1004198

Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation

Macdonald, K. A., Pryce, J. E., Spelman, R. J., Davis, S. R., Wales, W. J., Waghorn, G. C., Williams, Y. J., II, Marett, L. C. and Hayes, B. J. (2014). Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation. Journal of Dairy Science, 97 (3), 1427-1435. doi: 10.3168/jds.2013-7227

Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations

Pryce, J. E., Johnston, J., Hayes, B. J., Sahana, G., Weigel, K. A., McParland, S., Spurlock, D., Krattenmacher, N., Spelman, R. J., Wall, E. and Calus, M. P. L. (2014). Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations. Journal of Dairy Science, 97 (3), 1799-1811. doi: 10.3168/jds.2013-7368

An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb

Knight, Matthew I., Daetwyler, Hans D., Hayes, Ben J., Hayden, Matthew J., Ball, Alex J., Pethick, David W. and McDonagh, Matthew B. (2014). An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb. Meat Science, 96 (2), 1025-1033. doi: 10.1016/j.meatsci.2013.07.008

Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

Amador, Carmen, Hayes, Ben J. and Daetwyler, Hans D. (2014). Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds. Evolutionary Applications, 7 (2), 227-237. doi: 10.1111/eva.12113

Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle

Raven, Lesley-Ann, Cocks, Benjamin G. and Hayes, Ben J. (2014). Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle. BMC Genomics, 15 (1) 62. doi: 10.1186/1471-2164-15-62

Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree

Nguyen, Thuy T. T., Hayes, Ben J. and Ingram, Brett A. (2014). Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree. Aquaculture, 420-421, 295-301. doi: 10.1016/j.aquaculture.2013.11.021

Erratum: Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels (J. Dairy Sci. 95:4114-4129)

Erbe, M., Hayes, B. J., Matukumalli, L. K., Goswami, S., Bowman, P. J., Reich, C. M., Mason, B. A. and Goddard, M. E. (2014). Erratum: Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels (J. Dairy Sci. 95:4114-4129). Journal of Dairy Science, 97 (10), 6622-6622. doi: 10.3168/jds.2014-97-10-6622

Genomic selection for feed efficiency in dairy cattle

Pryce, J. E., Wales, W. J., de Haas, Y., Veerkamp, R. F. and Hayes, B. J. (2014). Genomic selection for feed efficiency in dairy cattle. Animal, 8 (1), 1-10. doi: 10.1017/S1751731113001687

Short communication: Validation of genomic breeding value predictions for feed intake and feed efficiency traits

Pryce, J. E., Gonzalez-Recio, O., Thornhill, J. B., Marett, L. C., Wales, W. J., Coffey, M. P., de Haas, Y., Veerkamp, R. F. and Hayes, B. J. (2014). Short communication: Validation of genomic breeding value predictions for feed intake and feed efficiency traits. Journal of Dairy Science, 97 (1), 537-542. doi: 10.3168/jds.2013-7376

Thermoregulatory differences in lactating dairy cattle classed as efficient or inefficient based on residual feed intake

DiGiacomo, K., Marett, L. C., Wales, W. J., Hayes, B. J., Dunshea, F. R. and Leury, B. J. (2014). Thermoregulatory differences in lactating dairy cattle classed as efficient or inefficient based on residual feed intake. Animal Production Science, 54 (10), 1877-1881. doi: 10.1071/AN14311

Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

Druet, T., Macleod, I. M. and Hayes, B. J. (2014). Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity, 112 (1), 39-47. doi: 10.1038/hdy.2013.13

Author reply to A commentary on Pitfalls of predicting complex traits from SNPs

Wray, Naomi R., Yang, Jian, Hayes, Ben J., Price, Alkes L., Goddard, Michael E. and Visscher, Peter M. (2013). Author reply to A commentary on Pitfalls of predicting complex traits from SNPs. Nature Reviews Genetics, 14 (12), 894-894. doi: 10.1038/nrg3457-c2

Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle

Ross, Elizabeth M., Petrovski, Steve, Moate, Peter J. and Hayes, Ben J. (2013). Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiology, 13. doi: 10.1186/1471-2180-13-242

Effect of prior distributions on accuracy of genomic breeding values for two dairy traits

Nicolazzi, Ezequiel L., Negrini, Riccardo, Chamberlain, Amanda J., Goddard, Michael E., Marsan, Paolo Ajmone and Hayes, Ben J. (2013). Effect of prior distributions on accuracy of genomic breeding values for two dairy traits. Italian Journal of Animal Science, 12 (4) e91, 555-561. doi: 10.4081/ijas.2013.e91

Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle

Ross, Elizabeth M., Moate, Peter J., Marett, Leah C., Cocks, Ben G. and Hayes, Ben J. (2013). Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle. PLoS One, 8 (9) e73056, e73056. doi: 10.1371/journal.pone.0073056

Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors

MacLeod, Iona M., Larkin, Denis M., Lewin, Harris A., Hayes, Ben J. and Goddard, Mike E. (2013). Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Molecular Biology and Evolution, 30 (9), 2209-2223. doi: 10.1093/molbev/mst125

Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing

Ross, E. M., Moate, P. J., Marett, L., Cocks, B. G. and Hayes, B. J. (2013). Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. Journal of Dairy Science, 96 (9), 6030-6046. doi: 10.3168/jds.2013-6766

Genes of the RNASE5 pathway contain SNP associated with milk production traits in dairy cattle

Raven, Lesley-Ann, Cocks, Benjamin G., Pryce, Jennie E., Cottrell, Jeremy J. and Hayes, Ben J. (2013). Genes of the RNASE5 pathway contain SNP associated with milk production traits in dairy cattle. Genetics Selection Evolution, 45 (1) 25, 391-398. doi: 10.1186/1297-9686-45-25

Pitfalls of predicting complex traits from SNPs

Wray, Naomi R., Yang, Jian, Hayes, Ben J., Price, Alkes L., Goddard, Michael E. and Visscher, Peter M. (2013). Pitfalls of predicting complex traits from SNPs. Nature Reviews Genetics, 14 (7), 507-515. doi: 10.1038/nrg3457

Prospects for genomic selection in forage plant species

Hayes, Benjamin J., Cogan, Noel O. I., Pembleton, Luke W., Goddard, Michael E., Wang, Junping, Spangenberg, German C. and Forster, John W. (2013). Prospects for genomic selection in forage plant species. Plant Breeding, 132 (2), 133-143. doi: 10.1111/pbr.12037

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation

Hayes, Ben J., Lewin, Harris A. and Goddard, Michael E. (2013). The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends in Genetics, 29 (4), 206-214. doi: 10.1016/j.tig.2012.11.009

Latent biochemical relationships in the blood-milk metabolic axis of dairy cows revealed by statistical integration of 1H NMR spectroscopic data

Maher, Anthony D., Hayes, Benjamin, Cocks, Benjamin, Marett, Leah, Wales, William J. and Rochfort, Simone J. (2013). Latent biochemical relationships in the blood-milk metabolic axis of dairy cows revealed by statistical integration of 1H NMR spectroscopic data. Journal of Proteome Research, 12 (3), 1428-1435. doi: 10.1021/pr301056q

Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations

Haile-Mariam, M., Nieuwhof, G. J., Beard, K. T., Konstatinov, K. V. and Hayes, B. J. (2013). Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. Journal of Animal Breeding and Genetics, 130 (1), 20-31. doi: 10.1111/j.1439-0388.2013.01001.x

Accelerating improvement of livestock with genomic selection

Meuwissen, Theo, Hayes, Ben and Goddard, Mike (2013). Accelerating improvement of livestock with genomic selection. Annual Review of Animal Biosciences, 1 (1), 221-237. doi: 10.1146/annurev-animal-031412-103705

Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle

Bolormaa, S., Pryce, J. E., Kemper, K., Savin, K., Hayes, B. J., Barendse, W., Zhang, Y., Reich, C. M., Mason, B. A., Bunch, R. J., Harrison, B. E., Reverter, A., Herd, R. M., Tier, B., Graser, H. -U. and Goddard, M. E. (2013). Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. Journal of Animal Science, 91 (7), 3088-3104. doi: 10.2527/jas.2012-5827

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

Bolormaa, Sunduimijid, Pryce, Jennie E., Kemper, Kathryn E., Hayes, Ben J., Zhang, Yuandan, Tier, Bruce, Barendse, William, Reverter, Antonio and Goddard, Mike E. (2013). Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies. Genetics Selection Evolution, 45 (1) 43, 43.1-43.12. doi: 10.1186/1297-9686-45-43

Preface

Gondro, Cedric, Van Der Werf, Julius and Hayes, Ben (2013). Preface. Methods in Molecular Biology, 1019. doi: 10.1007/978-1-62703-447_0

Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation

Daetwyler, Hans D., Swan, Andrew A., van der Werf, Julius H. J. and Hayes, Ben J. (2012). Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genetics Selection Evolution, 44 (1) 33. doi: 10.1186/1297-9686-44-33

Genome position specific priors for genomic prediction

Brondum, Rasmus Froberg, Su, Guosheng, Lund, Mogens Sando, Bowman, Philip J., Goddard, Michael E. and Hayes, Benjamin J. (2012). Genome position specific priors for genomic prediction. BMC Genomics, 13 (1) 543. doi: 10.1186/1471-2164-13-543

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle

Khatkar, Mehar S., Moser, Gerhard, Hayes, Ben J. and Raadsma, Herman W. (2012). Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle. BMC Genomics, 13 (1) 538, 1-12. doi: 10.1186/1471-2164-13-538

Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets

de Haas, Y., Calus, M. P. L., Veerkamp, R. F., Wall, E., Coffey, M. P., Daetwyler, H. D., Hayes, B. J. and Pryce, J. E. (2012). Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets. Journal of Dairy Science, 95 (10), 6103-6112. doi: 10.3168/jds.2011-5280

A single nucleotide polymorphism on chromosome 10 is highly predictive for the polled phenotype in Australian Merino sheep

Dominik, S., Henshall, J. M. and Hayes, B. J. (2012). A single nucleotide polymorphism on chromosome 10 is highly predictive for the polled phenotype in Australian Merino sheep. Animal Genetics, 43 (4), 468-470. doi: 10.1111/j.1365-2052.2011.02271.x

Long-term selection strategies for complex traits using high-density genetic markers

Kemper, K. E., Bowman, R. J., Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2012). Long-term selection strategies for complex traits using high-density genetic markers. Journal of Dairy Science, 95 (8), 4646-4656. doi: 10.3168/jds.2011-5289

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

Ross, Elizabeth M., Moate, Peter J., Bath, Carolyn R., Davidson, Sophie E., Sawbridge, Tim I., Guthridge, Kathryn M., Cocks, Ben G. and Hayes, Ben J. (2012). High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genetics, 13 53. doi: 10.1186/1471-2156-13-53

Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels

Erbe, M., Hayes, B. J., Matukumalli, L. K., Goswami, S., Bowman, P. J., Reich, C. M., Mason, B. A. and Goddard, M. E. (2012). Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. Journal of Dairy Science, 95 (7), 4114-4129. doi: 10.3168/jds.2011-5019

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

Larkin, Denis M., Daetwyler, Hans D., Hernandez, Alvaro G., Wright, Chris L., Hetrick, Lorie A., Boucek, Lisa, Bachman, Sharon L., Band, Mark R., Akraiko, Tatsiana V., Cohen-Zinder, Miri, Thimmapuram, Jyothi, Macleod, Iona M., Harkins, Timothy T., McCague, Jennifer E., Goddard, Michael E., Hayes, Ben J. and Lewin, Harris A. (2012). Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proceedings of the National Academy of Sciences of the United States of America, 109 (20), 7693-7698. doi: 10.1073/pnas.1114546109

Discovery and trait association of single nucleotide polymorphisms from gene regions of influence on meat tenderness and long-chain omega-3 fatty acid content in Australian lamb

Knight, M. I., Daetwyler, H. D., Hayes, B. J., Hayden, M. J., Ball, A. J., Pethick, D. W. and McDonagh, M. B. (2012). Discovery and trait association of single nucleotide polymorphisms from gene regions of influence on meat tenderness and long-chain omega-3 fatty acid content in Australian lamb. Animal Production Science, 52 (7), 591-600. doi: 10.1071/AN11229

Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

Pryce, J. E., Arias, J., Bowman, P. J., Davis, S. R., Macdonald, K. A., Waghorn, G. C., Wales, W. J., Williams, Y. J., Spelman, R. J. and Hayes, B. J. (2012). Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers. Journal of Dairy Science, 95 (4), 2108-2119. doi: 10.3168/jds.2011-4628

Design of a bovine low-density snp array optimized for imputation

Boichard, Didier, Chung, Hoyoung, Dassonneville, Romain, David, Xavier, Eggen, Andre, Fritz, Sebastien, Gietzen, Kimberly J., Hayes, Ben J., Lawley, Cynthia T., Sonstegard, Tad S., Van Tassell, Curtis P., VanRaden, Paul M., Viaud-Martinez, Karine A. and Wiggans, George R. (2012). Design of a bovine low-density snp array optimized for imputation. PLoS One, 7 (3) e34130, e34130. doi: 10.1371/journal.pone.0034130

A review of how dairy farmers can use and profit from genomic technologies

Pryce, Jennie and Hayes, Ben (2012). A review of how dairy farmers can use and profit from genomic technologies. Animal Production Science, 52 (3), 180-184. doi: 10.1071/AN11172

Design and phenotyping procedures for recording wool, skin, parasite resistance, growth, carcass yield and quality traits of the SheepGENOMICS mapping flock

