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Proceedings of the AAABG 26th Conference

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Preliminary pages
President's Message	iii
26^th Conference Committee and Citation of Papers	iv
Reviewers	v
Sponsors	vi
AAABG Rules	viii
AAABG Fellows	x
AAABG Honorary Members	xxi
Helen Newton Turner Medal	xxii
Helen Newton Turner Bright Futures Award	xxiii
2023 Helen Newton Turner Medalist Oration	xxiv
John Vercoe Memorial Lecture	xxviii
Table of Contents	xxix

Papers
Plenary Papers
Global regulations governing genome editing in food animals	1
A.L. Van Eenennaam
Growing Aotearoa New Zealand's aquaculture industry through breeding and genomics: Progress, challenges and opportunities	6
J.E. Symonds, M.R. Scholtens, K.G Dodds, S.M. Clarke, R. Costilla, S.P. Walker, N. King, N.L.C. Ragg, M. Camara, J.A. Ericson, J. Vignier, M. Wellenreuther, Z. Waddington, J. Bailey, R.D. Roberts, E. Malpot, M.L. Tate and T. Slattery
John Vercoe Memorial Lecture
Climate change mitigation through genetic improvement – A deeply worthwhile challenge in the spirit of John Vercoe	13
R.G. Banks
Sustainability – Feed Efficiency and Methane
Measurement of feed intake in sheep using "off the shelf" technologies	18
P.T. Fitzgerald, R.L. Hergenhan and J.H.J. van der Werf
Feed-intake and methane efficiency for weight and growth pre-slaughter of MLA resource flock lambs	22
B. Paganoni, B. Bolt, A. Bowden, P. Fitzgerald, S.F. Walkom and J.H.J. van der Werf
Selecting for efficiency in long-fed cattle is important	26
W.S. Pitchford
Genetic insights into methane emission traits in indoor-fed growing cattle	30
S.B. Crowley. D.C. Purfield, S.B. Conroy, D.N. Kelly, R.D. Evans and D.P. Berry
Methane emissions of low and high methane yield selection line sheep fed ryegrass-based pasture across multiple periods	34
A. Jonker, S. Hickey, J.C. McEwan, E. Sandoval, S. MacLean and S. Rowe
Effect of winter forage brassica grazing on methane selection line sheep	38
F.L. Booker, S.M. Hickey, T.P. Bilton, I. Hampton, B. Bryson, M. Ward, P.L Johnson, J.C. McEwan and S.J. Rowe
Portable accumulation chambers for measuring enteric methane in cattle	42
T.P. Bilton, S.M. Hickey, A. Searle, I. Hampton, F. Booker, C. Rodgers, S. Sevier, S. Gebbie, K.G. Dodds, G.M. Jenkins, J.A. Archer, J.C. McEwan and S.J. Rowe
Factors affecting methane production of composite and crossbred cattle grazing tropical and subtropical pastures in Northern Australia	46
C. Whistler, K. McCosker, C. Warburton, D. Johnston, T. Grant, B. Taylor, K. Goodwin, M. Dayman, N. Scott, S. Cullen, M.H. Dekkers, S. Clark and B.J. Hayes
Novel Traits
Genetic analysis of sensor-based activity traits in Australian Merino sheep	50
H. Keshavarzi, E. Dehnavi, J. McNally, J.L. Smith and S. Schmoelzl
Assessing behavioural rigidity and its genetic influences in Australian Wagyu cattle	54
A. Lloyd, M. Facy and J. Grose
An examination of multibreed temperament measures recorded in the Southern Multi-Breed Resource Population	58
B.J. Walmsley, K.L. Moore, R. Woodgate, S.A. Clark, F.E.M. Haynes and K.A. Donoghue
Genetic risk factors for tail biting in Australian pigs as determined by binomial regression models	62
D. van Winden, R.Y. Galea, M.N. Aldridge, P.M. Gurman and S. Hermesch
Genetic parameters of being a tail-biting recipient in pigs	66
A.A. Reda, M.N. Aldridge, P.M. Gurman and S. Hermesch
Genetic correlations between purebred and crossbred pre- and post-weaning piglet mortality	70
J. Harper and K.L. Bunter
Genetic analysis of sow udder treatments	74
A.M.G. Bunz, J. Harper and K.L. Bunter
