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Proceedings of the AAABG 20th Conference

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Preliminary pages
AAABG and President's Message i
Conference Sponsors vii
AAABG Rules ix
AAABG Fellows and Honorary members xi
Helen Newton Turner Medal xvii
Translating Science into Action
Understanding how farmers learn 1
H.T. Blair, A.M. Sewell, R.A. Corner-Thomas, P. Kemp, B.A. Wood, D.I. Gray, S.T. Morris, A.W. Greer, C.M. Logan, A.L. Ridler and R.E. Hickson, P.R. Kenyon  
Modelling farmer information transfers with network analysis: an exploratory farmlet study 6
B.A. Wood, H.T. Blair, D.I. Gray, P. Kemp, P.R. Kenyon, S.T. Morris and A.M. Sewell 
The California commercial beef cattle ranch project 10
A.L. Van Eenennaam, K.L. Weber and D.J. Drake 
Genomics for the Australian sheep industry: from design to delivery 14
J.B. Rowe, S. Gill, R.G. Banks, and J.H.J. van der Werf 
A survey examining the New Zealand breed composition, management tool use and 18 research needs of commercial sheep farmers and ram breeders 18
R.A. Corner-Thomas, P.R. Kenyon, S.T. Morris, A.W. Greer, C.M. Logan, A.L. Ridler, R.E. Hickson and H.T. Blair 
Acknowledging and honouring the contribution of Dave Johnson to animal evaluation
Dr Dave Johnson's contribution to dairy cattle genetic evaluation in New Zealand 22
B. Harris 
Effect of daughter misidentification on dairy sire evaluation 25
A.M. Winkelman 
The effects of using male and female genotypes in genomic evaluations 29
D.L. Johnson 
Improving the reliability of fertility breeding values in Australian dairy cattle 33
J.E. Pryce, M. Haile-Mariam, P. Bowman, T. Nguyen, K. Konstantinov, G.J. Nieuwhof and B.J. Hayes 
New approaches to genetic analysis of fertility traits in New Zealand dairy cattle 37
F.E. Bowley, P.R. Amer and S. Meier 
A Bayes-A like method in ASREML 41
Arthur R Gilmour 
Industry 1
A very simple model for examining potential impacts of value chain parameters on 45 direction of selection and genetic change 45
R.G. Banks, P.R. Amer and J.H.J. van der Werf 
Business metrics for Sheep Improvement Limited (SIL) ram breeders 49
T.J. Byrne, N.B. Jopson and M.J. Young 
Can selection for brighter, whiter more photostable wool replace oxidative bleaching during wool processing? 53
S. Hatcher, J.W.V. Preston and K.R. Millington 
Characteristics of extended lactation and persistency in Australian dairy cows 57
M. Abdelsayed, P.C. Thomson and H.W. Raadsma 
Modelling variation in bovine milk fat composition predicted using mid-infrared spectrometry 62
G. Johnstone, M. Coffey and E. Wall 
Strategies to objectively group merino flocks in sheep genetics 66
D.J. Brown, A.A. Swan, J.S. Gill and R.B. Banks 
Analyses of ewe stayability in flocks of New Zealand sheep 70
M.A. Lee, N.G. Cullen, S.A. Newman, J.C. McEwan and G.H. Shackell 
Modification of lactation yield estimates for improved selection outcomes in developing dairy sectors 74
D.M. McGill, P.C. Thomson, H.A. Mulder and J.J. Lievaart 
Increasing prolificacy of Awassi and Assaf breeds by introgression of the fecb 78 (Booroola) mutation: achievements and challenges 78
E. Gootwine, A. Rosov, M. Abu Siam and E. Seroussi 
Yearling and adult expressions of reproduction in maternal sheep breeds are genetically different traits 82
K.L. Bunter and D.J. Brown 
Age at first oestrus. A useful trait for early reproductive performance? 86
J.E. Newton, D.J. Brown, S. Dominik and J.H.J. van der Werf 
Potential economic return from use of fixed-time artificial insemination as part of a genetic improvement programme 90
S.A.A Edwards, B.M. Burns, J. Allen and M.R. McGowan 
