Application of New Genetic Technologies to Animal Breeding:

Proceedings of the 16th Biennial Conference of the Association for the Advancement of Animal Breeding and Genetics (AAABG) 25-28 September 2005

Edited by Association for the Advancement of Animal Breeding and Genetics
Application of New Genetic Technologies to Animal Breeding
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The 16th Biennial Conference of the Association for the Advancement of Animal Breeding and Genetics (AAABG) gathers together scientists, extension workers, producers and industry personnel to review developments in the application of new technologies to animal breeding. Conference presentations include 30 invited reviews and papers, and 95 contributed papers. All papers are peer-reviewed, and cover session topics that focus on genetic evaluation systems, gene expression profiling, identification and manipulation of quantitative trait loci, progress in applied programs and advanced statistical and computing techniques.

Industry applications are discussed for improvement in production, health and reproduction of domestic livestock, aquaculture species and even crocodiles and ostriches. Institutions and industries in Australia, New Zealand, USA, South Africa, South-East Asia and Japan are represented with significant participation of major Cooperative Research Centres.

These proceedings contain the full text of all contributed papers and summaries of the invited reviews which are published separately in the Australian Journal of Experimental Agriculture.

  1. Page 1
    Keynote Paper
    1. Page 1
      Application and impact of new genetic technologies on beef cattle breeding: a “real world” perspective
      By E. J. Pollak
  2. Page 2
    Genetic Evaluation Systems
    1. Page 2
      Genetic evaluation for the beef industry in Australia
      By H.-U. Graser, B. Tier, D.J. Johnston and S. A. Barwick
    2. Page 3
      Practical aspects of a genetic evaluation system using parentage assigned from genetic markers
      By K.G. Dodds, J.A. Sise and M.L. Tate
    3. Page 4
      Implementing genetic evaluation in the New Zealand deer industry
      By J.A. Archer, J.F. Ward, S-A.N. Newman, G.J. Cruickshank and A.J. Pearse
    4. Page 8
      The alliance central progeny test (CPT): an evaluation of sheep meat genetics in New Zealand
      By A.W. Campbell, N.B. Jopson, N. J. McLean, K. Knowler, M. Behrent, T. Wilson, G. Cruickshank, C.M. Logan, P.D. Muir and J.C. McEwan
  3. Page 12
    Genetic Parameters in Merino Sheep
    1. Page 12
      Genetic relationships between carcass quality and wool production traits in Australian Merino rams
      By J.C. Greeff, G. Cox, L. Butler and M. Dowling
    2. Page 16
      Merino strains with high wool production have lower lifetime reproduction rates
      By J.C. Greeff
    3. Page 20
      Reliability of estimates of correlations between reproduction and production traits from a Merino resource flock
      By M.J. Kelly, A.A. Swan and S. Dominik
    4. Page 24
      Genetic parameters and trends for hogget traits in Merino lines divergently selected for multiple rearing ability
      By S.W.P. Cloete, J.J. Olivier, J.B. van Wyk, S.J. Schoeman and G.J. Erasmus
    5. Page 28
      Analysis of lamb survival in Australian Merinos
      By E. Safari, K.D. Atkins, N.M. Fogarty and A.R. Gilmour
    6. Page 32
      Genetic parameters for ultrasound scan and wool traits at yearling and hogget age in Merino sheep
      By A.E. Huisman and D.J. Brown
  4. Page 36
    Poultry CRC
    1. Page 36
      Chicken functional genomics
      By R.J. Moore, K. Granger, T.M. Crowley, S. Riddell and T.J. Doran
    2. Page 40
      RNA interference as a tool for chicken functional genomics
      By T. Doran, D. Schafer, T. Wise and R. Moore
    3. Page 44
      Application of immunogenomic technologies to poultry: building a better chicken
      By J. W. Lowenthal, A. G. D. Bean, T. J. Doran and R. J. Moore
    4. Page 48
