AAABG 2023 Animal Breeding at the Crossroads

Proceedings of the AAABG 21st Conference

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Preliminary pages
AAABG and President's Message i
Conference Sponsors vi
AAABG Rules viii
AAABG Fellows and Honorary members x
Helen Newton Turner Medal xviii
Table of Contents xxiii
Breeding Objectives and Economics
Selection strategies for breeding objectives in growing pigs 1
S. Hermesch, M.M.A. Arnal, V. Börner and S. Dominik
A genetic line of Nile Tilapia undergoing seven generations of selection under moderate salinity water environment 5
N.P. Thoa, N.H. Ninh, W. Knibb and N.H. Nguyen
Non-linear calving difficulty weightings in the Irish dairy industry 9
F.S. Hely, R. Evans, P.R. Amer and A. Cromie
Extended cow liveweight modelling for beef cattle breeding objectives 13
B.J. Walmsley, M.L. Wolcott, W.S. Pitchford, D.J. Johnston and S.A. Barwick
Evaluation of alternative selection indexes for non-linear profit traits approaching their economic optimum 17
D. Martin-Collado, B. Visser, T. Byrne and P. Amer
A review of the national breeding objective and selection Indexes for the Australian dairy industry 21
T. Byrne, D. Martin-Collado, B. Santos, P. Amer, J. Pryce and M. Axford
Feed saved breeding values for Australian dairy cattle 25
J.E. Pryce, O. Gonzalez-Recio, G. Nieuwhof, W.J. Wales, M.P. Coffey, B.J. Hayes and M.E. Goddard
Breeding to improve meat eating quality in terminal sire sheep breeds 29
A. Swan, T. Pleasants , and D. Pethick
Accounting for the cost of reproductive technologies during selection in sheep breeding programs 33
T. Granleese, S.A. Clark, A.A. Swan, J.H.J. van der Werf
Genetic expressions and economic impact of performance recording in multi-tiered sheep breeding schemes 37
B.F.S. Santos, T.J. Byrne, B. Visser, J.H.J. van der Werf, J.P. Gibson and P.R. Amer
Detecting causal variants
Why can we impute some rare sequence variants and not others? 41
B.J. Hayes, P.J. Bowman, H.D. Daetwyler and M.E. Goddard
From sheep SNP chips, genome sequences and transcriptomes via mechanisms to improved sheep breeding and management 45
B.P. Dalrymple, V.H.Oddy, J.C. McEwan, J.W. Kijas, R. Xiang, J. Bond, N. Cockett, K. Worley, T. Smith and P.E. Vercoe
Pleiotropic multi-trait genome-wide association reveals putative candidate genes for fatty acid composition in Australian sheep 49
S. Bolormaa, J.H.J. van der Werf, B.J. Hayes, M.E. Goddard and H.D. Daetwyler
Fine-mapping single nucleotide polymorphisms on Bos taurus chromosome 26 affecting adipose myristic acid 53
D. Lu, S.M. Hickey, N.G. Cullen and S.P. Miller
Effects of TEX11 and AR polymorhisms on reproduction and growth traits in Australian beef cattle 57
L.T. Nguyen, G.M.F.D Camargo, R.E. Lyons, S.A. Lehnert and M.R.S. Fortes
Using protein QTL to disentangle variants effecting protein percentage in milk near the casein complex 61
K.E. Kemper, M.J. Carrick and M.E. Goddard
A comparison of genotypes generated by infinium beadchips and a targeted genotype by sequencing method in cattle 65
A.J. Chamberlain, P. Beatson, B.A. Mason, C. Prowse-Wilkins, C.M. Reich, C. Schrooten, B.J. Hayes, J. Tibbits and M. Hayden
Identification of loci associated with parasite resistance in Australian sheep 69
M. Al Kalaldeh, J.H.J. van der Werf and C. Gondro
Non-synonimous polymorphism in HELB is associated with male and female reproductive traits in cattle 73
M.R.S. Fortes, F.B. Almughlliq, L.T. Nguyen, L.R. Porto Neto and S.A. Lehnert
Detecting variants associated with complex traits through changing gene expression in cattle 77
M. Khansefid, J.E. Pryce, S. Bolormaa, Y. Chen and M.E. Goddard
Multi-breed GWAS and meta-analysis using whole-genome sequences of five dairy cattle breeds 81
I. van den Berg, D. Boichard and M.S. Lund
Feed efficiency, methane emission and fertility
Visualisation of rumen microbiome data 85