Benefits of MOET and JIVET in optimised sheep breeding programs 94
T. Granleese, S.A. Clark and J.H.J. van der Werf 
Analysis of a South African Merino flock divergently selected for reproductive 98 potential 98
L. Sandenbergh, R. Roodt-Wilding, A.E. Van der Merwe and S.W.P. Cloete 
Current flock effects on lifetime reproductive performance of simulated selection at 102 hogget age in Merino sheep, for fleece weight, fibre diameter, body weight and relevant selection indexes. III High rainfall region results. 102
L.R. Piper, A.A. Swan and H.G. Brewer 
Genetic estimates for along and across fibre diameter variation and its use to improve staple strength in Merino sheep 106
J.W.V Preston and S. Hatcher 
Genetic correlations across ages for greasy fleece weight and fibre diameter in Merino sheep 110
D.J. Brown, A.A. Swan and J.S. Gill 
Genetic and non-genetic effects on flight speed and agitation in weaned lambs 114
C.L. Dodd, J.E. Hocking Edwards, S.J. Hazel and W.S. Pitchford 
Genetic estimates for along and across fibre diameter variation and correlations with subjective wool quality traits in Merino sheep 118
J.W.V Preston and S. Hatcher 
Genomic Selection - design
Genetic architecture and evolution of quantitative traits 122
M.E. Goddard 
Combining multiple test-statistics increases the power of selective sweep analyses in cattle 126
I.A.S. Randhawa, P.C. Thomson, M.S. Khatkar and H.W. Raadsma 
Bovine fat depots discriminate by gene expression patterns 130
N.J. Hudson, A. Reverter, D.W. Pethick, J.P. Siddell, P.L Greenwood and Brian P Dalrymple 
Using two different approaches to infer the genetic structure of populations with 134 complex relationships: the case of the Avileña-Negra Ibérica 134
D. Martin-Collado, K.J. Abraham, S.T. Rodriguez-Ramilo, M.A. Toro, M.J. Carabaño and C. Diaz 
Crossbreeding and Crossbreds
Across-breed genomic evaluation based on bovine high density genotypes, and phenotypes of bulls and cows 138
C. Schrooten, G.C.B. Schopen, A. Parker, A. Medley and P. Beatson 
Lactational performance of straightbred Angus cows and three Angus-dairy-cross 142 genotypes 142
F.J. Roca Fraga, R.E. Hickson, N. Lopez-Villalobos, P.R. Kenyon and S.T. Morris 
opulation stratification and breed composition of Australian tropically adapted cattle 147
L.R. Porto-Neto, S.A. Lehnert, M.R.S Fortes, M. Kelly and A. Reverter 
Integrated assembly of positively selected genes in cattle 151
I.A.S. Randhawa, M.S. Khatkar, P.C. Thomson and H.W. Raadsma 
John Vercoe Memorial Session
Genetic parameters for faecal worm egg count and objectively measured wool traits in South African Merinos 155
P.A.M. Matebesi-Ranthimo, S.W.P. Cloete, J.B. van Wyk and J.J. Olivier 
Improving milk production and lactation persistency of Philippine dairy buffaloes using random regressions 159
E.B. Flores and J.H.J. van der Werf 
The prediction of genetic structure of East African smallholder 163
W.M.S.P. Weerasinghe, C. Gondro, M.G. Jeyaruban, O. Mwai, D. F. Mujibi and J.P. Gibson 
The fecb mutation increases lamb production in smallholder subsistence flocks in Maharashtra state of India 167
C. Nimbkar, R.S. Kataria, B.P. Mishra, B.K. Joshi and P.M. Ghalsasi 
Accuracy of genomic predictions in Nellore beef cattle 171
R. Carvalheiro, J. C. McEwan, H.H.R. Neves, Y.T. Utsunomiya, A.M. Pérez O´Brien, S. A. Boison, J. Sölkner, F.S. Schenkel, C.P. Van Tassell, T.S. Sonstegard and J.F. Garcia 
Animal Health
The impact of genomic selection on genetic gain in the New Zealand sheep dual purpose selection index 175
N.K. Pickering, K.G. Dodds, B. Auvray and J.C. McEwan 
Comparison of the power of pooled genotyping strategies to detect significant SNP effects for flystrike resistance in merino sheep 179