      Immunogenomics in the chicken: innate immune molecule analysis
      By A.G.D. Bean, K.A. Jenkins, A.J. Karpala, S.G. Tyack and J.W. Lowenthal
  5. Page 52
    Cattle and Sheep Growth
    1. Page 52
      Estimates of covariance functions for growth of Angus cattle from random regression analyses fitting b-spline functions
      By Karin Meyer
    2. Page 56
      Reduced rank estimates of the genetic covariance matrix for live ultra-sound scan traits
      By Karin Meyer
    3. Page 60
      Variation among maternal sires for lamb and wool gross margin performance of their crossbred daughters
      By N.M. Fogarty, V. Ingham, L. McLeod, G. Gaunt and L. Cummins
    4. Page 64
      Using assortative matings to maximise sales of homozygous favourable sheep sires, a simulation study
      By P.R. Amer, R.G. Sherlock and M.L. Tate
  6. Page 68
    Young Scientists 1
    1. Page 68
      Dust penetration is not genetically and phenotypically the same trait as dust content: 3 years of data
      By M.E. Dowling, A.C. Schlink and J.C. Greeff
    2. Page 72
      Breeding for body condition score in dairy cows
      By J.E. Pryce, B.L. Harris and W. Montgomerie
    3. Page 76
      Sire breed differences for net feed intake in feedlot finished beef cattle
      By K.L. Moore, D.J. Johnston and H.M. Burrow
    4. Page 80
      Multi-trait selection of crocodiles using CROCPLAN
      By S.R. Isberg, P.C. Thomson, F.W. Nicholas, E.M. Gray, F. Ahmadi-Esfahani, S.G. Barker and C. Moran
    5. Page 84
      Expression of body weight, fleece weight and fibre diameter in across flock genetic evaluation
      By D. J. Brown, K. Atkins and A.E. Huisman
  7. Page 88
    Genomics: The advent of new genetic technologies
    1. Page 88
      Harnessing the bovine genome sequence for the Australian cattle and sheep industries
      By B. P. Dalrymple
    2. Page 89
      Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics
      By A. E. Lew, L. A. Jackson and M. I. Bellgard
  8. Page 90
    Pig Genetics 1
    1. Page 90
      Insulin-like growth factor-I (IGF-I) measured in juvenile pigs is genetically correlated with economically important performance traits
      By K. L. Bunter, S. Hermesch, B. G. Luxford, H.-U. Graser and R. E. Crump
    2. Page 91
      Potential quantitative genetic indicators of pig temperament
      By R.E. Crump, A.C. Hansson, H.-U. Graser and R. Sokolinski
    3. Page 95
      Genetic correlations between juvenile insulin-like growth factor-I (IGF-I) and measures of sow reproductive performance are low
      By K.L. Bunter, C. Bennett and B.G. Luxford
    4. Page 99
      Genetic correlations between the performance of purebred and crossbred pigs
      By S. Nakavisut, R. Crump, M. Suarezand and H-U. Graser
  9. Page 103
    Young Scientists 2
    1. Page 103
      Estimation of the distribution of QTL effects
      By A.J. Chamberlain, T.H.E. Meuwissen and M.E. Goddard
    2. Page 107
      Combining two markov chain monte carlo approaches for linkage and association studies with a complex pedigree and multi marker loci
      By S.H. Lee, J.H.J. Van der Werf and B. Tier
    3. Page 111
      QTL for meat colour and pH in Bos taurus cattle
      By A. Esmailizadeh Koshkoih, W.S. Pitchford, Z.A. Kruk, C.A. Morris, N.G. Cullen, A.M. Crawford and C.D.K. Bottema
    4. Page 115
      A genome scan for quantitative trait loci for resistance to the gastrointestinal parasite Haemonchus contortus in sheep
      By K. Marshall, J. H. J. van der Werf, J.F. Maddox, H-U. Graser, Y. Zhang, S. W. Walkden-Brown and L. Kahn
    5. Page 119
      A study on the association of genotypes at the interferon gamma microsatellite locus with faecal strongyle egg counts in sheep
      By V.S.R. Dukkipati, H.T. Blair, P.L. Johnson, A. Murray and D.J. Garrick
  10. Page 123
    General Issues
    1. Page 123
      Adaptability in tropical beef cattle: genetic parameters of growth, adaptive and temperament traits in a crossbred population