White, Jason D., Allingham, Peter G., Gorman, Chris M., Emery, David L., Hynd, Philip, Owens, John, Bell, Amy, Siddell, Jason, Harper, Greg, Hayes, Ben J., Daetwyler, Hans D., Usmar, Jonathan, Goddard, Mike E., Henshall, John M., Dominik, Sonja, Brewer, Heather, van der Werf, Julius H. J., Nicholas, Frank W., Warner, Robyn, Hofmyer, Chris, Longhurst, Terry, Fisher, Troy, Swan, Paul, Forage, Rob and Oddy, V. Hutton (2012). Design and phenotyping procedures for recording wool, skin, parasite resistance, growth, carcass yield and quality traits of the SheepGENOMICS mapping flock. Animal Production Science, 52 (2-3), 157-171. doi: 10.1071/AN11085

Components of the accuracy of genomic prediction in a multi-breed sheep population

Daetwyler, H. D., Kemper, K. E., van der Werf, J. H. J. and Hayes, B. J. (2012). Components of the accuracy of genomic prediction in a multi-breed sheep population. Journal of Animal Science, 90 (10), 3375-3384. doi: 10.2527/jas.2011-4557

Accuracy of genotype imputation in sheep breeds

Hayes, B. J., Bowman, P. J., Daetwyler, H. D., Kijas, J. W. and van der Werf, J. H. J. (2012). Accuracy of genotype imputation in sheep breeds. Animal Genetics, 43 (1), 72-80. doi: 10.1111/j.1365-2052.2011.02208.x

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

Kijas, James W., Lenstra, Johannes A., Hayes, Ben, Boitard, Simon, Neto, Laercio R. Porto, San Cristobal, Magali, Servin, Bertrand, McCulloch, Russell, Whan, Vicki, Gietzen, Kimberly, Paiva, Samuel, Barendse, William, Ciani, Elena, Raadsma, Herman, McEwan, John, Dalrymple, Brian and Int Sheep Genomics Consortium (2012). Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. PLoS Biology, 10 (2) e1001258, e1001258. doi: 10.1371/journal.pbio.1001258

Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle

Chamberlain, A. J., Hayes, B. J., Savin, K., Bolormaa, S., McPartlan, H. C., Bowman, P. J., Van der Jagt, C., MacEachern, S. and Goddard, M. E. (2012). Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle. Journal of Dairy Science, 95 (2), 864-875. doi: 10.3168/jds.2010-3786

Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information

Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2012). Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science, 95 (1), 377-388. doi: 10.3168/jds.2011-4254

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

Lien, Sigbjorn, Gidskehaug, Lars, Moen, Thomas, Hayes, Ben J., Berg, Paul R., Davidson, William S., Omholt, Stig W. and Kent, Matthew P. (2011). A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics, 12 (1) 615. doi: 10.1186/1471-2164-12-615

Impacts of stock enhancement strategies on the effective population size of Murray cod, Maccullochella peelii, a threatened Australian fish

Ingram, B. A., Hayes, B. and Rourke, M. L. (2011). Impacts of stock enhancement strategies on the effective population size of Murray cod, Maccullochella peelii, a threatened Australian fish. Fisheries Management and Ecology, 18 (6), 467-481. doi: 10.1111/j.1365-2400.2011.00798.x

Use of a microsatellite-based pedigree in estimation of heritabilities for economic traits in Australian blue mussel, Mytilus galloprovincialis

Nguyen, T. T. T., Hayes, B. J., Guthridge, K., Ab Rahim, E. S. and Ingram, B. A. (2011). Use of a microsatellite-based pedigree in estimation of heritabilities for economic traits in Australian blue mussel, Mytilus galloprovincialis. Journal of Animal Breeding and Genetics, 128 (6), 482-490. doi: 10.1111/j.1439-0388.2011.00948.x

Using the genomic relationship matrix to predict the accuracy of genomic selection

Goddard, M. E., Hayes, B. J. and Meuwissen, T. H. E. (2011). Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics, 128 (6), 409-421. doi: 10.1111/j.1439-0388.2011.00964.x

Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12

Olsen, H. G., Hayes, B. J., Kent, M. P., Nome, T., Svendsen, M., Larsgard, A. G. and Lien, S. (2011). Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Animal Genetics, 42 (5), 466-474. doi: 10.1111/j.1365-2052.2011.02179.x

Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle

Sodeland, M., Kent, M. P., Olsen, H. G., Opsal, M. A., Svendsen, M., Sehested, E., Hayes, B. J. and Lien, S. (2011). Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle. Animal Genetics, 42 (5), 457-465. doi: 10.1111/j.1365-2052.2010.02165.x

Imputation of missing genotypes from sparse to high density using long-range phasing

Daetwyler, Hans D., Wiggans, George R., Hayes, Ben J., Woolliams, John A. and Goddard, Mike E. (2011). Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics, 189 (1), 317-327. doi: 10.1534/genetics.111.128082

Variation in residual feed intake in Holstein-Friesian dairy heifers in southern Australia

Williams, Y. J., Pryce, J. E., Grainger, C., Wales, W. J., Linden, N., Porker, M. and Hayes, B. J. (2011). Variation in residual feed intake in Holstein-Friesian dairy heifers in southern Australia. Journal of Dairy Science, 94 (9), 4715-4725. doi: 10.3168/jds.2010-4015

Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle

Sodeland, Marte, Grove, Harald, Kent, Matthew, Taylor, Simon, Svendsen, Morten, Hayes, Ben J. and Lien, Sigbjorn (2011). Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle. BMC Genetics, 12 70. doi: 10.1186/1471-2156-12-70

Genetic parameters for growth and survival in Penaeus monodon cultured in India

Krishna, Gopal, Gopikrishna, Gopalapillay, Gopal, Chavali, Jahageerdar, Shrinivas, Ravichandran, Pitchaiyappan, Kannappan, Sudalyandi, Pillai, Subramaniapillai M., Paulpandi, Sivagnanam, Kiran, Remanibhaskaran P., Saraswati, Ramamoorthy, Venugopal, Gundaboena, Kumar, Dilip, Gitterle, Thomas, Lozano, Carlos, Rye, Morten and Hayes, Ben (2011). Genetic parameters for growth and survival in Penaeus monodon cultured in India. Aquaculture, 318 (1-2), 74-78. doi: 10.1016/j.aquaculture.2011.04.028

Effect of stocking density, water exchange rate and tank substrate on growth and survival of post-larvae of Penaeus monodon (Fabricius, 1798)

Gopikrishna, G., Gopal, C., Krishna, G., Jahageerdar, S., Rye, M., Lozano, C., Gitterle, T., Venugopal, G., Paulpandi, S., Ravichandran, P., Pillai, S. M., Ponniah, A. G. and Hayes, B. (2011). Effect of stocking density, water exchange rate and tank substrate on growth and survival of post-larvae of Penaeus monodon (Fabricius, 1798). Indian Journal of Fisheries, 58 (3), 57-61.