S. Dominik, J.M. Henshall and J. Smith 
Inheritance of flystrike recorded in a non-seasonal rainfall environment 183
T.L. Bird-Gardiner, D.J. Brown, J.L. Smith and S.I. Mortimer 
The effect of breed, ewe age and season on tick counts of indigenous and commercial sheep in South Africa 187
J.J.E. Cloete, S.W.P. Cloete, A.J. Scholtz and S. Matthee 
Improving facial eczema tolerance in New Zealand dairy cattle 191
N.G. Cullen, P.R. Beatson, R.T. Courtney and C.A. Morris 
Whole genome association analysis of susceptibility to paratuberculosis in New Zealand dairy cattle 195
R.G. Sherlock, S. Loker, P.J. Back, H. Voges, and R.J. Spelman 
Genetic evaluation for resistance to metabolic diseases in Canadian Holsteins 199
F. Miglior, A. Koeck, J. Jamrozik, D.F. Kelton4 S. Loker, K. Stachowicz and F.S. Schenkel 
Bovine neuronal ceroild lipofusinosis in Australian Devon cattle 203
H. Okazaki, E. Jonas, P.C. Thomson and I. Tammen 
Genomic Selection - accuracy
Accuracies of genomic predictions in US beef cattle 207
M. Saatchi and D.J. Garrick 
Accuracy of Igenity direct genomic values in Australian Angus 211
V. Boerner and D. J. Johnston 
Will sequence SNP data improve the accuracy of genomic prediction in the presence of long term selection? 215
I.M. MacLeod, B.J. Hayes and M.E. Goddard 
Accuracy of genomic prediction from multi-breed sheep reference population 220
N. Moghaddar, A.A. Swan and J.H.J. van der Werf 
Using male performance to improve genomic selection for female fertility in Brahman cattle 224
Y.D. Zhang, D.J. Johnston, S. Bolormaa, A. Reverter, M.R.S. Fortes and B. Tier 
Implications of genetic architecture on the efficacy of genomic selection 229
F.S. Hely, S.A. Clark and P.R. Amer 
The impact of measuring adult fleece traits with genomic selection on economic gain in Merino selection indexes 233
A.A. Swan and D.J. Brown 
Genetic relationships between lamb survival and meat traits 237
F.D. Brien, D.L. Rutley, S.I. Mortimer and J.E. Hocking Edwards 
Genetic parameters for body weight, carcass and wool traits in Dohne Merino 241
L. Li, D.J. Brown and J.S. Gill 
Estimates of heritability for colour CIE a* measurements at four time points for chill 245 aged lamb 245
M.J. Bixley, J.C. McEwan, W.E. Bain, E. Young, N.J. McLean and P.L. Johnson 
Genetic associations of early growth and ultrasound scanned traits in several beef breeds 249
M.G. Jeyaruban and D.J. Johnston 
Selection opportunities from using abattoir carcass data 253
E. Wall, M. Coffey and T. Pritchard 
Genomic Selection - relationships
Comparison of measures of relatedness using pedigree or genomic data in a multi-breed 257 sheep population 257
B. Auvray and K.G. Dodds 
Comparisons of identical by state and identical by descent relationship matrices derived from SNP markers in genomic evaluation 261
S.A. Clark, B.P. Kinghorn and J.H.J. van der Werf 
A study on effects of family and haplotype blocks on conservation of gene expression 266 traits in half sib sheep families 266
H.A. Al-Mamun, Paul Kwan, Ross L. Tellam, James W. Kijas and Cedric Gondro 
Utility of graphics processing units for dense matrix calculations In computing and inverting genomic relationship matrices 270
Karin Meyer and Bruce Tier 
Breeds of New Zealand sheep - as recorded or by genomic prediction 274
K.G. Dodds, S.-A.N. Newman, B. Auvray and J.C. McEwan 
Success rates of commercial SNP based parentage assignment in sheep 278
A. M. Bell, J.M. Henshall, S. Gill, K. Gore and J.W. Kijas 
Novel phenotyping techniques for enhancing genetic and genomic predictions of traits 282 that are difficult to measure in grazing livestock 282