      By K.C. Prayaga and J.M. Henshall
    2. Page 124
      Productive, reproductive and economic performance of dairy cattle in Bangladesh
      By M.K.I. Khan, H.T. Blair, N. Lopez-Villalobos and P.L. Johnson
    3. Page 128
      Calving traits and their relationship with production, conformation and workability traits in Holstein-Friesian cows
      By S. E. McClintock, K. T. Beard and M. E. Goddard
    4. Page 132
      Genetic parameters for reproduction in ostriches
      By S.W.P. Cloete, K.L. Bunter and Z. Brand
  11. Page 136
    Pig Genetics 2
    1. Page 136
      Breeding Robust Pigs
      By Pieter W. Knap
    2. Page 137
      Genetic parameters for characteristics of pork bellies
      By S. Hermesch and J.M. O’Shea
    3. Page 141
      Relationships among temperament and production traits of pigs
      By A. C. Hansson, R. E. Crump, H.-U. Graser and R. Sokolinski
    4. Page 145
      Estimates of genetic parameters for reproductive traits at different parities in Australian hyperprolific Large White sows
      By Matías Suárez, Susanne Hermesch, Jeffrey A. Braun and Hans-Ulrich Graser
    5. Page 149
      Construction of more refined comparative maps for pig chromosomes 9 and 10
      By Jaclyn Aldenhoven, Yizhou Chen and Chris Moran
  12. Page 153
    Gene Expression Profiling for Beef
    1. Page 153
      Molecular And Bioinformatic Strategies For Gene Discovery For Meat Traits; A Reverse Genetics Approach
      By I.J. Hagen, A. Zadissa, J.C. McEwan, B.A. Veenvliet, S.M Hickey, N.G. Cullen, C.A. Morris and T. Wilson
    2. Page 154
      Transcriptional profiling of adult muscle in Japanese Black cattle to identify genes involved with the development of intramuscular fat
      By Y.H. Wang, A. Reverter, H. Mannen, M. Taniguchi, G.S. Harper, K. Oyama, K.A. Byrne, A. Oka, S. Tsuji and S.A. Lehnert
    3. Page 155
      Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data
      By A. Reverter, W. Barris, N. Moreno-Sánchez, S. McWilliam, Y. H. Wang, G. S. Harper, S. A. Lehnert and B. P. Dalrymple
  13. Page 156
    Selection Index and Genetic Progress
    1. Page 156
      Development successes and issues for the future in deriving and applying selection indexes for beef breeding
      By S. A. Barwick and A. L. Henzell
    2. Page 157
      Response to selection for age at puberty in an Angus herd
      By C. A. Morris and N. C. Amyes
    3. Page 161
      “Stocktake” – genetic audit software for Australian seedstock beef producers
      By D. J. Johnston and K.L. Moore
    4. Page 165
      Genetic progress in the T13 Merino breeding program
      By A.A. Swan and I.W. Purvis
    5. Page 169
      Quantifying the selection response using a residual feed intake DNA marker for two Australian breeding objectives
      By B.J Wood, J.H.J. van der Werf and P.F. Parnell
  14. Page 173
    Advanced Statistical Techniques in Genetics
    1. Page 173
      Advances in methodology for random regression analyses
      By Karin Meyer
    2. Page 174
      The use of linkage disequilibrium to map quantitative trait loci
      By M.E. Goddard and T.H.E. Meuwissen
    3. Page 175
      Using mixture models to detect differentially expressed genes
      By G.J. McLachlan, R.W. Bean, L. Ben-Tovim Jones and J.X. Zhu
  15. Page 176
    Sheep CRC and Genomics Program 1
    1. Page 176
      Optimal development of the Australian sheep genetic resources
      By J.H.J. van der Werf
    2. Page 180
      Preliminary genetic parameters for clean fleece weight, fibre diameter, hogget weight and number of lambs born in merinos
      By E. Safari, N.M. Fogarty, A.R. Gilmour, K.D. Atkins, S. I. Mortimer, A. A. Swan, F. Brien, J. C. Greeff and J. H.J. van der Werf
    3. Page 184
      Heritabilities for skin follicle traits and their correlations with production traits in Australian fine wool Merino sheep
      By M. Asadi Fozi, J.H.J. Van der Werf and A.A. Swan
    4. Page 188
      Australian Piebald: incomplete penetrance or incomplete picture?