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

Qanbari, Saber, Gianola, Daniel, Hayes, Ben, Schenkel, Flavio, Miller, Steve, Moore, Stephen, Thaller, Georg and Simianer, Henner (2011). Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, 12 (1) 318. doi: 10.1186/1471-2164-12-318

Short communication: Genomic selection using a multi-breed, across-country reference population

Pryce, J. E., Gredler, B., Bolormaa, S., Bowman, P. J., Egger-Danner, C., Fuerst, C., Emmerling, R., Soelkner, J., Goddard, M. E. and Hayes, B. J. (2011). Short communication: Genomic selection using a multi-breed, across-country reference population. Journal of Dairy Science, 94 (5), 2625-2630. doi: 10.3168/jds.2010-3719

Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data

Hayes, B. J. (2011). Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data. Journal of Dairy Science, 94 (4), 2114-2117. doi: 10.3168/jds.2010-3896

Polymorphic regions affecting human height also control stature in cattle

Pryce, Jennie E., Hayes, Ben J., Bolormaa, Sunduimijid and Goddard, Michael E. (2011). Polymorphic regions affecting human height also control stature in cattle. Genetics, 187 (3), 981-984. doi: 10.1534/genetics.110.123943

Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array

Gidskehaug, Lars, Kent, Matthew, Hayes, Ben J. and Lien, Sigbjorn (2011). Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics, 27 (3) btq673, 303-310. doi: 10.1093/bioinformatics/btq673

Recent and historical recombination in the admixed Norwegian Red cattle breed

Sodeland, Marte, Kent, Matthew, Hayes, Ben J., Grove, Harald and Lien, Sigbjorn (2011). Recent and historical recombination in the admixed Norwegian Red cattle breed. BMC Genomics, 12 (1) 33. doi: 10.1186/1471-2164-12-33

The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

Kemper, Kathryn E., Emery, David L., Bishop, Stephen C., Oddy, Hutton, Hayes, Benjamin J., Dominik, Sonja, Henshall, John M. and Goddard, Michael E. (2011). The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections. Genetics Research, 93 (3), 203-219. doi: 10.1017/S0016672311000097

Genomic selection in livestock populations

Goddard, Michael E., Hayes, Ben J. and Meuwissen, Theo H. E. (2010). Genomic selection in livestock populations. Genetics Research, 92 (5-6), 413-421. doi: 10.1017/S0016672310000613

Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population

Daetwyler, H. D., Hickey, J. M., Henshall, J. M., Dominik, S., Gredler, B., van der Werf, J. H. J. and Hayes, B. J. (2010). Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Animal Production Science, 50 (12), 1004-1010. doi: 10.1071/AN10096

Deterministic models of breeding scheme designs that incorporate genomic selection

Pryce, J. E., Goddard, M. E., Raadsma, H. W. and Hayes, B. J. (2010). Deterministic models of breeding scheme designs that incorporate genomic selection. Journal of Dairy Science, 93 (11), 5455-5466. doi: 10.3168/jds.2010-3256

Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers

Moser, Gerhard, Khatkar, Mehar S., Hayes, Ben J. and Raadsma, Herman W. (2010). Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers. Genetics Selection Evolution, 42 (1) 37, 37.1-37.15. doi: 10.1186/1297-9686-42-37

Limited evidence for genetic variation for resistance to the white spot syndrome virus in Indian populations of Penaeus monodon

Hayes, Ben J., Gitterle, Thomas, Gopikrishna, Gopalapillay, Gopal, Chavali, Krishna, Gopal, Jahageerdar, Shrivinas, Lozano, Carlos, Alavandi, Shankar, Paulpandi, Sivagnanam, Ravichandran, Pitchaiyappan and Rye, Morten (2010). Limited evidence for genetic variation for resistance to the white spot syndrome virus in Indian populations of Penaeus monodon. Aquaculture Research, 41 (11), e872-e877. doi: 10.1111/j.1365-2109.2010.02611.x

Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits

Hayes, Ben J., Pryce, Jennie, Chamberlain, Amanda J., Bowman, Phil J. and Goddard, Mike E. (2010). Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genetics, 6 (9) e1001139, e1001139. doi: 10.1371/journal.pgen.1001139

Multivariate analysis of a genome-wide association study in dairy cattle

Bolormaa, S., Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2010). Multivariate analysis of a genome-wide association study in dairy cattle. Journal of Dairy Science, 93 (8), 3818-3833. doi: 10.3168/jds.2009-2980

Testing options for the commercialization of abalone selective breeding using bioeconomic simulation modelling

Robinson, Nick, Li, Xiaoxu and Hayes, Ben (2010). Testing options for the commercialization of abalone selective breeding using bioeconomic simulation modelling. Aquaculture Research, 41 (9), e268-e288. doi: 10.1111/j.1365-2109.2010.02528.x

A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes

Pryce, J. E., Bolormaa, S., Chamberlain, A. J., Bowman, P. J., Savin, K., Goddard, M. E. and Hayes, B. J. (2010). A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. Journal of Dairy Science, 93 (7), 3331-3345. doi: 10.3168/jds.2009-2893

A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle

Olsen, H. G., Hayes, B. J., Kent, M. P., Nome, T., Svendsen, M. and Lien, S. (2010). A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle. Animal Genetics, 41 (3), 273-280. doi: 10.1111/j.1365-2052.2009.01998.x

Genetic markers for lactation persistency in primiparous Australian dairy cows

Pryce, J. E., Haile-Mariam, M., Verbyla, K., Bowman, P. J., Goddard, M. E. and Hayes, B. J. (2010). Genetic markers for lactation persistency in primiparous Australian dairy cows. Journal of Dairy Science, 93 (5), 2202-2214. doi: 10.3168/jds.2009-2666

Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms

MacLeod, I. M., Hayes, B. J., Savin, K. W., Chamberlain, A. J., McPartlan, H. C. and Goddard, M. E. (2010). Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms. Journal of Animal Breeding and Genetics, 127 (2), 133-142. doi: 10.1111/j.1439-0388.2009.00831.x

Weight and time of onset of female-superior sexual dimorphism in pond reared Penaeus monodon

Gopal, Chavali, Gopikrishna, Gopalapillay, Krishna, Gopal, Jahageerdar, Shrinivas S., Rye, Morten, Hayes, Ben J., Paulpandi, Sivagnanam, Kiran, Remanibhaskaran P., Pillai, Subramaniapillai M., Ravichandran, Pitchaiyappan, Ponniah, Alphis G. and Kumar, Dilip (2010). Weight and time of onset of female-superior sexual dimorphism in pond reared Penaeus monodon. Aquaculture, 300 (1-4), 237-239. doi: 10.1016/j.aquaculture.2010.01.007

A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors

MacLeod, I. M., Meuwissen, T. H. E., Hayes, B. J. and Goddard, M. E. (2009). A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genetics Research, 91 (6), 413-426. doi: 10.1017/S0016672309990358

LASSO with cross-validation for genomic selection

Usai, M. Graziano, Goddard, Mike E. and Hayes, Ben J. (2009). LASSO with cross-validation for genomic selection. Genetics Research, 91 (6), 427-436. doi: 10.1017/S0016672309990334

Reliability of genomic predictions across multiple populations

de Roos, A. P. W., Hayes, B. J. and Goddard, M. E. (2009). Reliability of genomic predictions across multiple populations. Genetics, 183 (4), 1545-1553. doi: 10.1534/genetics.109.104935

Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species

Hayes, B. J., MacLeod, I. M. and Baranski, M. (2009). Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species. Genetics Research, 91 (6), 367-371. doi: 10.1017/S0016672309990310

Using LASSO to estimate marker effects for Genomic Selection

Usai, Mario Graziano, Goddard, Mike E. and Hayes, Ben J. (2009). Using LASSO to estimate marker effects for Genomic Selection. Italian Journal of Animal Science, 8 (SUPPL. 2), 168-170.

