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Proceedings of the AAABG 19th Conference

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Preliminary pages
AAABG and President's Message	i
Conference Sponsors	vi
AAABG Rules	vii
AAABG Fellows and Honorary members	ix
Helen Newton Turner Medal	xiv
Author Index	490

Papers
Animal Breeding and Selection
Genetic architecture of complex traits	1
M.E. Goddard
Animal breeding objectives: balancing productivity and ecological impact	7
J.A.M. van Arendonk
Automated mate selection analyses	15
B.P. Kinghorn
Breeding Objectives
Experience in breeding objectives for beef cattle, sheep and pigs, new developments and future needs	23
S.A. Barwick, A.A. Swan, S. Hermesch and H.-U. Graser
Is breeding for profit still the answer?	31
P.R. Amer
Preference-based approaches to deriving breeding objectives: application to sheep and plant breeding	35
T.J. Byrne, P.F. Fennessy, K.F. Smith, P. Hansen, and P.R. Amer
Breeding objectives and breeding strategies for Philippine dairy buffaloes	39
E.B. Flores and J.H.J. van der Werf
The impacts on selection for economic merit of including residual feed intake traits in breeding objectives and of having records available	43
S.A. Barwick, M.G. Jeyaruban, D.J. Johnston, M.L. Wolcott and H.-U. Graser
Cattle I
Associations between residual feed intake on ad libitum, pasture and restricted feeding in Angus cows	47
R.M. Herd, P.F. Arthur and J.A. Archer
The effect of breed on the onset of puberty in heifers	51
R.E. Hickson, C.C. Balcomb, K.R. Fraser, N. Lopez-Villalobos, P.R. Kenyon and S.T. Morris
Bull traits measured early in life as indicators of herd fertility	55
N.J. Corbet, B.M. Burns, D.H. Corbet, J.M. Crisp, D.J. Johnston, M.R. McGowan, B.K. Venus and R.G. Holroyd
Effect of previous reproductive status of dam on the preadjustment of weaning weight for genetic evaluation in tropical beef breeds	59
M.G. Jeyaruban, M.L. Wolcott, D.J. Johnston and H–U. Graser
The effect of imprinted genes on carcass traits in Australian Angus and Hereford cattle	63
B. Tier and K. Meyer
Genetic parameters of post-partum reproductive status in beef cattle from northern Australia	67
Y. Zhang, B. Tier and R. Hawken
Statistical Genetics
Multivariate estimation of genetic parameters – quo vadis?	71
Karin Meyer
Effects of ascertainment bias when testing for polled in Australian beef cattle	79
J.M. Henshall, E. Piper and C.A. McDonald
Performance of cross-validation and likelihood based strategies to select tuning factors for penalized estimation	83
Karin Meyer, Mark Kirkpatrick and Daniel Gianola
Penalized maximum likelihood estimates of genetic covariance matrices with shrinkage towards phenotypic dispersion	87
Karin Meyer
Partitioning genetic variance in composite sheep	91
S.F. Walkom, A.P. Verbyla, F.D. Brien, M.L. Hebart and W.S. Pitchford
Genetic Parameters I
Genetic variation in growth patterns is associated with sow lifetime performance	95
K.L. Bunter and C.R.G. Lewis
Survival analysis for the productive life of commercial sows	99
C.R.G Lewis and K.L. Bunter
Genetic parameters associated with adult ewe liveweight and body condition	103
G.H. Shackell, N.G. Cullen and G.J. Greer
Heritability estimates for retail colour stability of lamb meat	107
S.I. Mortimer, R.H. Jacob, R.D. Warner, K.L. Pearce, D.W. Pethick, J.H.J. van der Werf, A.J. Ball and D.L. Hopkins
Genetic relationships between objectively measured and subjectively assessed traits in the South African Dorper sheep breed	111