Implementation and delivery of the Wagyu Feeder Check	78
C.F. Teseling, M.B. McDonagh and D.P. Garrick
Genomic Prediction 1
Cost-benefit of a genomic reference population for goats in Australia	82
T. Granleese and S.F. Walkom
Genomic models for estimating genetic parameters for lifetime wool traits in Merino sheep	86
P.K. Wahinya, D.J. Brown, B.E. Clarke, J.L. Smith, T. Bird-Gardiner, A.A. Swan
Evaluating the accuracy of SNP-BLUP and admixture for breed composition prediction in rare and well-represented cattle breeds	90
C.A. Ryan
IBS versus IBD - new insights from whole genome sequence data	94
C.L. Warburton, R. Costilla, M.E. Goddard, B.J. Hayes and T.H.E. Meuwissen
The molecular cattle for precision breeding	98
R. Xiang, M.E. Goddard, A.J. Chamberlain and J.E. Pryce
Recovering the obscured genetic architectures through deconvolution of GWAS statistics	102
Z. Loh
Sort & Paste: A numerical method to render any random variable heritable given a genotype	106
A. Reverter and P.A. Alexandre
Assessing the effectiveness of low-coverage nanopore sequencing in genomic selection: A comparison between Clair3 and QUILT pipelines	110
L.T. Nguyen, H. Lamb, J. Copley, B.J. Hayes and E.M. Ross
Aquaculture
Estimating thermal tolerance in selectively-bred New Zealand Greenshell mussels (Perna canaliculus)	114
M.R. Scholtens, R. Roberts, N.J. Delorme, N. King, N.L.C. Ragg, R. Costilla and J.A.Ericson
Genotype-by-environment interactions in Yellowtail Kingfish: Implications for genetic improvement.	118
M. Camara, A. Setiawan, J.W.M. Bastiaansen and N.K. Jacob
Marker-based family assignment without parent genotypes	122
K.G. Dodds, J.E. Symonds, S.J. Rowe and J.C. McEwan
Applying machine learning to unlock genomic insights in snapper breeding	126
J. Blommaert and M. Wellenreuther
Fast-tracking farmed king salmon climate change adaptation	130
J.E. Symonds, M.R. Scholtens, K.G Dodds, R. Costilla, S.M. Clarke, J. Arinez, N.J. Kenny, S.P. Walker and Z. Waddington
Sustainability – Methane
Methane and carbon dioxide emissions in Australian Angus – past and present	134
M.D. Madsen, C.J. Duff, M. Samaraweera, L.A. Mowbray, T. Granleese, R. Hergenhan, T. Bird-Gardiner, P.F. Arthur and S.A. Clark
Validation of genomic prediction for methane emissions in Australian Merino sheep	138
M.N. Aldridge, S.I. Mortimer, D.J. Brown, P.T. Fitzgerald, E.H. Clayton, A. Donaldson, B. Paganoni, A. Thompson, V.H. Oddy and J.H. van der Werf
Building a reference population to enable genomic selection for methane related traits in beef cattle	142
S. Clark, M. Madsen, R. Hergenhan, C. Duff and T. Granleese
Repeatability and heritability of dairy cow methane concentration using sniffer sensors	146
F. Almasi, S.R.O. Williams, C.J. Vander Jagt, L.C. Marett, J.L. Jacobs and J.E. Pryce
Methane index explorer: Optimising a breeding value format for simultaneous inclusion of enteric methane emissions in breeding schemes and national inventories	150
P.C. Ariyarathne, S.M. Hickey, T.P. Bilton, P. Johnson, N.K. Pickering, S.J. Rowe and J.C. McEwan
Incorporation of direct methane traits in national breeding objectives	154
F. Hely, D. Kenny, N. Howes and P. Amer
The Green Cow project: developing a methane efficiency genomic breeding value for the Australian dairy industry	158
C.J. Vander Jagt, F. Almasi, B.J. Sepulveda, L.C. Marett, S.R.O. Williams, R. Xiang, S. Bolormaa, M. Shaffer, J. Penry, C. Hill, D. Gibson, J.L. Jacobs and J.E. Pryce
Dairy
Industry perspectives on calf traits	162
M.M. Axford, M. Khansefid and J.E. Pryce
Correlation of cow mortality and culling (sale) rate with selected type traits in Australian Holstein and Jersey cattle	166