I.W. Purvis, P. Valencia, L. Overs and P.L. Greenwood 
Phenotypic associations between methane production traits, volatile fatty acids and 286 animal breeding traits 286
R.M. Herd, S.H. Bird, K.A.Donoghue, P.F. Arthur and R.F. Hegarty 
Preliminary genetic parameters for methane production in Australian beef cattle 290
K.A. Donoghue, R.M. Herd, S.H. Bird, P.F. Arthur and R.F. Hegarty 
A potential practical system to estimate pasture intake of individual animals 294
D.J. Cottle 
Accuracy of genomic prediction for residual feed intake in a multi-breed cattle population 298
M. Khansefid, J.E. Pryce, S.P. Miller and M.E. Goddard 
Genetic solutions to improve resource efficiency in dairy cattle 303
Y. de Haas, J.E. Pryce, J. Dijkstra, E. Wall and R.F. Veerkamp 
Industry 2
Female, male and genomic measures for use in genetic selection to improve lifetime weaning rate of Brahman cattle 307
S.A. Barwick, D.J. Johnston, R.G. Holroyd, J.R.W. Walkley and H.M. Burrow 
Liveweight loss in adult ewes is affected by their sires breeding values for fat and muscle 311
S.E. Blumer, G.E. Gardner, M.B. Ferguson and A.N. Thompson 
Genetics of body condition score and its relationship with fertility, milk and survival in Australian Holstein cattle 315
M. Haile-Mariam, R. Butler and J.E. Pryce 
Productive and genetic differences between cows managed organically or conventionally 319
J.G. García-Muñiz, N. Lopez-Villalobos, R.G. Sherlock, N. Martin, C.W. Holmes and N.M. Shadbolt 
Genotype by environment interactions for average daily gain using multiple-trait analyses in Australian pigs 323
L. Li and S. Hermesch 
Investigating the genetics of culling time and the effects of feeding level on osteochondrosis in sows 327
E.M. van Grevenhof, H.C.M. Heuven, D.B. de Koning, W. Hazeleger and B.J. Ducro 
Stayability to consecutive calvings as a measure of longevity In Canadian Simmentals 331
J. Jamrozik and S.P. Miller 
'Deer improvement' - genetic selection in a recently domesticated livestock species 336
B. Gudex, D. Johnson, D. Ford, T. Benton and J. Chardon 
Genomic Selection - techniques
Prediction of genomic breeding values across genetic groups 340
J.H.J. van der Werf, D.J. Brown and A.A. Swan 
Sequencing and genotyping for the whole genome selection in Canadian beef 344 populations 344
K. Stachowicz, S. Larmer, J. Jamrozik, S.S. Moore and S.P. Miller 
Use of high density genotyping and trait-dependent methods in genome-assisted evaluations 348
J.A. Jiménez-Montero, D. Gianola, K. Weigel, R. Alenda and O. González-Recio 
Application of whole genome sequence technology to dairy cattle breeding by LIC 352
M. Keehan, A. Scott, T. Lopdell, T. Johnson and R. Spelman 
Preliminary analysis of intensity signals from SNP data based on pooled DNA samples in beef and poultry 356
A. Reverter, J. Henshall, R. McCulloch, R. Hawken and S.A. Lehnert 
A genomic prediction cross-validation approach combining ewe repeated phenotypes and ram daughter trait deviations 360
H.D. Daetwyler, S. Bolormaa1, D. J. Brown, J.H.J. van der Werf and B. J. Hayes 
The extent and distribution of linkage disequilibrium in extensively raised chicken populations of southern Africa 364
K.S. Khanyile, E.F. Dzomba and F.C. Muchadeyi 
Microrna profiling in cattle divergently selected for residual feed intake 368
W. AL-Husseini, C. Gondro, R.M. Herd, J.P. Gibson, P.F. Arthur and Y. Chen 
Genome-wide epistasis association of ultrasound-scanned carcass traits in beef cattle: 372 two-stage models 372
A.A. Ali, M.S. Khatkar, H.N. Kadarmideen and P.C. Thomson 
Rumen differences between sheep identified as being low or high emitters of greenhouse gas 376