Accuracy of genomic breeding values in multi-breed dairy cattle populations

Hayes, Ben J., Bowman, Phillip J., Chamberlain, Amanda C., Verbyla, Klara and Goddard, Mike E. (2009). Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genetics Selection Evolution, 41 (1) 51, 321-329. doi: 10.1186/1297-9686-41-51

Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle

Verbyla, Klara L., Hayes, Ben J., Bowman, Philip. J. and Goddard, Michael E. (2009). Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle. Genetics Research, 91 (5), 307-311. doi: 10.1017/S0016672309990243

Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6

Nilsen, H., Olsen, H. G., Hayes, B., Nome, T., Sehested, E., Svendsen, M., Meuwissen, T. H. E. and Lien, S. (2009). Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6. Animal Genetics, 40 (5), 701-712. doi: 10.1111/j.1365-2052.2009.01908.x

A validated genome wide association study to breed cattle adapted to an environment altered by climate change

Hayes, Ben J., Bowman, Phil J., Chamberlain, Amanda J., Savin, Keith, van Tassell, Curt P., Sonstegard, Tad S. and Goddard, Mike E. (2009). A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS ONE, 4 (8) e6676, e6676. doi: 10.1371/journal.pone.0006676

Gene by environment interactions for production traits in Australian dairy cattle

Lillehammer, M., Hayes, B. J., Meuwissen, T. H. E. and Goddard, M. E. (2009). Gene by environment interactions for production traits in Australian dairy cattle. Journal of Dairy Science, 92 (8), 4008-4017. doi: 10.3168/jds.2008-1484

Mapping genes for complex traits in domestic animals and their use in breeding programmes

Goddard, Michael E. and Hayes, Ben J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics, 10 (6), 381-391. doi: 10.1038/nrg2575

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

MacEachern, Sean, Hayes, Ben, McEwan, John and Goddard, Mike (2009). 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. BMC Genomics, 10 181. doi: 10.1186/1471-2164-10-181

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

Gibbs, Richard A., Taylor, Jeremy F., Van Tassell, Curtis P., Barendse, William, Eversoie, Kallye A., Gill, Clare A., Green, Ronnie D., Hamernik, Debora L., Kappes, Steven M., Lien, Sigbjorn, Matukumalli, Lakshmi K., McEwan, John C., Nazareth, Lynne V., Schnabel, Robert D., Taylor, Jeremy F., Weinstock, George M., Wheeler, David A., Ajmone-Marsan, Paolo, Barendse, William, Boettcher, Paul J., Caetano, Alexandre R., Garcia, Jose Fernando, Hanotte, Olivier, Mariani, Paola, Skow, Loren C., Williams, John L., Caetano, Alexandre R., Diallo, Boubacar, Green, Ronnie D. ... Dodds, Ken G. (2009). Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324 (5926), 528-532. doi: 10.1126/science.1167936

A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle

Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., Sethuraman, L. and Goddard, M. E. (2009). A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics, 40 (2), 176-184. doi: 10.1111/j.1365-2052.2008.01815.x

Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009)

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009). Genetics Research, 91 (2), 143-143. doi: 10.1017/S0016672309000111

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

Nilsen, Heidi, Olsen, Hanne Gro, Hayes, Ben, Sehested, Erling, Svendsen, Morten, Nome, Torfinn, Meuwissen, Theo and Lien, Sigbjorn (2009). Casein haplotypes and their association with milk production traits in Norwegian Red cattle. Genetics Selection Evolution, 41 (1) 24. doi: 10.1186/1297-9686-41-24

Increased accuracy of artificial selection by using the realized relationship matrix

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. Genetics Research, 91 (1), 47-60. doi: 10.1017/S0016672308009981

Invited review: genomic selection in dairy cattle: progress and challenges

Hayes, B. J., Bowman, P. J., Chamberlain, A. J. and Goddard, M. E. (2009). Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science, 92 (2), 433-443. doi: 10.3168/jds.2008-1646

Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar)

Robinson, Nick and Hayes, Ben (2008). Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar). Aquaculture, 285 (1-4), 38-46. doi: 10.1016/j.aquaculture.2008.08.016

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

Baranski, M., Rourke, M., Loughnan, S., Hayes, B., Austin, C. and Robinson, N. (2008). Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling. Animal Genetics, 39 (6), 606-614. doi: 10.1111/j.1365-2052.2008.01773.x

Predicting unobserved phenotypes for complex traits from whole-genome SNP data

Lee, Sang Hong, van der Werf, Julius H. J., Hayes, Ben J., Goddard, Michael E. and Visscher, Peter M. (2008). Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genetics, 4 (10) e1000231, e1000231. doi: 10.1371/journal.pgen.1000231

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Robinson, N., Goddard, M. and Hayes, B. (2008). Use of gene expression data for predicting continuous phenotypes for animal production and breeding. Animal, 2 (10), 1413-1420. doi: 10.1017/S1751731108002632

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

de Roos, A. P. W., Hayes, B. J., Spelman, R. J. and Goddard, M. E. (2008). Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179 (3), 1503-1512. doi: 10.1534/genetics.107.084301

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

Moen, Thomas, Hayes, Ben, Baranski, Matthew, Berg, Paul R., Kjoglum, Sissel, Koop, Ben F., Davidson, Willie S., Omholt, Stig W. and Lien, Sigbjorn (2008). A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics, 9 223. doi: 10.1186/1471-2164-9-223

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

Nilsen, H., Hayes, B., Berg, P. R., Roseth, A., Sundsaasen, K. K., Nilsen, K. and Lien, S. (2008). Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal Genetics, 39 (2), 97-104. doi: 10.1111/j.1365-2052.2007.01686.x

The origin of selection signatures on bovine chromosome 6

Hayes, B. J., Lien, S., Nilsen, H., Olsen, H. G., Berg, P., Maceachern, S., Potter, S. and Meuwissen, T. H. E. (2008). The origin of selection signatures on bovine chromosome 6. Animal Genetics, 39 (2), 105-111. doi: 10.1111/j.1365-2052.2007.01683.x

Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection

Moen, Thomas, Hayes, Ben, Nilsen, Frank, Delghandi, Madjid, Fjalestad, Kjersti T., Fevolden, Svein-Erik, Berg, Paul R. and Lien, Sigbjorn (2008). Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genetics, 9 (1) 18. doi: 10.1186/1471-2156-9-18

Comparison of casein haplotypes between two geographically distant European dairy goat breeds