G.R. Wood, S. Kittelmann, C. Pinares-Patiño, K.G.Dodds, M.R. Kirk, S. Ganesh, S.M. Hickey, P.H. Janssen, J.C. McEwan and S.J. Rowe
Prediction of residual feed intake from genome and metagenome profiles in first lactation Holstein-Friesian dairy cattle 89
M. Wang, J. E. Pryce, K. Savin and B.J. Hayes
Associations of rumen volatile fatty acids with phenotypic and genetic variation in methane production traits in Angus cattle 93
H.C. Smith, R.M. Herd, K.A. Donoghue, T. Bird-Gardiner, P.F. Arthur and R.F. Hegarty
Liver microRNA expression revealed the difference in fat metabolism from cattle divergently selected for residual feed intake 97
Y. Chen, W. AL-Husseini, I. Barchia, C. Gondro, R.M. Herd and P.F. Arthur
Genetic selection for litter size in cattle 101
L.R. Piper, B.M. Bindon, A.A. Swan and H.G. Brewer
Towards a data set to investigate feed efficiency in New Zealand maternal sheep 106
P.L. Johnson, S.P. Miller and K. Knowler
Repeatabilities for methane emission in Merino ewes on pasture across different ages 110
S. Dominik and V.H. Oddy
Genetic parameters for methane production and relationships with production traits in Australian beef cattle 114
K.A. Donoghue, T.L. Bird-Gardiner, P.F. Arthur, R.M. Herd and R.F. Hegarty
Genomic estimated breeding values for methane production in Australian beef cattle 118
B.J. Hayes, K.A. Donoghue, C. Reich, B. Mason, R.M. Herd and P.F. Arthur
Divergent selection for methane yield in beef cattle 122
T. Bird-Gardiner, K.A. Donoghue, P.F. Arthur, R.M. Herd and R.F. Hegarty
Genomic prediction in practice
Big is beautiful: biology informed sequence exploitation 126
M. Perez-Enciso, M. Naval-Sanchez, J. Leno-Colorado and A. Reverter
High throughput genotyping-by-sequencing in livestock - Ion Ampliseq(tm) 133
K. Ridley, J. Walker and M. Hickenbotham
Using genomic information to estimate genotype by environment interactions 137
S.A. Clark, S.H. Lee and J.H.J. van der Werf
Lamb eating quality can be managed by using terminal sires with desirable breeding values for intramuscular fat and shear force 141
J.E. Hocking Edwards, B. Hancock, S. Gill, R. Apps and A. Ball
Genomic best linear unbiased prediction using differential evolution 145
H.A. Al-Mamun, P. Kwan, S. Clark, S.H. Lee, H.K. Lee, K.D. Song, S.H. Lee and C. Gondro
Improving the accuracy of across breed genomic predictions 149
M.E. Goddard, I.M. MacLeod, S. Bolormaa, B.J. Hayes and K.E. Kemper
Data compression: a new way to infer genomic relationship matrices and highlight regions of interest in commercial lines of broiler chicken 153
N.J. Hudson, R. Hawken R. Sapp and A. Reverter
John Vercoe Memorial Session
Relationship between change in trait definition and accuracy of genomic breeding value of type traits in Australian Holstein 157
M. Haile-Mariam, J.E. Pryce and B.J. Hayes
Predicting genomic selection accuracy from heterogeneous sources 161
J.H.J. van der Werf, S.A. Clark and S.H. Lee
Accuracy of genomic prediction for merino wool traits using high-density marker genotypes 165
N. Moghaddar, A.A. Swan and J.H.J. van der Werf
Genetics on the ground
Considerations in the use of commercial data for genetic evaluation in beef and sheep in Australia 169
R.G. Banks and B. Tier
What causes the negative genetic correlation between maternal and direct effects for lamb birth weight? 173
H.T. Blair
Genetic correlations between purebred and crossbred performance of Poll Dorset sheep 177
D.J. Brown and J.H.J. van der Werf
Animal Health
Using hump height to estimate Bos indicus content in the MSA beef grading model which predicts eating quality 181
M. Kelly, J.M. Thompson, L.R. Porto-Neto, R.E. Lyons and S.S. Moore
Are high Australian profit ranking sires best in all herds? Findings from the feeding the genes project 185
J.M. Morton, R.R. Woolaston, P. Brightling, S. Little, K.L. Macmillan, J.E. Pryce and G.J. Nieuwhof
