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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

Papers
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
Reproduction
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
Wool
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 B.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
Population 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
Meat
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, P. Kwan, R.L. Tellam, J.W. Kijas and C. Gondro
Utility of graphics processing units for dense matrix calculations In computing and inverting genomic relationship matrices	270
K. Meyer and B. 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
Efficiency
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
Posters
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
C. Massault, B.P. Kinghorn and J.H.J. 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
Objectives
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
K. Meyer and D. 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
M.H. Ferdosi, B.P. Kinghorn, J.H.J. van der Werf and C. 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