W.E. Bain, L Bezuidenhout, N.B. Jopson, C.S. Pinares-Patino and J.C. McEwan 
Genetic trends in a Merino line selected for a reduced fibre diameter relative to an 377 unselected control flock 377
S.W.P. Cloete, J.J. Olivier and E. du Toit 
Genetic parameters for slaughter and meat traits in ostriches 381
A. Engelbrecht, S.W.P. Cloete, K.L. Bunter, J.B. van Wyk and L.C. Hoffman 
Comparing genomic relationship matrices with relationship estimated from pedigree data 385
M.M. Farah, M.R.S. Fortes, L.R. Porto-Neto, C.T. Meira, M. Kelly, L.O.C. Duitama, A.V. Pires, R. Fonseca and S.S. Moore 
Genetic markers associated with male reproductive traits across 2 beef cattle breeds: Brahman and Tropical composite 389
M.R.S. Fortes, A. Reverter, L.R. Porto Neto, M. Kelly, S.S. Moore and S.A. Lehnert 
Genetic parameters for staple strength and coefficient of variation of fibre diameter in Merino wool of different staple length 393
J.C. Greeff and A.C. Schlink 
Dogs can differentiate between odours from sheep that are resistant or susceptible to breech strike 397
J.C. Greeff, A. Biggs, W. Grewar, P. Crumblin, L.J.E. Karlsson, A.C.Schlink and J. Smith 
The role of AI in genetic progress - new opportunities from new technologies and new approaches 401
R.E. Green, P.R. Amer and P.F. Fennessy 
In-silico approach identified polymorphism associated with wool traits in sheep 405
E. Jonas, P.C. Thomson and H.W. Raadsma 
Fibre diameter corrected wool clean colour - the impact on genetic parameters 408
A.Jones and S.Hatcher 
Partitioning the genetic variance into genomic and pedigree components for parasite resistance in sheep 412
M. Al Kalaldeh, J.P. Gibson, J.H.J. van der Werf and C. Gondro 
Managing cost of phenotyping 416
Cécile Massault, Brian Kinghorn and Julius van der Werf 
A genome-wide association study for height at withers in racing quarter horse 420
C.T. Meira, M.R.S. Fortes, M.M. Farah, L.R. Porto-Neto, R.A. Curi, S.S. Moore and M.D.S. Mota 
Post-estimation penalization: more 'PEP' for estimates of genetic covariance matrices 424
Karin Meyer 
Penalized estimation of covariance matrices with flexible amounts of shrinkage 428
Karin Meyer 
A new approach to connect between multi-trait mixed model and principal component analysis for describing variation in carcass quality of crossbred cattle 432
H.R. Mirzaei and W.S. Pitchford 
The milk fatty acid composition and conjugated linoleic acid content of Jersey and Fleckvieh x Jersey cow milk in a pasture based feeding system 435
C.J.C. Muller, B. Sasanti, S. Abel and A. Schmulian 
Reproductive performance of Holstein and Fleckvieh x Holstein heifers and cows in a total mixed ration feeding system 439
C.J.C. Muller, J.P. Potgieter, S.W.P Cloete, and J.A. Botha 
The beef production of a Jersey herd as affected by crossbreeding using Fleckvieh sires 443
C.J.C. Muller, S. Goni, K. Dzama and J.A. Botha 
A preliminary study on breed differences in susceptibility of sheep to Mycotoxin sporidesmin 447
S.H. Phua, H. Henry and K.G. Dodds 
Genetic origin of Arapawa sheep and adaptation to a feral lifestyle 451
N.K. Pickering, E.A. Young, J.W. Kijas, D.R. Scobie and J.C. McEwan 
Composite signatures of directional selection identified multiple genes for stature on bovine chromosome 13 and 14 455
I.A.S. Randhawa, M.S. Khatkar, P.C. Thomson and H.W. Raadsma 
Genetic analysis of absence of breech strike and breech strike indicator traits in South African Merino sheep 459
A.J. Scholtz, S.W.P. Cloete, J.B. van Wyk and E. du Toit 
Using cross-validation in a fast EM algorithm for genomic selection and complex trait prediction 463
R.K. Shepherd, M.J. Drumm and J. Yang 
Post-weaning growth in beef and dairy crossbred steers 467
