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Proceedings of the AAABG 24th Conference

Proceedings of the AAABG 24th Conference

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Note: An additional 29 papers have been published in a special edition of Animal Production Science. The 24th AAABG Conference Organising Committee instigated the choice for authors to publish full article papers in the AAABG special edition in Animal Production Science or contribute papers to the AAABG proceedings.

Preliminary pages
AAABG and President's Message iii
Conference Sponsors vi
AAABG Rules vii
AAABG Fellows and Honorary members ix
Helen Newton Turner Medal xi
Table of Contents xiii
John Vercoe Memorial Lecture
Breeding Australian cattle for production in the year 2050 1
B. J. Hayes, K.E. Kemper and L. Prada E Silva
Plenary Papers
Advancing livestock well-being – The role of genetic improvement 6
S. Dominik
Measurement enabled precision interventions: A future opportunity for livestock farming 10
M.R. Hutchinson
The future of genotyping 14
J.C. McEwan, K.G. Dodds, T.P. Bilton, R. Brauning, S.J. Rowe, M.K. Hess, K.M. McRae, A.F. McCulloch, R.A. Anderson and S.M. Clarke
The contribution animal breeding can make to industry carbon neutrality goals 15
S.J. Rowe, S.M. Hickey, P.L. Johnson, T.P. Bilton, A. Jonker, W. Bain, B. Veenvliet, G. Pile, B. Bryson, K. Knowler, N.C. Amyes, S.A. Newman and J.C. McEwan
What can research on the genetic of human well=being tell us about improving livestock well-being? 19
P.M. Visscher and N.R. Wray
Contributed Papers
Assessment of genomic predictions for feedlot and carcase traits in Australian Angus steers 22
P.A. Alexandre, Y. Li, B.C. Hine, C.J. Duff, A.B. Ingham, L.R. Porto-Neto and A. Reverter
Genetic association between ultrasound and carcase muscle dimension measures in sheep 26
P. Alexandri, S.F. Walkom and D.J. Brown
Merits of developing a genetic evaluation for the Australian dairy sheep and goat industries 30
P. Alexandri, R.G. Banks, D.J. Brown and S.F. Walkom
Genetic progress for environmental outcomes – How do we get it? 34
P.R. Amer
Trait prioritisation methods used in animals also work in plants 38
I.A. Balogun, T.J. Byrne, B.F.S. Santos, P.R. Amer, P.F. Fennessy, D. Martin-Collado, B. Abolore, B. Okoye, B. Teeken, O.D. Olaosebikan, T. Madu, D. Owoade, A. Ogunade, M. Ejechi, N. Onyemauwa, S. Onwuka, B. Ukeje, P. Kulakow, C. Egesi, J. Onyeka, I. Rabbi, J. Jannink and H.A. Tufan
Impact of breeding for divergent methane yield on milk composition in breeding ewes 42
T.P. Bilton, S.M. Hickey, P.H. Janssen, A. Jonker, M.K. Hess, B. Bryson, W. Bain, E. Waller, K.M. McRae, S. Muetzel, M. Agnew, J.C. McEwan and S.J. Rowe
Phenotypic trade-offs between lambs and wool reflect weak antagonistic genetic correlations between reproductive and wool traits 46
K.L. Bunter and A.A. Swan
Using selected sequence variants to improve genomic prediction of heat tolerance in dairy cattle 50
E.K. Cheruiyot, M. Haile-Mariam, B.G. Cocks, I.M. MacLeod and J.E. Pryce
Split paternity is high in twins born from syndicate mated Merino ewes 54
B.E. Clarke, K.L. Egerton-Warburton, J.L. Smith, B. Paganoni, G.B. Martin and A.N. Thompson
Visual classing grades are heritable and visually classed Merino sheep born and reared as twins are graded lower than singles 58
B.A. Metcalfe, J.C. Greeff, A.N. Thompson and B.E. Clarke
Responses to heat in ewes from indigenous and commercial South African sheep breeds: Preliminary results 62
S.W.P. Cloete, D.A. van der Merwe, S. Steyn, A. Muller, J. Melgar, C.K. Cornwallis and T.S. Brand
Genetic parameters for reproduction in intensively and extensively managed Dohne Merino flocks in South Africa 66
S.W.P. Cloete, C.L. Nel, J.J. Olivier and G.J. Delport
Addressing scur phenotypic challenges with the Southern Multi-Breed Project 70
N.K. Connors, B.J. Walmsley and K.A. Donoghue
Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in Northern Australia 74