O.T. Zishiri, S.W.P. Cloete, J.J. Olivier and K. Dzama
Piglet traits at birth are associated with their survival until weaning	115
P. Tabuaciri, K.L. Bunter and H-U. Graser
Cattle II
Comparison of genetic parameters for calving difficulty in Angus, Charolais, Hereford and Limousin	119
M.G. Jeyaruban, D.J. Johnston and H.–U. Graser
Observed trends in estimated breeding values in response to selection using visual muscle score in beef cattle	123
B.J. Walmsley and W.A. McKiernan
Milk and weight EBVs are associated with cow and calf gain during lactation but carcass EBVs are not	127
S.J. Lee, K. Donoghue, M.L. Hebart and W.S. Pitchford
The effective management of deleterious genetic conditions in cattle	131
C.F. Teseling and P.F. Parnell
Information empowers – Arthrogryposis multiplex in Angus Australia	135
J.M. Allen and C.F. Teseling
Managing deleterious genetic conditions at the herd level	139
J.M. Allen, P.F. Parnell and C.F. Teseling
Sheep I
Genetic frontiers in the development of ‘clean, green and ethical’ management systems for the extensive sheep industry	143
G.B. Martin and J.C. Greeff
Selection strategies for the genetic improvement of reproductive performance in sheep	151
F.D. Brien, G.N. Hinch, J.H.J. van der Werf, D.J. Brown and A.A. Swan
Factors affecting variability in feed intake of sheep with ad libitum access to feed and the relationship with daily methane production	159
D.L. Robinson, S.L. Bickell, A.F. Toovey, D.K. Revell and P.E. Vercoe
Genetic and phenotypic parameters for temperament in weaned lambs	163
J.E. Hocking Edwards, F.D. Brien, M.L. Hebart, G.N. Hinch, J. Hoad, K.W. Hart, G. Gaunt, M. Robertson, G. Refshauge, and T. Bird-Gardiner
Genetic Parameters II
Genetic (co)variances for yearling traits and reproduction in the South African Dohne Merino breed	167
J.J. Olivier and S.W.P. Cloete
Different methods detected different loci involved in resistance to facial eczema disease of sheep	171
S.H. Phua and K.G. Dodds
Genetic parameters for breech strike indicator traits and yearling production traits in Merinos	175
A.J. Scholtz, S.W.P. Cloete, J.J.E. Cloete, A.C.M. Kruger, J.B. van Wyk and T.C. de K. van der Linde
Is there a relationship between temperament and internal parasite resistance in Merinos?	179
J.E. Newton, S. Dominik, J.M. Henshall and J.H.J. van der Werf
Genetic variation and heritability of ostrich weight traits	183
A. Engelbrecht, S.W.P. Cloete, K.L. Bunter and J.B. van Wyk
Cattle III
Breeding Angus cattle that naturally emit less methane	187
R.M. Herd, K.A. Donoghue, S.H. Bird, R.F. Hegarty and P.F. Arthur
The effect of duration and frequency of milk yield recording on lactation curve modelling	191
P.C. Thomson, E. Jonas, M. Abdelsayed and H.W. Raadsma
Breeding for extended lactation in Australian dairy cows: a review	195
M. Abdelsayed, H.W. Raadsma and P.C. Thomson
Age at first calving and its relationship with other dairy traits in Holstein cattle in Australian herds	199
M. Haile-Mariam and J.E. Pryce
Gene Expression
Characterisation in the New Zealand dairy industry of a polymorphism modulating the transcription rate of a chromosome domain encompassing PLAG1	203
R.J. Spelman, T. Druet, W. Coppieters and M. Georges
Expression of candidate genes for residual feed intake in beef cattle	207
W. Al-Husseini, K. Quinn, R.M. Herd, C. Gondro, J.P. Gibson, L.M. Cafe, P.L. Greenwood and Y. Chen
Recent ancestry for the 821del11 double muscling allele	211