C.G. Vazquez, R.E. Hickson, S.T. Morris, N. Lopez-Villalobos, P.R. Kenyon and J.G. García-Muñiz 
Updates to the New Zealand national breeding objective for dairy cattle 471
P.R. Amer, B. Santos, T.J. Byrne, C. Ludemann, B. Visser, B.L. Harris, and J. Bryant 
Deriving economic values for reaction norms of growth in pigs 475
S. Hermesch and P.R. Amer 
The economic value of body condition score in New Zealand seasonal dairying systems 479
T.J. Byrne, B. Santos, P.R. Amer, and J.R. Bryant 
Economic weights for maternal pig traits in Australia motivate genetic improvement for robustness 483
C.I. Ludemann, P.R. Amer and S. Hermesch 
Economic impact of changes to the breeding objectives used within the New Zealand 487 beef breeding industry 487
J.A. Sise, T.J. Byrne, M.J Young and P.R. Amer 
Heritability of track condition affinity in the Australian thoroughbred racing population 491
B.D. Velie, N.A. Hamilton and C. M. Wade  
Genomic Selection - trait associations
Genome wide association study using the ovine SNP50 beadchip and lambs selected for extremes for carcass lean meat yield 495
P.L. Johnson, T.C. Van Stijn, H. Henry, N.J. McLean and M. Lee 
Genomic regions associated with differences in fat percentage in milk between Holstein and Jersery cattle 499
K.E. Kemper, B.J. Hayes and M.E. Goddard 
Searching for SNPs that affect sheep robustness: cyp17 SNP affects behavioural responses to psychological stress 503
D. Hough, P. Swart, J.J.E. Cloete and S.W.P. Cloete 
Association Study Verifies a Major Locus for Fleece Diameter on OAR 25 in Sheep 507
H.W. Raadsma, E. Jonas and P.C. Thomson 
A binary classifier using SNP data for prediction of phenotypic outcomes in Hanwoo (Korean) cattle 511
D.C. Detterer, S.H. Lee, P. Kwan and C. Gondro 
Multi-trait QTL mapping in beef cattle 515
S. Bolormaa, J.E. Pryce, A. Reverter, Y.D. Zhang, W. Barendse and M.E. Goddard 
Animal Breeding and Genetics Techniques
Handling a subset of a large dairy industry dataset for quantitative genetic analyses of extended lactation traits in Australian dairy cattle 519
M. Abdelsayed, H.W. Raadsma and P.C. Thomson 
Sampling based approximation of confidence intervals for functions of genetic covariance matrices 523
Karin Meyer and David Houle 
A preliminary evaluation of a method for incorporating genetic information into phenotypic prediction models 527
B.J. Walmsley, B.P. Kinghorn, V.H. Oddy, M.J. McPhee and W.A. McKiernan 
Improved reporting method for genetic connectedness 531
B. Visser, T.J. Byrne, M.J. Young and P.R. Amer 
A method for maximising average flock reproduction by optimising culling policies across age groups 534
.S. Richards, K.D Atkins, B.P. Kinghorn and J.H.J. van der Werf 
Genetic control of residual variance for teat number in pigs 538
M. Felleki and N. Lundeheim 
Genomic Selection - imputation
Across- and within-breed imputation across several genotyping densities in dairy and beef cattle 542
D.P. Berry, M.P. Mullen and A.R. Cromie 
Effect of genotype and pedigree error on detection of recombination events, sire imputation and haplotype inference using the hsphase algorithm 546
Mohammad H. Ferdosi, Brian P. Kinghorn, Julius H.J. van der Werf and Cedric Gondro 
Accuracy of imputation in a population of tropical composite cattle with particular emphasis on the use of allelic r2 as a quality control metric 550
M. Kelly, M.R.S. Fortes and S.S. Moore 
Utility of imputed SNP genotypes for genome-wide association studies in dairy cattle 554
M.S. Khatkar, P.C. Thomson and H.W. Raadsma 
How Angus breeders have reduced the frequency of deleterious recessive genetic conditions 558
C.F. Teseling and P.F. Parnell