M. Haile-Mariam, M.E. Goddard, M. Axford, J. Newton and M. Khansefid
Updating the genetic prediction model for cow survival in Australia	170
M. Khansefid, J.E. Pryce, J.E. Newton, M. Axford, G. Nieuwhof, M.E. Goddard and M. Haile-Mariam
Selection for first parity linear-type traits in the New Zealand dairy cattle population	174
M.A. Nilforooshan, R.G. Sherlock and B.L. Harris
Evaluating genetic and phenotypic relationships of six traits other than production (TOP) in dairy cattle prior to their adoption in New Zealand	178
R.C. Handcock, D.P. Garrick and M.A. Stephen
Dual-purpose Norwegian red cattle for sustainable dairy and beef productions in pasture-based systems	182
C. McKimmie, H.A. Najafabadi, E. Noble-Campbell, J. Hoffmann and J. Jenko
Agriculture Institute Australia's Student Compendium is building a sustainable research, development and adoption workforce	185
B. Hancock and T. Manning
Genomic Prediction 2
Multi-trait genomic models with trait and marker specific weights can substantially increase the accuracy of genomic breeding values	189
T. Meuwissen and V. Boerner
Integrating whole genome sequence variants selected from large-scale association analysis into a single-step marker model in New Zealand dairy cattle	193
Y. Wang, M.A. Nilforooshan, R.G. Sherlock, A.M. Winkelman and B.L. Harris
A linkage disequilibrium method to reposition single nucleotide polymorphism and improve genotype imputation accuracy	197
Y. Fazel, K. Moore, S. Miller and M.H. Ferdosi
Multi-breed genomic estimated breeding values predict liveweight production in North Australian beef cattle	201
B.J. Hayes, G. Fordyce, E. Dodd, S. Speight and K. McCosker
Estimates of accuracy for genomic-only breeding values and flock profiles in Australian Merino sheep	205
L. Li, P.M. Gurman, A.A. Swan and D.J. Brown
Helical: A full-stack agile platform enabling data flywheels and data sharing to empower modern breeding programs	209
D.P. Garrick, D.J. Garrick and J.E. Howse
Alignment of pedigree and genomic information in a combined terminal sire and maternal sheep analysis	213
P.M. Gurman, P. Alexandri, D.J. Brown, K.L. Bunter, S. de las Heras-Saldana, K.P. Gore, L. Li, A.J. McMillan, S.F. Walkom and A.A. Swan
Implementing genomic outcomes for simulated progeny to support mating decisions	217
D.P. Garrick, J.E. Howse and C.F. Teseling
Sustainability Methane Prediction
Association between rumen and faecal microbiome and enteric methane emissions in dairy cattle	221
B.J. Sepulveda, C.J. Vander Jagt, A.J. Chamberlain, J. Wang, L.C. Marett, S.R.O. Williams, J.L. Jacobs and J.E. Pryce
Metagenomic predictions for enteric methane emissions in sheep using long-read sequencing of rumen fluid samples	225
Y. Li, L.T. Nguyen, C.T. Ong, S. Yadav, M. Aldridge, P. Fitzgerald, J. van der Werf and E. M. Ross
Proxies in practice: Implementing rumen metagenomic profiles for genomic selection of methane emissions	229
T.P. Bilton, P.L. Johnson, H. Henry, B.J. Perry, F. Booker, J. Peers-Adams, M. Ward, B. Bryson, S.M. Clarke, J.C. McEwan, L.W. Coleman, N.K. Pickering, K.G. Dodds and S.J. Rowe
Tissue-specific RNA expression data enhances genomic prediction of methane emissions in sheep	233
S.W. Alemu, T.P. Bilton, B.J. Perry, H.M. Henry, K.M. McRae, K.G. Dodds, J.C. McEwan, S.M. Clarke and S.J. Rowe
Use of mid-infrared spectrocopy data for improving accuracy of genomic prediction for methane emissions	237
S. Bolormaa, P.N. Ho, I.M. MacLeod, M. Haile-Mariam, L.C. Marett, S.R.O. Williams, J.L. Jacobs, C.J. Vander Jagt, M.E. Goddard, R. Xiang, and J.E. Pryce