Selection for reduced mature cow weight will reduce body condition unless accompanied by selection for increased fat 189
W.S. Pitchford, S.J. Lee, K.A. Donoghue and B.J. Walmsley
Estimates of genetic parameters for seasonal weight changes of beef cows 193
K. Meyer and I.G. Colditz
Effects of production level on the expression of breed and heterosis for lactation yields of milk, fat and protein in cows milked once- and twice-daily 197
F. Lembeye, N. Lopez-Villalobos, J.L. Burke and S.R. Davis
Revisiting total weaning weight as a selection criterion 201
K.L. Bunter and D.J. Brown
Is fibre comfort factor required in merino breeding programs? 205
S. Hatcher and D.J. Brown
Genetic parameters for eating quality traits of Australian lamb 209
S.I. Mortimer, A.A. Swan, L. Pannier, A.J. Ball, R.H. Jacob, J.H.J. van der Werf and D.W. Pethick
Industry Focus
A public:private collaboration to evaluate the potential value of genomic information to a vertically-integrated commercial beef cattle enterprise 213
B.T Welly, M.D. MacNeil, A.R. McClain, R.C. Raymond, E.B. Simpson and A.L. Van Eenennaam
Production performance of Merino and Dohne Merino ewes and lambs in pure or crossbreeding systems 217
S.W.P. Cloete and J.J.E. Cloete
Has the beef genetic improvement pipeline been effective? 221
P.F. Parnell
Detailing a beef genetics extension strategy 225
S.J. Lee and W.S. Pitchford
Evaluating dairy herd genetic progress 229
M.M. Axford, P.W. Williams, D.P. Abernethy and G.J. Nieuwhof
Realising genetic improvement for the extensive livestock industries as a whole 233
R.G. Banks
Inheritance of tail length in Merino sheep 237
J.C. Greeff, L.J.E. Karlsson and A.C. Schlink
Testing an approach to account for daughter misidentification in the estimation of breeding values 241
N. Lopez-Villalobos, J.R. Bryant, B.L Harris and D.J. Garrick
Merino breeding objectives under climate change 245
P. Graham, A.A. Swan and R.G. Banks
SNP-based parentage in an Australian cattle industries context: does one size fit all? 249
R.E. Lyons, S. Buttsworth, D. Waine and M. Kelly
Impact of scanning lean cattle on the genetic correlation between scan and carcase intramuscular fat in Angus and Hereford cattle 253
S.F. Walkom, M.G. Jeyaruban and D.J. Johnston
Plenary Presentations
Integration of genomic information into national cattle and sheep evaluations - past, present and future 257
D.P. Berry, J.F. Kearney, N. McHugh, E. Wall, D. Purfield and A.R. Cromie
Sole haemorrhage, dermatitis and co.- How genomic information and precise phenotypes help to unscramble genetic background of health traits in dairy cattle 261
K. Schöpke
The opportunities and challenges of integrating genomics in a broiler breeding program 266
R.J. Hawken, R.L. Sapp, R. Okimoto, J. Chen, R. Borg, C-H. Huang, T. Wing, C. Wang, J. Henshall and M. Abrahamsen
Genomic prediction using sequence data in a multibreed context 270
M.S. Lund, I. van den Berg and D. Boichard
Poster Presentations
Selection patterns for Holstein sires in production-recorded Holstein herds with differing feeding systems 274
K.L. Macmillan, J.M. Morton and J.E. Pryce
Mildly penalized maximum likelihood estimation of genetic covariances matrices without tuning 278
Karen Meyer
Efficiency of a tactical phenotyping strategy for multi-stage selection 282
C. Massault and J.H.J van der Werf
A commercial comparison of ewe breeds for reproduction, wool and lamb growth 286
K.P. Ransom, F.D. Brien and W.S. Pitchford
Reproductive performance of Holstein and Jersey heifers and cows in a pasture-based system in South Africa 290
C.J.C. Muller, J.P. Potgieter, S.W.P Cloete and J.A. Botha
Genetic diversity and population structure of four South African sheep breeds 294
L. Sandenbergh, S.W.P. Cloete, R. Roodt-Wilding, M.A. Snyman, and A.E. Van der Merwe
Sheep phylogeography and domestication as inferred from complete genome sequences 298