Finocchiaro, R., Hayes, B. J., Siwek, M., Spelman, R. J., van Kaam, J. B. C. H. M., Adnoy, T. and Portolano, B. (2008). Comparison of casein haplotypes between two geographically distant European dairy goat breeds. Journal of Animal Breeding and Genetics, 125 (1), 68-72. doi: 10.1111/j.1439-0388.2007.00687.x

Technical note: prediction of breeding values using marker-derived relationship matrices

Hayes, B. J. and Goddard, M. E. (2008). Technical note: prediction of breeding values using marker-derived relationship matrices. Journal of Animal Science, 86 (9), 2089-2092. doi: 10.2527/jas.2007-0733

Genomic selection

Goddard, M. E. and Hayes, B. J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124 (6), 323-330. doi: 10.1111/j.1439-0388.2007.00702.x

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

Moen, Thomas, Sonesson, Anna K., Hayes, Ben, Lien, Sigbjorn, Munck, Hege and Meuwissen, Theo H. E. (2007). Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data. BMC Genetics, 8 (1) 53. doi: 10.1186/1471-2156-8-53

Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

Hayes, B. J., Chamberlain, A. J., McPartlan, H., Macleod, I., Sethuraman, L. and Goddard, M. E. (2007). Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle. Genetical Research, 89 (4), 215-220. doi: 10.1017/S0016672307008865

Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms

Gjuvsland, Arne B., Hayes, Ben J., Meuwissen, Theo H. E., Plahte, Erik and Omholt, Stig W. (2007). Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms. BMC Systems Biology, 1 (1) 32. doi: 10.1186/1752-0509-1-32

Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle

Olsen, Hanne Gro, Nilsen, Heidi, Hayes, Ben, Berg, Paul R., Svendsen, Morten, Lien, Sigbjorn and Meuwissen, Theo (2007). Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle. BMC Genetics, 8 (1) 32. doi: 10.1186/1471-2156-8-32

An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences

Hayes, B., Laerdahl, J. K., Lien, S., Moen, T., Berg, P., Hindar, K., Davidson, W. S., Koop, B. F., Adzhubei, A. and Hoyheim, B. (2007). An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture, 265 (1-4), 82-90. doi: 10.1016/j.aquaculture.2007.01.037

Optimisation of marker assisted selection for abalone breeding programs

Hayes, Ben, Baranski, Matt, Goddard, Mike E. and Robinson, Nick (2007). Optimisation of marker assisted selection for abalone breeding programs. Aquaculture, 265 (1-4), 61-69. doi: 10.1016/j.aquaculture.2007.02.016

Recent human effective population size estimated from linkage disequilibrium

Tenesa, Albert, Navarro, Pau, Hayes, Ben J., Duffy, David L., Clarke, Geraldine M., Goddard, Mike E. and Visscher, Peter M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17 (4), 520-526. doi: 10.1101/gr.6023607

Statistical epistasis is a generic feature of gene regulatory networks

Gjuvsland, Arne B., Hayes, Ben J., Omholt, Stig W. and Carlborg, Orjan (2007). Statistical epistasis is a generic feature of gene regulatory networks. Genetics, 175 (1), 411-420. doi: 10.1534/genetics.106.058859

Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10

Opsal, Monica Aa., Vage, Dag Inge, Hayes, Ben, Berget, Ingunn and Lien, Sigbjorn (2006). Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10. Gene, 384 (1-2), 45-50. doi: 10.1016/j.gene.2006.06.027

Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination

Hayes, Ben, Hagesaether, Nina, Adnoy, Tormod, Pellerud, Grunde, Berg, Paul R. and Lien, Sigbjorn (2006). Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination. Genetics, 174 (1), 455-464. doi: 10.1534/genetics.106.058966

Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males

Hayes, B. J., Gjuvsland, A. and Omholt, S. (2006). Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males. Heredity, 97 (1), 19-26. doi: 10.1038/sj.hdy.6800827

Use of molecular markers to maximise diversity of founder populations for aquaculture breeding programs

Hayes, Ben, He, Jie, Moen, Thomas and Bennewitz, Joern (2006). Use of molecular markers to maximise diversity of founder populations for aquaculture breeding programs. Aquaculture, 255 (1-4), 573-578. doi: 10.1016/j.aquaculture.2005.11.038

Evaluation of three strategies using DNA markers for traceability in aquaculture species

Hayes, Ben, Sonesson, Anna K. and Gjerde, Bjarne (2005). Evaluation of three strategies using DNA markers for traceability in aquaculture species. Aquaculture, 250 (1-2), 70-81. doi: 10.1016/j.aquaculture.2005.03.008

Break-even cost of genotyping genetic mutations affecting economic traits in Australian pig enterprises

Hayes, Ben and Goddard, Mike E. (2004). Break-even cost of genotyping genetic mutations affecting economic traits in Australian pig enterprises. Livestock Production Science, 89 (2-3), 235-242. doi: 10.1016/j.livprodsci.2004.01.005

Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records

Hayes, B. J., Carrick, M., Bowman, P. and Goddard, M. E. (2003). Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records. Journal of Dairy Science, 86 (11), 3736-3744. doi: 10.3168/jds.S0022-0302(03)73980-0

Evaluation of marker assisted selection in pig enterprises

Hayes, Ben and Goddard, Mike E. (2003). Evaluation of marker assisted selection in pig enterprises. Livestock Production Science, 81 (2-3), 197-211. doi: 10.1016/S0301-6226(02)00257-9

Novel multilocus measure of linkage disequilibrium to estimate past effective population size

Hayes, Ben J., Visscher, Peter M., McPartlan, Helen C. and Goddard, Mike E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13 (4), 635-643. doi: 10.1101/gr.387103

Look ahead mate selection schemes for multi-breed beef populations

Hayes, B., Shepherd, R. K. and Newman, S. (2002). Look ahead mate selection schemes for multi-breed beef populations. Animal Science, 74 (1), 13-23. doi: 10.1017/S1357729800052206

The distribution of the effects of genes affecting quantitative traits in livestock

Hayes, Ben and Goddard, Mike E. (2001). The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution, 33 (3), 209-229.

Prediction of total genetic value using genome-wide dense marker maps

Meuwissen, T. H. E., Hayes, B. J. and Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157 (4), 1819-1829.

Technical note: Constrained optimization of breed composition in composite populations to balance net merit and risk

Hayes B.J., Newman S. and Shepherd R.K. (2000). Technical note: Constrained optimization of breed composition in composite populations to balance net merit and risk. Journal of Animal Science, 78 (8), 2105-2107.

New diagnostic tools for bovine vibriosis

Tabor, Ala, Siddle, Hannah, Juli, Sogra Banu, Raza, Ali, Ong, Chian Teng, McCosker, Kieren, Hayes, Ben and Boe-Hansen, Gry (2023). New diagnostic tools for bovine vibriosis. Northern Beef Research Update Conference, Darwin, NT Australia, 22-25 August 2023.

Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis

Mantilla Valdivieso, E. , Nguyen, L., Ross, E., Raza, A., James, P., Hayes, B., Jonsson, N. and Tabor, A. (2022). Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_557

The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy

Lamb, H.J., Nguyen, L.T., Randhawa, I.A.S., Hayes, B.J. and Ross, E.M. (2022). The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_279

A conditional multi‑trait sequence GWAS of heifer fertility in tropically adapted beef cattle

Forutan, M., Engle, B., Goddard, M. E. and Hayes, B. J. (2022). A conditional multi‑trait sequence GWAS of heifer fertility in tropically adapted beef cattle. World Congress on Genetics Applied to Livestock Production, Rotterdam, The Netherlands, 3 July-8 July 2022.

Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in northern Australia

Copley, J.P., Engle, B.N., Speight, S., Fordyce, G., Ross, E.M., Voss-Fels, K.P. and Hayes, B.J. (2021). Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in northern Australia. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Genomic prediction of lifetime productivity in Brahman cows

Engle, B.N., Collins Snr, A. and Hayes, B.J. (2021). Genomic prediction of lifetime productivity in Brahman cows. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing

Lamb, H. J. , Nguyen, L. T., Engle, B. N., Hayes, B. J. and Ross, E. M. (2021). Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Assessing the potential of parentage testing using portable long read sequencing technologies

Ross, E. M., Lamb, H. J., Engle, B. N. , Nguyen, L. T. and Hayes, B. J. (2021). Assessing the potential of parentage testing using portable long read sequencing technologies. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Genome wide analysis of bovine enhancers and promoters across developmental stages in liver

Forutan, M., Vander Jagt, C.J., Ross, E., Chamberlain, A. J., Mason, B., Nguyen, L., Moore, S., Garner, J. B., Xiang, R. and Hayes, B. J. (2021). Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Multibreed genomic prediction for male fertility in tropical beef cattle

Porto-Neto, L. R., Bertram, J., McWilliam, S., Fortes, M. R. S., Alexandre, P., McGowan, M. R., Hayes, B. J. and Reverter, A. (2021). Multibreed genomic prediction for male fertility in tropical beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Genome-wide analysis of transcription start sites across Bos indicus tissues

Forutan, Mehrnush, Ross, Elizabeth, Nguyen, Loan and Hayes, Ben (2021). Genome-wide analysis of transcription start sites across Bos indicus tissues. 38th International Conference on Animal Genetics, Online, 26 - 30 July 2021.

A Bos indicus epigenetic clock predicts age from tail hair

Nguyen, Loan T., Forutan, Mehrnush, Hayes, Ben J. and Ross, Elizabeth M. (2021). A Bos indicus epigenetic clock predicts age from tail hair. 38th International Society of Animal Genetics (ISAG), Virtual, 26 - 30 July 2021.

Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle

Mantilla Valdivieso, E., Ross, E., Raza, A., Hayes, B., Jonsson, N., James, P. and Tabor, A. (2021). Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Factors affecting fertility in northern Australian beef herds

Copley, J., Engle, B., Ross, E., Landmark, S., Fordyce, G., Burns, B. and Hayes, B. (2021). Factors affecting fertility in northern Australian beef herds. 33rd Biennial Conference of the Australian Association of Animal Sciences, Fremantle, WA, Australia and online, 1-3 February 2020. Toowong, QLD, Australia: Australian Association of Animal Sciences.

The impact of physiological non-additivity on variance components for complex traits

Voss-Fels, Kai, Powell, Owen, Jordan, David, Hammer, Graeme, Barbier, Francois, Werner, Christian, Hayes, Ben, Beveridge, Christine and Cooper, Mark (2020). The impact of physiological non-additivity on variance components for complex traits. The 6th International Conference on Quantitative Genetics, Brisbane, QLD Australia, 3-13 November 2020.

Application of genomic selection to Vietnamese household dairy herds

Bang, N.N., Hayes, B.J., Randhawa, I.A.S., Lyons, R.E., Gaughan, J.B., Chanh, N.V., Trach, N.X., Khang, N.D. and McNeill, D.M. (2019). Application of genomic selection to Vietnamese household dairy herds. 23rd AABG Conference, Armidale, Australia, 27 October - 1 November 2019.

DNA testing and genetic evaluation for poll breeding in tropically adapted beef cattle

Randhawa, I. A. S, Hayes, B. J., McGowan, M. R., Porto-Neto, L. R. and Lyons, R. E. (2019). DNA testing and genetic evaluation for poll breeding in tropically adapted beef cattle. International Tropical Agriculture Conference (TROPAG2019), Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036098

Environmental characterization facilitate G × E interaction to highlight the role of stay-green traits for genetic gain

Amin, Asad, Christopher, Jack, Ababaei, Behnam, Cooper, Mark, Hayes, Ben, Voss-Fels, Kai, Hickey, Lee and Chenu, Karine (2019). Environmental characterization facilitate G × E interaction to highlight the role of stay-green traits for genetic gain. Translational Photosynthesis Conference: Innovations in Agriculture for Food Security (ASPS 2019), Brisbane, QLD, Australia, 30 June - 3 July 2019.

Improving poll gene testing in Australian cattle

Randhawa, I. A. S., Porto-Neto, L., Hayes, B., McGowan, M., Burns, B. and Lyons, R. (2019). Improving poll gene testing in Australian cattle. RSPCA Australian Animal Welfare Seminar, Canberra, ACT Australia, 22 February 2019.

New diagnostic tools helping poll breeding for sustainable beef production

Randhawa, I. A. S, Hayes, B. J., Porto-Neto, L. R., Schutt, K. M., McGowan, M. R., Burns, B. M. and Lyons, R. E. (2019). New diagnostic tools helping poll breeding for sustainable beef production. Northern Beef Research Update Conference (NBRUC2019), Brisbane, QLD Australia, 19-22 August 2019.

Poll diagnostics, scur genetics and production concurrence in naturally hornless cattle

Randhawa, I. A. S., McGowan, M. R., Porto-Neto, L. R., Hayes, B. J. and Lyons, R. E. (2019). Poll diagnostics, scur genetics and production concurrence in naturally hornless cattle. 37th International Society for Animal Genetics (ISAG) Conference, Lleida, Spain, 7-12 July 2019.

Poll testing efficiency, accuracy and trends in Australian cattle

Randhawa, I.A.S., McGowan, M.R., Porto-Neto, L.R., Hayes, B.J., Schutt, K.M. and Lyons, R.E. (2019). Poll testing efficiency, accuracy and trends in Australian cattle. Association for the Advancement in Animal Breeding Genetics, Armidale, Australia, 27 October - 1 November 2019.

Production and polledness: genetic correlations between target traits in beef cattle

Randhawa, Imtiaz A. S. , Porto-Neto, Laercio R. , McGowan, Michael R. , Hayes, Ben J. , Schutt, Karen M. and Lyons, Russell E. (2019). Production and polledness: genetic correlations between target traits in beef cattle. AAABG2019, Armidale, Australia, 27 October - 1 November 2019.