Exploring adaptive sequencing for efficient profiling of methanogenic microbiomes in cattle oral samples as a proxy for methane prediction and mitigation studies	241
Z. Chen, J. Silaban, E.M. Ross and C.T. Ong
Evaluating oral swabbing as a practical alternative to rumen sampling for large-scale methane emission studies in grazing animals	245
C.T. Ong, Z. Chen, A.S. Cavallaro, M.R.S. Fortes, M. Dekker, A. Boulton, B. Kniwesky and E.M. Ross
Maternal traits & survival
Effects of adding a new fertility trait to the Angus Australia HeiferSELECT index	249
C.D. Quinton, S. Harburg, L.E. Proctor, P.R. Amer, C.J. Duff and A.M. Samaraweera
The influence of spermatozoal motility on conception and scan count following artificial insemination in sheep	252
M.J. Hodge, S.J. Rindfleish, L. Li, C.P. Stephen, S.D. Pant and S. de las Heras-Saldana
Genetic parameters for cause of death traits in lambs and indicator traits linked to neonatal survival	256
M. Hebart, R. McEwin and F.D. Brien
A revisiting of the genetics of lamb survival and related traits, as part of the Fit to Lamb Project	260
R.A. McEwin, M.L. Hebart and F.D. Brien
An ex-post cost benefit analysis of the Ovita lamb survival project	264
K.M. McRae, J.M. Everett-Hincks, S.-A. Newman, W.E. Bain, G. Greer, H. Baird, H. Manley, G. Shackell, S.M. Clarke, K.G. Dodds, N. Amyes, N. Jopson, M. Lee, P.L. Johnson, S.J. Rowe and J.C. McEwan
Genetics parameters for gestation length with early in life growth traits in an Australian Wagyu population	268
M. Facy, A. Lloyd and J. Grose
Across-breed analysis of maternal traits in New Zealand beef cattle	272
J. Kang, D.J. Garrick, M.A. Lee, F. Weik and J.A. Archer
Breeding Programmes
Multi-trait selection with desired gains and non-linear indexes	276
J.H.J. van der Werf
Digital twin: Modelling breeding program approaches in Australian Wagyu	280
J. Copley, B. Hayes, G. Moser, B. Engle, K. Villiers and M. Kelly
Routine diagnosis of genetic evaluations and auto standardisation to non-linear cost function	284
X. Zhang, F. Hely, K. Stachowicz and P. Amer
Micron premiums and their role in Merino breeding programs	287
S.F. Hatcher, A.E. Casey, S.F. Walkom, D.J. Brown and A.A. Swan
Cost - benefit of genotyping commercial Merino sheep	291
G. Rose, S. Martin, D.J. Brown, L.P. Kahn and J.H.J. van der Werf
A comparison of progeny of selected and unselected sires within the setting of a community-based breeding programme catering to women smallholder goat rearers in Bihar, India	295
S. Abeykoon, P. Amer, P. Wilcox and C. Nimbkar
Optimal breeding programs for Lao native goats in smallholder systems	299
S.V. Le, S. de las Heras-Saldana, P. Alexandri and J.H.J. van der Werf
Genetic diversity & inbreeding
Identification of relationships and pedigree simplification using graph theory	303
M.H. Ferdosi and D. Johnston
Assessing the genetic diversity of Australian goats	307
P. Alexandri, T. Atkinson, D.J. Brown, K. Gore, K. Smith, S.F. Walkom and T. Granleese
Breed comparisons in combined LAMBPLAN: Genetic group and linkage assessment	311
A.J. McMillan, P. Alexandri, P.M. Gurman, D.J. Brown, K.L. Bunter, K.P. Gore, S. de las Heras-Saldana, L. Li, S.F. Walkom and A.A. Swan
Using genotyping by sequencing to monitor the genetic diversity of Australian honey bees	315
P. Alexandri, S.P. Miller, E.A. Frost, N.C. Chapman, S.F. Walkom, R.G. Banks and K.L. Bunter
Breed-of-origin of alleles and genomic breed composition estimation in New Zealand crossbred dairy cattle	319
Y. Wang, A.M. Winkelman and B.L. Harris