B.A. O’Rourke, P.L. Greenwood, P.F. Arthur and M.E. Goddard
Mapping of congenital contractural arachnodactyly in cattle	215
I. Tammen, M.S. Khatkar, J.A.L. Cavanagh, P.A. Windsor, P.C. Thomson and H.W. Raadsma
GDF8 c.1232 G>A mutation effect consistent in an industry collected resource	219
P.L. Johnson, T.C. Van Stijn, H. Henry and N.J. McLean
GDF8 c.1232 G>A frequency in commercially slaughtered lambs	223
P.L. Johnson, T.C. Van Stijn, H. Henry, N.J. McLean and K.G. Dodds
Sheep II
Genetic correlation estimates for lamb carcass composition	227
S.I. Mortimer, A.A. Swan, R.H. Jacob, R.D. Warner, K.L. Pearce, D.W. Pethick, J.H.J. van der Werf, J.E. Hocking Edwards, G.H. Geesink, G.E. Gardner, A.J. Ball and D.L. Hopkins
Pedigree Matchmaker: can it tell us more than just pedigree?	231
D.J. Brown, A.A. Swan and M.L. Mortimer
Will Merino sheep with smooth bare breeches grow soft, white, photostable wool?	235
S. Hatcher, K.J. Thornberry and S. Gabb
How do sheep breeders benefit from new technologies?	239
J.A. Sise, E.M. Linscott and P.R. Amer
Results of an exploratory study of the application of agent-based modelling of sheep genetic progress using network theory	243
A. Reverter, S. Dominik, S. Field and R.G. Banks
Biotechnology I
The effect of telomere length variation on lifetime productivity traits in sheep	247
G.S. Nattrass, R.G. Banks and W.S. Pitchford
Quantitative real-time PCR revealed differentially expressed genes between high and low residual feed intake Angus cattle	251
Y. Chen, K. Quinn, R.M. Herd, P.F. Parnell and P.F. Arthur
Use of snp chip technology for improved utilisation of livestock genetic resources in developing countries	255
K. Marshall
Using the GeSNP algorithm to quality control and prioritize differentially expressed genes from comparative genomics	259
Y. Li, N. Andronicos, A. Ingham, P. Hunt, R. Windon, W. Barris and A. Reverter
Accuracy of SNP imputation using a multi-tiered genotyping approach in dairy cattle	263
M.S. Khatkar, G. Moser, B. Hayes and H.W. Raadsma
Principal component analysis in a population of Brahman bulls genotyped with 50k SNP chip revealed a genetic structure	267
M.R.S. Fortes, S. Bolormaa L.R. Porto Neto. R.G. Holroyd and A. Reverter
The John Vercoe Memorial Lecture
Beef translational genomics: lessons from the literature	271
A.L. Van Eenennaam
Genomics
Beef cattle genetic evaluation in the genomics era	279
D.J. Johnston, B. Tier and H.–U. Graser
Effect of relationship and age structure between training and validation set on the accuracy of genomic breeding value prediction using genomic BLUP	287
M. Erbe, F. Seefried and H. Simianer
The relative importance of information on unrelated individuals on the prediction of genomic breeding values	291
S.A. Clark, J.M. Hickey and J.H.J. van der Werf
A kernel method for genome-wide selection using haplotypes	295
G. Moser, M.S. Khatkar and H.W. Raadsma
Maternal Efficiency
Merino ewes with higher breeding values for fatness and muscling have improved maternal efficiency	299
M.B. Ferguson, B.L. Paganoni, K.L. Kennedy and A.N. Thompson
Selection for superior growth advances the onset of puberty in Merino ewes	303
C.A. Rosales Nieto, M.B. Ferguson, C.A. Macleay, J.R. Briegel, G.B. Martin and A.N. Thompson
The potential value of genetic differences in liveweight loss during summer and autumn in Merinos ewes differs with production environment	307
J.M. Young, M.B. Ferguson and A.N. Thompson