J.P. Copley, B.N. Engle, S. Speight, G. Fordyce, E.M. Ross, K.P. Voss-Fels and B.J. Hayes
Genotyping dairy cattle with skim whole-genome sequencing and imputation 78
H.D. Daetwyler, J. Li, C.J. Vander Jagt, I.M. MacLeod, J. Pickrell, M. Vasquez, J.Hoff and A.J. Chamberlain
The impact of genotype by environment interaction on breeding vales for 150-day weight in Katahdin sheep in Mexico 82
L. De La Cruz, S.F. Walkom and A.A. Swan
Genome-wide association analysis for temperament in Australian sheep 86
S. de las Heras-Saldana, N. Moghaddar, S.A. Clark and J.H.J. van der Werf
A genomic comparison of Australian, New Zealand and Norwegian dairy goat populations 90
K.G. Dodds, J.H. Jakobsen, M. Wheeler, T. Blichfeldt, R. Brauning, H.J. Baird and J.C. McEwan
The benefit of a slick hair coat for heat tolerance in New Zealand dairy cattle 94
E.G. Donkersloot, G.M. Worth, A.F. Yeates, M.D. Littlejohn, L.R. McNaughton, R.J. Spelman and S.R. Davis
Southern Multi-breed resource population: Generation of cohorts one and two 98
K.A. Donoghue, B.J. Walmsley, J.P. Siddell, T. Granleese, L. Penrose and P.F. Arthur
The value of live-animal ultrasound scanning of breeding candidates for carcase traits in the age of genomics 102
C.J. Duff, B.J. Crook, A.I. Byrne and M.J. Reynolds
Reducing lameness and urinary nitrogen excretion through selection on next generation national dairy selection indices 106
J.E. Newton, M. Dunstan, P.N. Ho, M. Khansefid, I. van den Berg, S.S. Chauhan and J.E. Pryce
Genomic predictions of lifetime productivity in Braham cows 110
B.E. Engle, A. Collins Snr and B.J. Hayes
The effects of number of reference individuals on the accuracy of imputation from low and medium densities to high density 114
M.H. Ferdosi, N.K. Connors and M. Khansefid
Evaluation of haplotype diversity of Australian beef populations using medium-density SNP genotypes 118
M.H. Ferdosi, N.K. Connors and M. Khansefid
Phenobank: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle 122
K.B. Wockner, M.S. Tahir, J. Kour, W.L.A. Tan, B.S. Olasege, L.R. Porto-Neto, B.A. Little, C.R. Wilson, W. Dollemore, A. Reverter, B. Hayes and M.R.S. Fortes
Genome wide analysis of bovine enhancers and promoters across developmental stages in liver 126
M. Forutan, C.J Vander Jagt, E. Ross, A.J. Chamberlain, B. Mason, L. Nguyen, S. Moore, J.B. Garner, R. Xiang and B.J. Hayes
Is sex determination in Merinos heritable? 131
T. Granleese, M.R. Mortimer and S.F. Walkom
Multivariate analyses using two genomic relationship matrices to weight predictive SNP markers 135
P.M. Gurman, L. Li, A.A. Swan, N. Moghaddar and J.H.J. van der Werf
Characterizing the quantity and quality of data used in Merino sheep genetic evaluation systems 139
S.Z.Y. Guy and D.J. Brown
Maximising genetic gains with data quantity and quality in Merino flocks 143
S.Z.Y. Guy and D.J. Brown
Genomic evaluation of male fertility of Australian Holstein-Friesian and Jersey bulls 147
M. Haile-Mariam, K. Konstantinov, E.G Jewell, G.J Nieuwhof and J.E. Pryce
Quantifying genetic variation in urination traits of grazing dairy cattle 151
R.C. Handcock, L.A. Box, C.M. Thomas and D.J. Garrick
Group records with genomic prediction convert accuracy into genetic gain more efficiently than pedigree prediction 155
M. Henryon, G. Su, A.C. Sørensen and T. Ostersen
Economic values for farrowing rate to improve seasonal fertility 159
S. Hermesch
Across-country prediction of methane emissions using rumen microbial profiles 163
M.K. Hess, A. Donaldson, H.M. Henry, D.L. Robinson, A.S. Hess, J.C. McEwan, V.H. Oddy and S.J. Rowe
Characterisation of spermatozoal transcriptomes in sheep and the influence of breed and semen quality 167
M.J. Hodge, S. de-las Heras-Saldana, S.J. Rindfleish, C.P. Stephen, and S.D. Pant
The predicted responses to genomic selection in growing pigs 171
M. Shariful-Islam, J.H.J. van der Werf, V. Boerner and S. Hermesch