Ascertaining the breed composition of an admixed sheep populations using genomic information: a simulation study	323
S. Sahoo, M.H. Ferdosi, J.H.J. van der Werf and S. de las Heras-Saldana
Genomic inbreeding measures for Australian Wagyu - methods and implications	327
D.P. Garrick, D.J. Garrick and C.F. Teseling
Absence of C>T polymorphism in the intron (5′-UTR) region of the MTHFR gene in Indian Barbari goats	331
A. Kumar, S.P. Singh, D. Sharma, G. K. Gupta, Pooja, A. Chauhan, V. Aditya and B. Kumari
Meat and Growth
Genetic correlations of Merino meat colour traits with lean meat yield and eating quality	335
S.I. Mortimer, S.M. Fowler, B.W.B. Holman, T.I.R.C. Alvarenga, D.L. Hopkins, K.L. Egerton-Warburton, J.L. Smith, B.C. Hine and A.A. Swan
Genetic parameter estimation of carcase quality phenotypes measured with cameras in Australian Wagyu	339
E. de Bruyn, K.L. Moore and S.P. Miller
Multibreed genomic evaluation for sensory eating quality of lamb using consumer assessments	343
D.J. Brown, S.Z.Y. Guy, S.I. Mortimer, L. Pannier, P. McGilchrist, D. Pethick and A.A. Swan
Estimated frequencies of myostatin mutations (double muscling) in Australian tropically adapted beef breeds	347
K.L. Moore, D.J. Johnston and T. Grant
Identification of genes habouring mutations affecting eating quality traits in beef cattle using Bayesian genomic prediction methods	351
M. Forutan, H. Aliloo, S. Clark, P. McGilchrist and B. Hayes
Genetic correlations between mature body condition, weight, and hip height and early fat-depth traits in Australian Angus cattle	355
M. Samaraweera, H. Aliloo, C.J. Duff and S.A. Clark
Joint modelling of mean and dispersion increases the accuracy of random regression on simulated growth curves	359
C.L. Nel and A.R. Gilmour
Accuracy of genomic predictions for beef eating quality traits	363
H. Aliloo, M. Forutan, P. McGilchrist, B. Hayes and S. Clark
Yearling weight and horn traits in South African Merino lines divergently selected for and against number of lambs weaned	367
S.W.P. Cloete, C.L. Nel and J.J.E. Cloete
Alternative Omics Approaches
Microbiability and heritability of deer seasonality traits	371
J.L. Clarke, T.P. Bilton, H. Henry, K.M. McRae, F. Booker, B. Veenvliet, W. Bain, J.A. Ward, B. Thompson, D. Stevens, J.C. McEwan, B.J. Perry, M.A. Black and S.J. Rowe
Characterisation of short tandem repeats (STRs) in cattle using long read sequencing	375
Q.H. Tran, I.M. MacLeod, T.V. Nguyen, J. Wang and A.J. Chamberlain
Considerations in imputation of Skim Sequenced data	379
M.S. Tahir, J. Wang, A.J. Chamberlain, C.M. Reich, B.A. Mason and I.M. MacLeod
The feasibility of an imputation reference population for structural variation in cattle	383
A.J. Chamberlain, T.V. Nguyen, J. Wang, X. Wang, C.J. Vander Jagt and I.M. MacLeod
Insights from population-scale long-read sequencing: structural variant characterisation and annotation	387
T. Nguyen, J. Wang, A. Chamberlain and I. Macleod
Exploring blood biomarkers as potential intermediate phenotypes for transition cow diseases: a foundation for future multi-omics integration	391
A. Kudriashova, A.J. Chamberlain, J.A.A. McArt, J.E. Hemsworth, C. M. Reich and M.E. Goddard
Using multi-omics data to identify candidate genes for milk lactose percentage in dairy cattle	395
M. Ghoreishifar, R. Xiang, T. Lopdell, M. Littlejohn, A. Chamberlain, J. Pryce and M. Goddard
Evidence of chromosome x association with knobbed acrosomes	399
B.S. Firewski, W.L.A. Tan, T. Melo, L.R. Porto-Neto, A. Reverter, M. McGowan and M.R.S. Fortes
Health and Welfare
Preliminary investigation of the genetics of shedding in maternal sheep	402