Variation in floral and growth traits in a macadamia breeding population

O’Connor, K.M., Hardner, C.M., Alam, M.M., Hayes, B.J. and Topp, B.L. (2018). Variation in floral and growth traits in a macadamia breeding population. International Symposia on Tropical and Temperate Horticulture (ISTTH), Cairns, QLD, Australia, 20-25 November, 2016. Leuven, Belgium: International Society for Horticultural Science (ISHS). doi: 10.17660/actahortic.2018.1205.77

Accuracy of multi-trait genomic predictions for age at puberty in Northern Australian beef heifers

Engle, B., Corbet, N., Allen, J., Laing, A., Fordyce, G., McGowan, M., Burns, B. and Hayes, B. (2018). Accuracy of multi-trait genomic predictions for age at puberty in Northern Australian beef heifers. 2018 ASAS-CSAS Annual Meeting and Trade Show, Vancouver, Canada, 8-12 July 2018. Cary, NC, United States: Oxford University Press (OUP). doi: 10.1093/jas/sky404.231

The use of multi-breed reference populations and multi-omic data to maximize accuracy of genomic prediction

Goddard, M.E., MacLeod, I.M., Kemper, K.E., Xiang, R., van den Berg, I., Khansefid, M., Daetwyler, H.D. and Hayes, B.J. (2018). The use of multi-breed reference populations and multi-omic data to maximize accuracy of genomic prediction. 11th World Congress of Genetics Applied to Livestock Production, Auckland, New Zealand, 11-16 February 2018. Auckland, New Zealand: WCGALP.

Indirect prediction of macadamia yield through a genome wide association study of component traits

O'Connor, Katie, Hayes, Ben, Hardner, Craig, Mobashwer Alam and Topp, Bruce (2017). Indirect prediction of macadamia yield through a genome wide association study of component traits. International Macadamia Research Symposium, Hawaii, United States, 13-14 September 2017.

Improving the selection efficiency in potato breeding

Slater, A. T., Cogan, N. O.I., Rodoni, B. C., Hayes, B. J. and Forster, J. W. (2016). Improving the selection efficiency in potato breeding. 29th International Horticultural Congress on Horticulture - Sustaining Lives, Livelihoods and Landscapes (IHC) / International Symposium on Plant Breeding in Horticulture, Brisbane, QLD, Australia, 17-22 August 2014. LEUVEN 1: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2016.1127.37

Optbr: computationally efficient genomic predictions and QTL mapping in multi-bred populations

Wang, Tingting, Yi-Ping, Phoebe Chen, Kemper, Kathryn E., Godard, Michael E. and Hayes, Ben J. (2015). Optbr: computationally efficient genomic predictions and QTL mapping in multi-bred populations. Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Lorne, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.

Genomic selection in crops, trees and forages: a review

Lin, Z., Hayes, B. J. and Daetwyler, H. D. (2014). Genomic selection in crops, trees and forages: a review. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/CP13363

Resources and strategies for implementation of genomic selection in breeding of forage species

Forster, J. W., Hand, M. L., Cogan, N. O. I., Hayes, B. J., Spangenberg, German C. and Smith, K. F. (2014). Resources and strategies for implementation of genomic selection in breeding of forage species. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/CP13361

Genomic evaluations in the Australian sheep industry

Swan, A. A, Brown, D. J., Daetwyler, H. D., Hayes, B. J., Kelly, M., Moghaddar, N. and van der Werf, J. H. J. (2014). Genomic evaluations in the Australian sheep industry. 10th World Congress of Genetics Applied to Livestock Production, Vancouver Canada, 2014.

Mapping QTL in Australian dairy cattle using genomic selection methodologies

Kemper, K. E., Vander Jagt, C. J., Bowman, P. J., Reich, C. M., Mason, B. A., Hayes, B. J. and Goddard, M. E. (2014). Mapping QTL in Australian dairy cattle using genomic selection methodologies. World Congress of Geneics Applied to Livestock Production, Vancouver, BC, Canada, 17-22 August 2014. Vancouver, BC, Canada: World Congress on Genetics Applied to Livestock Production.

Use of molecular technologies for the advancement of animal breeding: genomic selection in dairy cattle populations in Australia, Ireland and New Zealand

Spelman, Richard J., Hayes, Ben J. and Berry, Donagh P. (2013). Use of molecular technologies for the advancement of animal breeding: genomic selection in dairy cattle populations in Australia, Ireland and New Zealand. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/AN12304

Genomic regions associated with differences in fat percentage in milk between Holstein and Jersery cattle

Kemper, K. E., Hayes, B. J. and Goddard, M. E. (2013). Genomic regions associated with differences in fat percentage in milk between Holstein and Jersery cattle. Association for the Advancement of Animal Breeding and Genetics, Napier, New Zealand, 20-23 October 2013. Red Hook, NY, United States: Curran Associates.

The symbiotic rumen microbiome and cattle performance: a brief review

Bath, C., Morrison, M., Ross, E. M., Hayes, B. J. and Cocks, B. G. (2013). The symbiotic rumen microbiome and cattle performance: a brief review. Clayton, VIC, Australia: CSIRO Publishing. doi: 10.1071/AN12369

The importance of population structure on the accuracy of genomic prediction in a multi-breed sheep population

Daetwyler, H. D., Kemper, K. E., van der Werf, J. H. J. and Hayes, B. J. (2011). The importance of population structure on the accuracy of genomic prediction in a multi-breed sheep population. Association for the Advancement of Animal Breeding and Genetics, Perth, Australia, 19-21 July 2011. Perth, Australia: Association for the Advancement of Animal Breeding and Genetics.

Genome-wide association and genomic selection in animal breeding

Hayes, Ben and Goddard, Mike (2010). Genome-wide association and genomic selection in animal breeding. International Conference on Exploiting Genome-Wide Association in Oilseed Brassicas - A Model for Genetic Improvement of Major OECD Crops for Sustainable Future Farming, Perth Australia, Nov 09-12, 2009. doi: 10.1139/G10-076

SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates

Hayes, Ben J., Nilsen, Kjetil, Berg, Paul R., Grindflek, Eli and Lien, Sigbjorn (2007). SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. doi: 10.1093/bioinformatics/btm154

Design of a whole genome scan experiment for a multi-breed beef cattle population with a complex pedigree

Kelly, M.J., Hayes, B.J. and Miller, S.P. (2007). Design of a whole genome scan experiment for a multi-breed beef cattle population with a complex pedigree. 17th Conference: Genetic Improvement - Making it Happen, Armidale, N.S.W., 23-26 September 2007. Armidale NSW: Association for the Advancement of Animal Breeding Genetics.

SNP and phenotype data, and GWAS results for macadamia breeding progeny population

O'Connor, Katie, Hayes, Ben, Hardner, Craig, Alam, Mobashwer and Topp, Bruce (2019). SNP and phenotype data, and GWAS results for macadamia breeding progeny population. The University of Queensland. (Dataset) doi: 10.14264/uql.2019.808