Adult Merino ewes can be bred for live weight change to be more tolerant to climate change	311
G. Rose, A. Kause, J.H.J. van der Werf, A.N. Thompson, M.B. Ferguson and J.A.M. van Arendonk
Genomics - Sheep
Optimizing sheep breeding programs with genomic selection	315
J.H.J. van der Werf, B.J. Horton and R.G. Banks
The value of genomic selection for stud and commercial Merino rams	323
S. Dominik, J.H.J. van der Werf and R.G. Banks
The importance of population structure on the accuracy of genomic prediction in a multi-breed sheep population	327
H.D. Daetwyler, K.E. Kemper, J.H.J. van der Werf and B.J. Hayes
Use of genomic information to estimate breeding values for carcass traits in sheep	331
A.A. Swan, D.J. Brown, B. Tier, and J.H.J. van der Werf
Sheep III
Effects on lifetime reproductive performance of phenotypic selection for fleece weight, fibre diameter, body weight and related selection indexes. II. Selection group x environment interaction	335
L.R. Piper, A.A. Swan, and H.G. Brewer
Different mature ewe sizes require different stocking rates and lamb slaughter weights to maximise whole-farm profit	339
A.J. Kennedy, M.B.Ferguson, G.B. Martin, A.N. Thompson and D.J. Pannell
The mobilisation of fat in response to adrenaline is greater in Merino ewes with higher breeding values for coefficient of variation of fibre diameter	343
M.B. Ferguson, J.R. Briegel, A.N. Thompson and G.E. Gardner
Use of automatic feeder data for activity studies in sheep	347
E. Jonas, E. Webster, P.C. Thomson and H.W. Raadsma
Does the lamb birth weight response to mid pregnancy shearing differ in two breeds of disparate size?	351
P.R. Kenyon, H.T. Blair and C.M.C. Jenkinson
The necessary paradigm change in quantitative genetics	355
R.G. Beilharz
Genomics - Dairy Cattle
Choice of parameters for removal of inflation in genomic breeding values for dairy cattle	359
B.L. Harris, D.L. Johnson and R.J. Spelman
Implementation of genomics in Australian dairy cattle	363
G.J. Nieuwhof, M. Haile-Mariam, K.T.Beard, K.V. Konstantinov and B.J. Hayes
Accuracy of genomic selection for residual feed intake and 250-day liveweight in dairy heifers using high density (630k) SNP	367
J.E. Pryce, J. Arias, P.J. Bowman, K.A. Macdonald, G.C.Waghorn, Y.J. Williams, W.J. Wales, R.J. Spelman and B.J. Hayes
Optimising multistage dairy cattle breeding programs with regard to genomic selection	371
V. Börner and N. Reinsch
Biotechnology II
Towards a comprehensive recombination map of hotspots in sheep	375
C. Massault, J. Henshall, C. Gondro and J.H.J. van der Werf
Imputation of single nucleotide polymorphism genotypes in a crossbred dairy cattle population using a reference panel	379
D.L. Johnson, R.J. Spelman, M.K. Hayr and M.D. Keehan
Single nucleotide polymorphisms in the bovine leptin gene and their association with carcass and efficiency traits, and endocrine profiles, in female Angus cows	383
M. Laurence, J.M. Accioly, A.L. Barnes, D. Blache, N.D. Costa1, F.M. Jones, E.J. Speijers and W.S. Pitchford
Association between SNP intensity data and growth and meat yield traits in sheep	387
G.M. Payne, M.E. Goddard, J.C. McEwan, M.A. Black and K. G. Dodds
Industry I
Increasing uptake of genetic technologies across the beef value chain	391
H.M. Burrow and R.G. Banks
Progress in implementation of a beef information nucleus portfolio in the Australian beef industry	399
R.G. Banks
Genetic progress in Australian young sire programs: a model for increasing the rate of genetic improvement	403