      By L.D. Brash, J.H.J. van der Werf, Y. Li and B.J. Norris
    5. Page 192
      Observations on white spotting in a Damara x Merino family
      By M.R. Fleet, D.I. Våge, H. Klungland, R.O. Olsen, G.S. Nattrass and M.J. Bennie
    6. Page 196
      Optimising selection on growth and carcase development trajectories in lamb
      By T.M. Fischer and J.H.J. van der Werf
  16. Page 200
    Aquaculture
    1. Page 200
      The Potential of Microarrays to Assist Shrimp Breeding And Production: A Review
      By Kate Wilson and Enrique de la Vega
    2. Page 201
      Rates of inbreeding using DNA fingerprinting in aquaculture breeding programs at various broodstock fitness levels – a simulation study
      By M. Macbeth
    3. Page 202
      Live weight genetic parameters in two production environments in the gift strain of Nile Tilapia (Oreochromis niloticus)
      By R. W. Ponzoni, A. Hamzah, N. Kamaruzzaman and Hooi Ling Khaw
    4. Page 206
      Response to selection in two production environments in the gift strain of Nile tilapia (Oreochromis niloticus)
      By R. W. Ponzoni, A. Hamzah, N. Kamaruzzaman and Hooi Ling Khaw
  17. Page 209
    Sheep CRC and Genomics Program 2
    1. Page 209
      Sheep genomics – core technologies and resources
      By V.H. Oddy, T.J. Longhurst, F.W. Nicholas, J.F. Maddox and M. B. McDonagh
    2. Page 213
      Expression of imprinted genes surrounding the Callipyge mutation in ovine skeletal muscle
      By Tony Vuocolo, Noelle E. Cockett and Ross L. Tellam
    3. Page 214
      Gene expression profiling of ovine skin and wool follicle development using a combined ovine-bovine skin cDNA microarray
      By B.J. Norris, N.I. Bower, W.J.M. Smith, G.R. Cam and A. Reverter
  18. Page 215
    Young Scientists 3
    1. Page 215
      A comparison of different non-genetic models to describe lamb weights when using DNA to assign sire
      By P.L. Johnson and H.T. Blair
    2. Page 219
      The effect of different reproductive technologies on the efficiency of marker assisted introgression in Merino breeding
      By S. Dominik, J.G. O’Grady and J.M. Henshall
    3. Page 223
      The role of selected wether flocks in Merino wool enterprises
      By J.S. Richards and K.D. Atkins
    4. Page 227
      Relationships between LAMBPLAN EBVS for rams and post weaning performance of their crossbred progeny
      By V. M. Ingham, N.M. Fogarty, A.R. Gilmour, D.J. Brown, L.J. Cummins, G.M. Gaunt, J. Stafford and J.E. Hocking Edwards
    5. Page 231
      Breed differences and crossbreeding effects for liveweight traits in Australian meat sheep breeds
      By M. Khusro, D. J. Brown, J.H.J. Van der Werf and H -U. Graser
  19. Page 235
    New Genetic Technologies for Pigs
    1. Page 235
      The potential of new genetic technologies in selecting for stress resistance in pigs
      By C. A. Kerr and B. M. Hines
    2. Page 236
      Westran - highly inbred pigs for xenotransplantation research
      By Chris Moran
  20. Page 237
    QTL in Cattle
    1. Page 237
      The Transition From Quantitative Trait Loci to Diagnostic Test in Cattle and Other Livestock
      By W. Barendse
    2. Page 238
      QTL analyses of growth traits on cattle chromosome 14
      By N. G. Cullen, C. A. Morris, W.S. Pitchford, C.D.K. Bottema, T.R. Manley, B.C. Glass and M.A. Lee
    3. Page 242
      Phenotype definition and the identification of QTL for puberty traits in crossbred dairy cattle
      By L.R. McNaughton, R. Bennett, G. Stanley, S. Harcourt and R.J. Spelman
  21. Page 246
    Young Scientists 4
    1. Page 246
      Associations between plasma concentrations of IGF-1 in young Holstein-Friesian heifers and productive and reproductive parameters in their first lactations