M. Naval-Sanchez, S. McWilliam, A. Reverter, M. Perez-Enciso, N. J. Hudson and J. Kijas
Assessing imputation accuracy using a 15K low density panel in a multi-breed New Zealand sheep population 302
R.V. Ventura, M. Lee, S.P. Miller, S.M. Clarke and J.C. McEwan
Estimating the genetic (co)variance explained per chromosome for two growth traits using a half sib data structure in sheep 306
C. Esquivelzeta-Rabell, N. Moghaddar, S. Clark and J.H.J. van der Werf
Runs of homozygosity in Swakara pelt producing sheep: implications on sub-vital performance 310
F.C. Muchadeyi, M.T. Malesa, P. Soma and E.F. Dzomba
Genetic diversity and effective population size of eight Iranian cattle breeds 314
E.M. Strucken, K. Karimi, A.K. Esmailizadeh, N. Moghaddar and C. Gondro
Arthrospira platensis: a novel feed supplement influences gene expression in the heart, kidney and liver of prime lambs 318
A.E.O. Malau-Aduli and A. Kashani
Environmental effects on post weaning fleece traits of a Merino sire evaluation flock 322
S.I. Mortimer and A.E. Casey
Methane emissions estimated based on milk fatty acids of Jersey and Fleckvieh x Jersey cows in a pasture-based system 326
S. Abel, C.J.C. Muller and B. Sasanti
Comparison of survival phenotypes in specific dairy production systems 330
B. Visser, K. Stachowicz, J.R. Bryant and P.R. Amer
Modelling of longitudinal liveweight data using regression with Legendre and eigenvector functions 334
M.D. Price, M.E. Olayemi and J.B. Bryant
Fibre diameter measured in the post-weaning age window is genetically the same trait as yearling fibre diameter 338
A.A. Swan
Measurement of methane traits in the beef information nucleus cattle 342
P.F. Arthur, R.M. Herd, C. Weber, H. Smith and R.F. Hegarty
Reproduction, behaviour and health
Regions impacting inbreeding depression and their association with additive genetic effects for Jersey cattle from the United States of America and Australia 346
J. T. Howard, J. E. Pryce, M. Haile-Mariam and C. Maltecca
Use of high density genotyping and trait-dependent methods in genome-assisted evaluations 350
M.N. Aldridge, D.J. Brown and W.S. Pitchford
Genetic relationships between breech cover, wrinkle and lamb survival in Merino sheep 354
S. Hatcher, D.J. Brown, F.D. Brien and M.L. Hebart
A genome-wide association study of non-additive effects for milk yield and fertility in Holstein and Jersey dairy cattle 358
H. Aliloo, J.E. Pryce, O. González-Recio, B.G. Cocks and B.J. Hayes
Effects of selection for fertility on lactation curves 362
E.M. Strucken, Y.C.S.M. Laurenson and G.A. Brockmann
Benchmarking cow health status with dairy herd summary data 366
K.L. Parker Gaddis, J.B. Cole, J.S. Clay and C. Maltecca
Proposed changes in the genetic evaluation of dairy fertility in New Zealand 370
K. Stachowicz, G.M. Jenkins, P.R. Amer, J.R. Bryant and S. Meier
Using sequence data to improve accuracy of genomic prediction and QTL discovery for dairy cow fertility 374
I.M. MacLeod, B.J. Hayes, M. Haile-Mariam, P. Bowman, A.J.Chamberlain, C.J Vander Jagt, C. Schrooten and M.E. Goddard
Genomic breeding values of heat tolerance in Australian dairy cattle 378
T.T.T. Nguyen, P.J. Bowman, M. Haile-Mariam, J.E. Pryce and B.J. Hayes
Improving the accuracy of genomic selection for lactation anoestrous interval in Brahman cattle 382
M.L. Wolcott, Y.D. Zhang and D.J. Johnston
Australian sheep breeding values for worm egg count retain predictive power across flocks in the presence of GxE 386
L. Li, A.A. Swan, D.J. Brown, and J.H.J. van der Werf
Speed talks
BESSiE a program for multivariate linear model BLUP and Bayesian analysis of large scale genomic data 390
V. Boerner and B. Tier
Collection of data for the genetic improvement of health traits in Australian dairy cattle 393
M. Abdelsayed, P. Douglas and J.E. Pryce
Quantifying between animal variation for male semen traits and female egg traits in an ostrich flock used to develop an artificial insemination protocol 397