New Zealand national dairy breeding objective review stakeholder survey 175
G.M. Jenkins, B.F.S. Santos, P.R. Amer, K. Stachowicz, A. Young and B. Wickham
Evaluation of Australian breeding values for heat tolerance under US conditions 179
L.M. Jensen, E.A. Jannaman, J.E. Pryce, A. De Vries and P.J. Hansen
Investigation of the pathogenesis of suspected inherited neurological diseases in Australian sheep 183
L.K. Manning, B.A. O’Rourke, M. Krockenberger, K.L.M. Eager and I. Tammen
A genome-wide association study (GWAS) for carcass traits in Hanwoo cattle using imputed whole genome sequence data 187
H. Kim, S. de las Heras-Saldana, N. Moghaddar and J.H.J van der Werf
Management of inbreeding and coancestry to target short-term and long-term genetic gains 191
B.P. Kinghorn and A.J. Kinghorn
Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low- coverage nanopore sequencing 195
H.J. Lamb, L.T. Nguyen, B.N. Engle, B.J. Hayes and E.M. Ross
Evaluating the benefits of including predictive SNP markers in single step evaluation in sheep using cross-validation 200
L. Li, P.M. Gurman, A.A. Swan, N. Moghaddar and J.H.J. van der Werf
Ranking Brahman bulls for female reproductive performance in northern Australian commercial environments using DNA pooling 204
Y. Li, L. Porto-Neto, R. McCulloch, S. McWilliam, P. Alexandre, J. McDonald, A. Reverter and S. Lehnert
A deterministic algorithm for optimality of threshold in a GWAS experiment 208
Z. Loh, J. H. J. van der Werf and S. Clark
Current challenges for imputation of SNP chips to whole-genome sequence in cattle and sheep 212
I.M. MacLeod, S. Bolormaa, C.J. Vander Jagt, T.V. Nguyen, A.J. Chamberlain and H.D. Daetwyler
Macro- and micro-genetic environmental sensitivity for 400 day weight in Australian Angus 217
M.D. Madsen, J.H.J. van der Werf, V. Börner and S. Clark
Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle 222
E. Mantilla Valdivieso, E. Ross, A. Raza, B. Hayes, N. Jonsson2, P. James and A. Tabor
Genetic parameters for feed efficiency and weight in Jersey cows using 3D cameras in commercial Danish farms 226
C.I.V. Manzanilla-Pech, R.B. Stephansen and J. Lassen
Revealing phenotypic and genetic relationships underlying the thermotolerance - production complex in beef cattle 230
R.G. Mateescu, F.M. Rezende, K.M. Sarlo Davila, S. Dikmen, A.N. Nunez Andrade, A. Hernandez and M.A. Elzo
A new tool to select Angus bulls to breed to dairy cows 234
S.P. Miller, J.A. Archer, F. Hely, C. Quinton, K. Retallick, D. Moser and P. Amer
The effect of GDF9 on litter size in Australian sheep 238
N. Moghaddar, K. L. Bunter, A. A. Swan L. Li, P. M. Gurman and J. H. J. van der Werf
Dairyfarmer perceptions and attitudes to female genomic testing 242
L.C. Monks, B. A. Scott, S.L. Bullen, J. J. Andony and M.M. Axford
Genetic analysis of body condition and growth traits in beef females within and across ages and physiological states 247
K.L. Moore, T.P. Grant and D.J. Johnston
Ewe reproduction status and its impact on greasy fleece weight breeding values 251
S.I. Mortimer, A.A. Swan and K.L. Bunter
Variation between Merino sires in lamb carcass value 255
S.I. Mortimer, J. L. Smith, B.C. Hine, S.M. Fowler, B.W.B. Holman, D.L. Hopkins, K.L. Egerton-Warburton and A.A. Swan
The importance of early environmental effects on Merino fleece trains across two shearings 259
K.L. Egerton-Warburton, J.L. Smith, S.I. Mortimer, A.A. Swan and B.C. Hine
Using mid-infrared spectroscopy predictions of fertility to optimise semen allocation in dairy herds 263
J.E. Newton, P.N. Ho and J.E. Pryce
Exploring imputation accuracy across the bovine X chromosome 267
T.V. Nguyen, S. Bolormaa, C.M. Reich, A.J. Chamberlain, A. Medley, C. Schrooten, H. D. Daetwyler and I.M. MacLeod
Genetic improvement of goats owned by smallholder goat keeper women in Bihar, India, with the help of a database tool 272
C. Nimbkar, P. Amer, A. Schurink, T. Sawhney and R. Azam