S.F. Walkom, J.R. Keiller, M.P. Kelly and D.J. Brown
Genetic evaluation of tail length in Australian sheep	407
M.J. Hodge, D.J. Brown and S.F. Walkom
Assessing genetic variability in flystrike resistance across expression levels in Australian Merino sheep	411
E. Dehnavi, A.A. Swan, B.C. Swain, J.C. Greeff, J.L. Smith, G. Burbidge, A.M.M. Ramsay, T.L. Bird-Gardiner and D.J. Brown
The role of conformation traits in evaluating heat tolerance in dairy cattle	415
L.M. Jensen, M. Haile-Mariam, S. Bolormaa and J.E. Pryce
Linear analysis of rumen themologger data to compare tolerance to heat challenge in eight sheep breeds	419
C.L. Nel, K. Mafunga, S.K. Maloney, T.S. Brand, K. Dzama, P.G. Theron and S.W.P. Cloete
The effect of tree shade and breed on heat stress indicators in Dormer and South African Meat Merino ewes and lambs	423
K. Mafunga, C.L. Nel, K. Dzama and S.W.P. Cloete
Preliminary analysis of immune competence traits in northern Australian tropically adapted beef breeds	427
K.L. Moore, D.J. Johnston, T. Grant and J. Croaker
Associations between immune competence breeding values and health traits in Australian Angus cattle	431
L.A Mowbray, M. Samaraweera, C. Duff, B.C. Hine, A. Reverter, P.A. Alexandre, L.R. Porto-Neto and A.B. Ingham
Including resilience in the breeding objective of sustainable Merino sheep	435
E.G. Smith, S.F. Walkom, A.A Swan and S.A. Clark
Genetic Evaluation
Latest developments in genomic tools for Angus Australia: SteerSELECT, HeiferSELECT and BreedCHECK	438
A. Reverter, C. Duff, M. Samaraweera, P.A. Alexandre, B.C. Hine, A.B. Ingham, L.A Mowbray and L.R. Porto-Neto
The 2025 National Breeding Objective review for Australian dairy cattle: insights from stakeholder consultation	443
T.T.T. Nguyen, M. Axford, P. Thurn, L. Monks, G. Nieuwhof, P. Williams, D. Watson, H. McLaren and M. Shaffer
Exploring adoption factors, and preferences to the use of beef genetic tools in Northern Australia	447
P. Menchon, J.K. Manning, D.L. Swain and A. Cosby
Combined LambPlan: Expanding the mulit-breed nature of the LambPlan evaluation	451
S.F. Walkom, P. Alexandri, D.J. Brown, K.L. Bunter, N.K. Connors, S. de las Heras-Saldana, K.P. Gore, P.M. Gurman, L. Li, A.J. McMillan, S.P. Miller, P.E. Bradley and A.A. Swan
Expanding Australian sheep genomic reference population	455
P. Alexandri, P.M. Gurman, D.J. Brown, K.L. Bunter, K.P. Gore, S. de las Heras-Saldana, L. Li, A.J. McMillan, S.F. Walkom and A.A. Swan
Fixed effects and genetic parameters for the combined LambPlan evaluation of Australian sheep	459
S. de las Heras-Saldana, D.J. Brown, P.M. Gurman, P. Alexandri, K.L. Bunter, K.P. Gore, L. Li, A.J. McMillan, S.F. Walkom and A.A. Swan
Genotyping reduces preselection bias on MERINOSELECT ASBVs in Merino flocks	463
B.E. Clarke, D.J. Brown, P. Bradley and A.A. Swan
Implementation of genomic mate selection and other non-additive issues	467
B.P. Kinghorn and A.J. Kinghorn
Factors affecting genetic gain by geographic location for Australian and New Zealand MERINOSELECT flocks	471
C.J. Bunter, P.E. Bradley, M.J. Hodge and K.L. Rummery
Genetic progress in industry
Seven Years On: What has Single-Step BREEDPLAN meant for the Australian Brahman breed?	475
C.A. Millen, B.J. Crook and P.J. Williams
BREEDPLAN: 40 years of accelerating genetic progress in the beef industry	479
B.W. Gudex, C.A. Millen, D.J. Johnston and N. Turner
Genetic trends in Australian beef cattle and sheep populations and their impact	483
R.G. Banks, D.J. Brown, K.L. Moore, B.J Walmsley and A.A. Swan
Breeding for facial eczema tolerance - A success story	487
P.L. Johnson and R. Proffit