S.W.P. Cloete, M. Bonato, A.M.J. Smith and I.A. Malecki
Genomic predictions for meat colour traits in New Zealand sheep 401
L.F. Brito, S.P. Miller, M.A. Lee, D. Lu, K.G. Dodds, N.K. Pickering, W.E. Bain, F.S. Schenkel, J.C. McEwan and S.M. Clarke
Genotype by birth or rearing type interaction in Merino sheep 405
A. Dakhlan, N. Moghaddar and J.H.J. van der Werf
Genetic analyses on carcase characters of Australian Wagyu beef cattle 409
Y.D. Zhang, B. Tier and R.G. Banks
Change in accuracy of estimated breeding values for viascan lean-meat yield when estimated from half-sib records 413
H.J.B. Craig, N.B. Jopson and M.J. Young
Effect of different data exclusion policies on the heritability of fat depth in maternal, Merino and terminal sheep 417
A.J. McMillan and D.J. Brown
How precise are enteric methane emission phenotypes or breeding values estimated from spot flux measures? 421
D.J. Cottle, J.I. Velazco, D. Mayer, R.S. Hegarty and R.M. Herd
Implications of manipulating the ewe live weight penalty in maternal sheep indexes in New Zealand 425
J.I. Kerslake, P.R. Amer, M.J. Young and T.J. Byrne
Statistical methods and computations
Computing for multi-trait single-step genomic evaluation of Australian sheep 429
K. Meyer, A.A. Swan and B. Tier
Using random forests to identify SNP associated with leg defect in broiler chicken: impact of correcting for population structures 433
Y. Li, A. George, R. Hawken, R. Sapp, S.A. Lehnert and A. Reverter
Missing heritability of adaptation phenotypes in tropical cattle 437
L.R. Porto-Neto, N.J. Hudson, W. Barendse, S.A. Lehnert and A. Reverter
Imputation accuracy measurement and post-imputation quality in imputed SNP genotypes for dairy cattle 441
K.M. Tiplady and R.G. Sherlock
Inbreeding depression in adaptation phenotypes of tropical beef cattle using genome wide data 445
L.R. Porto-Neto, N.J. Hudson, W. Barendse, M.A.R. de Cara, S.A. Lehnert and A. Reverter
OPTBR: Computationally efficient genomic predictions and QTL mapping in multi-breed populations 449
T. Wang, Y.-P.P. Chen, K.E. Kemper, M.E. Goddard and B.J. Hayes
The impact of fitting incorrect models on the partitioning of genetic variance components for bionomial lamb traits 453
P.R. Amer, K. Stachowicz, P. Pierard and G.M. Jenkins
Backfat as an environmental descriptor in defining growth rate of the pig: a GxE analysis 457
S.Z.Y. Guy, S. Hermesch and P.C. Thomson
Which genomic relationship matrix? 461
B. Tier, K. Meyer and M.H. Ferdosi
Detection and validation of structural variation in cattle whole-genome sequence data 465
L. Chen, A.J. Chamberlain, C.M. Reich, H.D. Daetwyler and B.J. Hayes
A comparison of genetic connectedness measures using data from the NZ sheep industry 469
J.B. Holmes, B. Auvray, S.A. Newman, K.G. Dodds and M.A. Lee
Evolving to the best SNP panel for Hanwoo breed proportion estimates 473
C. Esquivelzeta-Rabell, H.A. Al-Mamun, S.H. Lee, H.K. Lee, K.D. Song and C. Gondro
Systems Biology
Allele specific expression is pervasive in cattle 477
C.J. Vander Jagt, A.J. Chamberlain, B.J. Hayes, L.C. Marett and M.E. Goddard
A map of bovine long non coding RNA across 18 tissues 481
L.T. Koufariotis, Y.-P.P. Chen, A.J. Chamberlian, C.J. Vander Jagt and B.J. Hayes
Potential role of lncRNA cyp2c91-protein interactions on immune diseases and obesity 485
P. Suravajhala, L.J.A. Kogelman, G. Mazzoni and H.N. Kadarmideen
Connecting gene expression and phenotype - preliminary results from RNA sequencing of 150 lambs 489
S. Bolormaa, R. Behrendt, M.I. Knight, B.A. Mason, C.P. Prowse-Wilkins, L. Slocombe, C.J. Vander Jagt, B.J. Hayes, A.J. Chamberlain and H.D. Daetwyler
What's next in genomics? Functional annotation of animal genomes 493
J. Kijas, B. Barendse, C. Bottema, R. Brauning, A. Chamberlain, S. Clarke, B. Dalrymple, R. Tellam, B. Hayes, J. McEwan and S. Moore