Identification of genetic variants linking dairy fertility and milk production traits 276
E. Ooi, J.E. Pryce and M.E. Goddard
Investigation of methods for inclusion of fixed effects for ultrasound scan carcass traits in large scale sheep genetic evaluation 280
U. Paneru, D.J. Brown, N. Moghaddar and J.H.J. van der Werf
Identifying the breeding preferences and attitudes of the Australian beef cattle producer 284
J.E. Peart, A.I. Byrne, M.J. Reynolds and C.J. Duff
How are you feeling, girls? – Behavioural traits as emergent properties of the community 288
G.E.L. Petersen, A.C.L. Walters, P.F. Fennessy and P.K. Dearden
Industry consultation as the basis of a breeding objective for the New Zealand beekeeping industry 292
G.E.L. Petersen, I.A. Balogun, P.F. Fennessy and P.K. Dearden
An evaluation of the effect of the Booroola gene, FecB, on productivity in a Border Leicester x Merino prime lamb production system 296
L.R. Piper, A.A. Swan, J.M. Elsen, L. Bodin, H.G. Brewer and B.M. Bindon
Multibreed genomic prediction for male fertility in tropical beef cattle 300
L.R. Porto-Neto, J. Bertram, S. McWilliam, M.R.S. Fortes, P. Alexandre, M.R. McGowan, B.J. Hayes and A. Reverter
Narrowing the search space: putative causal variants are enriched in annotated functional regions from 6 bovine tissues 304
C.P. Prowse-Wilkins, J. Wang, M.E. Goddard, R. Xiang, J.B. Garner and A.J. Chamberlain
Indexes supporting genomic tools for selecting commercial Angus heifer replacements and identifying steers for long-fed programmes in Australia 308
C.D. Quinton, J.A. Archer, P.R. Amer, S. Harburg, G. Petersen, A. Byrne, C. Duff and P. Parnell
Defining longevity and estimating genetic parameters in Australian Merino ewes 312
M.O.A. Rahman, D.J. Brown and S.F. Walkom
Circular and genomic permutations can limit the confounding effects of the reference population in the analyses of selection signatures 316
I.A.S. Randhawa, M.S. Khatkar, P.C. Thomson and H.W. Raadsma
Genome-wide analyses of scur genetics in cattle 320
I.A.S. Randhawa, M.R. McGowan and R.E. Lyons
Efficiency of optimized poll testing assay in Australian beef cattle 324
I.A.S. Randhawa, K.M. Schutt, M.R. McGowan and R.E. Lyons
Effects of poll breeding on reproductive traits in beef cattle 328
I.A.S. Randhawa, R.E. Lyons and M.R. McGowan
EBVs predict progeny performance differences 332
M.J Reynolds, C.J Duff, P.F Parnell and A.I Byrne
Economic analysis of Merino ewe performance from diverse industry sires using GrassGro 337
J.S. Wallace, K.L. Egerton-Warburton, and A.A. Swan
Assessing the potential of parentage testing using portable long read sequencing technologies 341
E.M. Ross, H.J. Lamb, B.N. Engle, L.T. Nguyen and B.J. Hayes
Estimation of optimum polygenic and genomic weights in single-step genetic evaluation of carcass traits in Australian Angus beef cattle 345
A.M. Samaraweera, J.A. Torres-Vázquez, M G. Jeyaruban, D.J. Johnston and V. Boerner
Supporting data-driven sustainable livestock industries in developing countries 349
B. Santos, G. Jenkins, T. Byrne, M. Teviotdale, A. Haile, C. Nimbkar and P. Amer
Improving carcase value by incorporating primal weights into pig breeding objectives 353
N.R. Sarker, B.J. Walmsley and S. Hermesch
Integration of GWAS, Network and Pathway analysis reveals novel insights into thermotolerance in beef cattle 357
K.M. Sarlo Davila, E.E. Rodriguez, A.N. Nunez Andrade, G. Zayas, D. Rodriguez and R.G. Mateescu
Does selecting for the A2 Β-casein allele increase inbreeding 361
B.A. Scott, M. Haile-Mariam, I.M. MacLeod and J.E. Pryce
Genomic breeding values for residual feed intake in Australian maternal composite ewes 365
B.J. Sepulveda, S.K. Muir, S. Bolormaa, M.I. Knight, R. Behrendt, I.M. MacLeod, J.E. Pryce and H.D. Daetwyler
Exploring machine learning approaches to predict the incidence of lameness in dairy cows 369
S. Shahinfar, M. Khansefid, M. Haile-Mariam and J.E. Pryce
New model for genetic evaluation of fertility in New Zealand dairy cattle 373