A.J. Ball, R.B. Banks, D.J. Brown and S.R. Field
Ram breeding in New Zealand two decades after the introduction of exotic sheep breeds	407
H.T. Blair
Posters
Genetic, phenotypic and environmental correlations between footrot and fleece traits in sheep	411
M. Abdelsayed, P.C. Thomson and H.W. Raadsma
Four week repeatability of daily and one hour methane production of mature merino wethers fed ad libitum	415
S.L. Bickell, D.L. Robinson, A.F. Toovey, J.P. Goopy, R.S. Hegarty, D.K. Revell and P.E. Vercoe
Genetic and environmental parameters of milk production and milk composition in South African Merinos	419
S.W.P. Cloete, M.A. Snyman and A.J. Scholtz
Use of residual feed intake as an indirect selection trait for reduction of methane emissions in grazing beef cattle	423
D.J. Cottle
QTL analyses of beef taste panel data	426
N.G. Cullen, C.A. Morris and H.V. Henderson
The expression of genes encoding lipid storage proteins is correlated with intramuscular fat percentage in Brahman steers	430
N. De Jager, N.J. Hudson, A. Reverter, R. Barnard, L.M. Cafe, P.L. Greenwood and B.P. Dalrymple
Carcase quality of two year old steer progeny of Angus heifers divergently selected on rib fat estimated breeding values and subjected to two levels of nutrition pre-weaning	434
M.P.B. Deland, K. Copping, J.F. Graham and W.S. Pitchford
The effect of subcutaneous fat, muscle and body weight during mating on fertility in Merino and Border Leicester x Merino lambs	438
K.W. Hart and J.C. Greeff
Genetic diversity in Alpacas: can inbreeding explain the high prevalence of congenital defects?	442
F.C. Jackling, J.L. Vaughan, M.E. Goddard and B.R. Appleton
Opportunities for genetic management of the retail colour stability of lamb meat	446
R.H. Jacob, S.I. Mortimer, D.L. Hopkins, R.D. Warner, and M.F. D’Antuono
Fluctuation in ewe liveweight during periods of restricted nutrition is influenced by sire	450
S.E. John, M.B. Ferguson, G.E. Gardner and A.N. Thompson
Analysis of udder health in dairy ewes	454
E. Jonas, P.C. Thomson, H.W. Raadsma
Does dam age, ewe birth rank and sex of a co-twin affect a ewe’s lifetime performance?	458
P.R. Kenyon, L.M. Cave, H.T. Blair, N. Lopez-Villalobos and G.B. Nicoll
Functional genomics of estimated breeding value for eye muscle depth in sheep	462
L.J.A. Kogelman, N.S. Watson-Haigh, H.N. Kadarmideen, J.W. Kijas, T. Vuocolo, K. Byrne, H. Oddy, G.E. Gardner, C. Gondro and R.L. Tellam
Genetic variation in growth and the optimisation of snp molecular markers for parentage assignment in pasture-based crossbred sheep	466
A.E.O. Malau-Aduli, A. Kashani, S. McCammon and A. Smolenski
Constraints associated with the improvement of animals through breeding as perceived by poor livestock keepers of West Africa	470
K. Marshall and M. Ejlersten
Variation in Merino wethers for growth and carcase traits	474
S.J. Martin, C.A. Wilson, M.J. Moses, R. van de Ven and D.L Hopkins
Reproduction traits in Holstein cows: Towards the development of a genetic evaluation system for cow fertility	478
C.J.C. Muller, J.P. Potgieter, O.T. Zishiri and S.W.P. Cloete
Exploring fertility traits other than calving interval for inclusion in a national genetic evaluation for South African Holstein cows	482
J.P. Potgieter, C.J.C. Muller, S.W.P. Cloete, O.T. Zishiri and K. Dzama
Genetic parameters for ostrich chick mortality to six months post hatch	486
M.D. Wang, S.W.P. Cloete, and K. Dzama
Author Index	490