      By T.E. Moyes, S. Humphrys and K.L. Macmillan
    2. Page 250
      Multiple trait linkage across flocks
      By A.E. Huisman, B. Tier and D.J. Brown
    3. Page 254
      South African Merinos divergently selected for multiple rearing ability: a preliminary study of divergence based on rapd markers
      By P. Naidoo, S. W. P. Cloete and A. Fossey
    4. Page 258
      Association of the exon 9 single-nucleotide polymorphism of CAPN1 with beef tenderness
      By A. Esmailizadeh Koshkoih, C.D.K. Bottema, Z.A. Kruk, C.A. Morris, N.G. Cullen, A.M. Crawford and W.S. Pitchford
    5. Page 262
      Analysis of microarrays incorporating adjustments for spatial effects
      By A.F. Woolaston, R. Murison and B. Tier
  22. Page 266
    Dairy Cattle
    1. Page 266
      Review: bovine mammary epithelial cells, initiators of innate immune response to mastitis
      By Christian Gray, Ylva Strandberg, Laurelea Donaldson and Ross Tellam
    2. Page 267
      Quantifying energy balance in crossbred dairy cows
      By B. Harris, J. E. Pryce, L. McNaughton, G Stanley, S. Harcourt and R. Spelman
    3. Page 271
      Hidden costs of dystocia: fertility and long term survival in dairy cows
      By S. E. McClintock, K. T. Beard, M.E. Goddard and D.J. Johnston
    4. Page 275
      Interactions between gestation length, calf size, dystocia and calf mortality
      By S. E. McClintock, K. T. Beard, M.E. Goddard and D.J. Johnston
  23. Page 279
    Cattle and Beef Quality CRC 1
    1. Page 279
      Genetics research in the cooperative research centre for cattle and beef quality
      By H. M. Burrow and B. M. Bindon
    2. Page 280
      Maternal productivity of Angus cows divergently selected for postweaning residual feed intake
      By P. F. Arthur, R. M. Herd, J. F. Wilkins and J. A. Archer
    3. Page 281
      CRC “Regional Combinations” project – effects of genetics and growth paths on beef production and meat quality: experimental design, methods and measurements
      By WA McKiernan, JF Wilkins, SA Barwick, GD Tudor, BL McIntyre, JF Graham, MPD Deland and L Davies
  24. Page 282
    Computing Techniques: Developments and Validations
    1. Page 282
      Ordering strategies to reduce computational requirements in variance component estimation
      By Karin Meyer
    2. Page 286
      Sampling behaviour of reduced rank estimates of genetic covariance functions
      By Karin Meyer
    3. Page 290
      Developments in utilizing pedigrees in genetic analysis within ASReml
      By A. Gilmour
    4. Page 294
      Predicted and observed responses in BLUP estimates of genetic gain
      By J.W. James
    5. Page 298
      Implementing look ahead mate selection
      By R.K. Shepherd
    6. Page 302
      A method that predicts the genetic composition and inbreeding of the future Australian dairy herd
      By M. Haile-Mariam, P.J. Bowman, K. Beard and M.E. Goddard
  25. Page 306
    Breeding and Genetics of Sheep
    1. Page 306
      The influence of ewe weight at mating on lamb performance and reproduction of the ewe
      By D. J. Brown, A. Ball and A. E. Huisman
    2. Page 310
      Genetic parameters for body weight and carcase traits in Australian based south African meat Merino sheep
      By D. J. Brown and M. Asadi Fozi
    3. Page 314
      Age changes in wool traits of Merino sheep in western NSW
      By S. Hatcher, K.D. Atkins and K.J. Thornberry
    4. Page 318
      Inheritance of yarn shrinkage of Merino wool
      By J.C. Greeff, A.C. Schlink and M.E. Dowling
    5. Page 322
      Selection demonstration flocks - what have we learnt?