K. Stachowicz, P.R. Amer, B. Falconer and D.P. Garrick
Next generation feed saved Australian breeding values evaluated in Holstein dairy cattle 377
S. Bolormaa, I.M. MacLeod, M. Khansefid, L. Marett, B. Wales, G.J. Nieuwhof, C.F. Baes, F.S. Schenkel, M.E. Goddard and J.E. Pryce
Deriving breeding values for net reproduction rate form component traits in sheep 382
A.A. Swan and K.L. Bunter
The Anstee Hub for Inherited Diseases of Animals (AHIDA) – development of a new online platform for surveillance, reporting and control of inherited diseases in animals 386
I. Tammen, C. Wade, B. Waud, M. Gimeno, B.D. Velie, B. O’Rourke and F.W. Nicholas
Curation of pig traits in the Online Mendelian Inheritance in Animals (OMIA) database 390
S.M. Shields, S. Hermesch, F.W. Nicholas and I. Tammen
Comparing genomic with pedigree relationship matrices and preliminary genome-wide association in Santa Gertrudis bull 397
W.L.A. Tan, L.R. Porto-Neto, G. C. Gouveia, A. Reverter and M.R.S. Fortes
Determination of optimum weighting factors for single-step genetic evaluation via genetic variance partitioning 402
J.A. Torres-Vázquez, A.M. Samaraweera, M G. Jeyaruban, D.J. Johnston, and V. Boerner
Economic benefit of additional recording for welfare traits in maternal breeding objectives for pigs 406
L. Vargovic, K.L. Bunter and S. Hermesch
Genetic parameters for urinalysis traits recorded on gestating sows 410
L. Vargovic, S. Hermesch and K.L. Bunter
Proposed genetic improvement strategies for dairy cattle in Kenya 414
P.K. Wahinya, A.A. Swan and M.G. Jeyaruban
Using matesel to aid sire allocation in Genomic reference populations – Southern Multi-breed an example 419
S.F. Walkom, K.A. Donoghue, P.F. Arthur, S.A. Clark and B.J. Walmsley
Initiating the Southern Multi-Bred Resource population 423
B.J. Walmsley, K.A. Donoghue, D.J. Johnston, S.A. Clark, J.P. Siddell, S.F. Walkom, T. Granleese and P.F. Arthur
Genomic analysis of genotype by environment interactions in post-weaning weight of Australian sheep 427
D.L. Waters, S.A. Clark, N.Moghaddar and J.H.J. van der Werf
Genome-wide association analysis of birth and weaning weights in Australia Taurine beef cattle 431
W.M.S.P. Weerasinghe, B.J. Crook and N. Moghaddar
Genetic parameters for structural traits in New Zealand beef cattle and their correlations with production traits 435
F. Weik, R.E. Hickson, S.T. Morris, D.J. Garrick and J.A. Archer
Genetics of heifer age at puberty in Australian Angus cattle 439
M.L. Wolcott, R. Banks and G. Alder
Methane emissions variation among New Zealand dairy farms and herds 443
X. Zhang, P.R. Amer, K. Stachowicz, C. Quinton and J. Crowley
The application of a sub-index weighted percent emphasis method to Australian dairy selection indexes 447
X. Zhang and P.R. Amer
Genetic diversity and trends of Australian Japanese Black cattle 451
Y.D. Zhang and R. Banks
HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV and CNVR 455
J. Zhou, L. Liu, T.J. Lopdell, D. Garrick and Y. Shi
Breeders Papers
Ewe lamb joining for selection 459
L. Arney
Performance Corriedale group genomics 463
P. Blackwood, C. Blackwood, J.M. Pitchford, H. Gordon, S.C. Welsh and W.S. Pitchford
Investigating the potential to utilise commercial carcass traits in genetic evaluation 467
S.J. Lee, M. Beattie, R.A. McEwin, R. Tearle and W.S. Pitchford
Genetics for self-replacing Maternals: Paradoo Prime 471
T. Leeming
MerinoLink/UNE DNA Stimulation Project: Doubling the rate of genetic gain – Where are we after 4 years? 476
S.J. Martin and T. Granleese
Popplewell tropical beef composite breeding program update 480
G.I. Popplewell, M.L. Facy,, R.G. Tearle, R.A. McEwin and W.S. Pitchford
Ewes for the future: A commercial comparison of ewe breeds for reproduction, wool and lamb growth 481
K.P. Ransom, F.D. Brien and W.S. Pitchford
Improve your social license – Breed sheep for disease resistance 486
S.F. Walkom and K.L. Bunter