      By F.D. Brien, K.S. Jaensch, R.J. Grimson, K.E. Kemper, D.H. Smith, M.L. Hebart and A.M.M. Ramsay
    6. Page 326
      The relationship of early lamb growth with ewe age and milk production
      By J. E. Morgan, N. M. Fogarty, S. Nielsen and A. R. Gilmour
  26. Page 330
    Cattle and Beef Quality CRC 2
    1. Page 330
      When pastures limit growth rate of steers those bred for low residual feed intake grow faster
      By R.M. Herd, P.F. Arthur and J.A. Archer
    2. Page 334
      Selection for residual feed intake can change methane production by feedlot steers
      By R.S. Hegarty, R.M. Herd, J.P. Goopy, B. McCorkell and P.F. Arthur
    3. Page 338
      Effect of post weaning growth and bulls selected for extremes in intramuscular fat and retail beef yield on liveweight and carcase traits
      By J.F. Graham, J. Byron, M.P.D. Deland and G Kearney
    4. Page 342
      Effect of time of calving and sire types on growth of progeny to weaning
      By D.M. Read, B.L. McIntyre, E.G. Taylor and G.D. Tudor
  27. Page 346
    QTL: Advanced Statistical Approaches
    1. Page 346
      Selective genotyping for determination of a major gene associated with cranial cruciate ligament disease in the Newfoundland dog
      By P.E. Macrossan, B.P. Kinghorn, V.L. Wilke and M.F. Rothschild
    2. Page 350
      On the power of QTL detection in outbred populations
      By B. Auvray and K.G. Dodds
    3. Page 354
      QTL mapping using logistic regression
      By Yuandan Zhang and Bruce Tier
    4. Page 358
      Constraints to multiple trait major gene models in outbred populations: a wool sheep example
      By J.M. Henshall, S. Dominik and I.W. Purvis
    5. Page 362
      A simple generalisation of Kinghorn’s genotypic probability index
      By Bruce Tier
    6. Page 366
      Limits to genotypic probabilities for single loci
      By Bruce Tier and John M. Henshall
  28. Page 370
    Visions
    1. Page 370
      Integrated and comparative maps in livestock genomics
      By F. W. Nicholas
    2. Page 371
      Animal biotechnologies and their potential impact on animal breeding and production: A Review
      By H. W. Raadsma and I. Tammen
    3. Page 372
      Challenges in investing in genetics and biotechnology for the Australian extensive livestock industries
      By R. G. Banks
  29. Page 373
    Posters
    1. Page 373
      Undesirable biological correlates of sheep with a high genetic value for clean fleece weight
      By N.R. Adams, J.C. Greeff, J.R. Briegel, E.N. Bermingham and S.M. Liu
    2. Page 377
      Fibre diameter and wool growth efficiency estimated from wa wether trials
      By L.G. Butler, M.F. D’Antuono, J.C. Greeff and S.R. Brown
    3. Page 381
      Sire selection for yield or intramuscular fat and beef quality
      By M.P.B. Deland, B. Siebert, J.F. Graham and M. Hebart
    4. Page 385
      Genetic and biological approaches to modulate nematode resistance mechanisms in sheep
      By D.L. Emery and K.J. Beh
    5. Page 389
      Merino breeding values – how do they compare?
      By J.E. Hocking Edwards, N.J. Edwards and T.M. Starbuck
    6. Page 393
      Annotation analysis of a bovine cDNA microarray for expression profiling of muscle and adipose tissue
      By S.M. McWilliam, S.A. Lehnert and A. Reverter
    7. Page 397
      Genetic parameters for physiological characters in Merino ewes in central and north west Queensland
      By Mary Rose and P.M. Pepper
    8. Page 401
      Feltball diameter measurement lacks repeatability over the lifespan of a Merino ewe
      By M.E. Dowling, J.C. Greeff and A.C. Schlink
    9. Page 405
      Delivering new CRC technologies to the northern beef industry
      By R.A. Farrell, V.J. Edmondston, J.D. Bertram, P. Venamore and S. Hudson
    10. Page 409
      The gametic covariance matrix between relatives for a chromosomal segment
      By M. Sargolzaei and H. Iwaisaki

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