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Using Variation in Cattle Growth to Develop a Predictive Model Of IJsing variation in cattle growth to develop a predictive model of carcass quality By Hamid Reza Mirzaei A thesis submitted to the University of Adelaide in total fulfilment of the requirements of the degree of Doctor of Philosophy fHI Uf'lruEfiSlTY $F AÐËLflNË ÂIJSTf,ÅLåA Disciptines of Animal Science and Biometrics The Llniversity of Adelaide Decemberr 2004 In the Name of Allah' the Most Beneficent, the Most Merciful. Read: in the name of your Lord who created. He created man from something which clings. Read and your Lord is the most Sienerous. Who taught with pen. Taught man what he knew not"'r' (The Holv Qur'an 96:1-5) Dedication First of all, most impofiantly,I am very much grateful to my Lord (Allah),who granted me so many things. He provided me the good genes and environment so I can make better use of life in this universe- I dedicate this study to the memory of all the people in my home countty that so generously allowed me to continue my study abroad. Also, this thesis is dedicate d to my parents who have supported me all the way since the beginning of my studies. and with all my love to ......my wfe my son, Ali my son, Reza. You øll keeP mY sPirit alive! o Lord! Benefit me through knowledge that You have bestowed on me, teach me whatever would benefit me' and increase my knowledge. My Lord, save me from the useless knowledge' 1 Table of Contents Dedication ....................1 Table of Contents.......... .. ... .. .. .... ...ii List of abbreviations ,.... ...................v List of Figures ............,.. ...vll List of Tables ................ ....ix Declaration ....xi Acknowledgments...... ...xii Abstract ..xiv 1 Chapter One: Introduction and review of literature ' 1 1. 1 Introduction....,......,..... 4 1.2. Review of literature..., 4 | .2.l . Y ariability in the growth traits . '. '. .. Pre-weaning growth pattern (Birth to weaning) "' "" "" "" 5 Post-weaning growth pattem (weaning to slaughter) """"""' 8 I.2.2.Yanability in the carcass quality traits.....'... 5 24 1.2.3. Relationships between growth and carcass quality traits...... t.2.4. Tecl-niques for describing variability in growth and carcass quality Random regression model (RRM) Principal component analysis (PCA) 1.3. Research questions......','.."..' 1.4. Thesis overview Chapter Two : Materials and methods.... 2.I. The Southern Crossbreeding Proj ect 2.2. Explor atory data analYsis 2.2.I. Live body weights....' 2.2.2. Carcass traits ......,.. chapter Three : Describing variation in growth using principal component analysis.6T 3.1. lntroduction.........,.... ...........67 ...........68 3.2, Statistical method..... J.J. Results..... ...........72 ...........78 3.4, Discussion 80 3.5 Conclusion 11 Chapter Four : Describing variation in carcass quality using principal component analysis..,.. ............81 4. 1 . Introduction......... ...,...,....81 4.2 Statistical method ............82 4.2 Results ............83 4.3 Discussion............ ............92 4.4 Conclusion .......... ............95 Chapter Five : Random regression models of growth ............96 ............96 5. 1 . Introduction...,.,... 5.2 Statistical method ............97 5.3. Results................ ..........103 5.4. Discussion........... ,..........1r2 5.5. Conclusion .......... ,..........72r Chapter Six : Multivariate models for analysis of carcass quality raits ..t22 6. I . Introduction......... ..t22 6.2. Statistical method ..t22 6.3. Results.........,...... ..t23 6.4. Discussion........... ..t32 6.5. Conclusion .......... ,..t39 6.6. Connection between multi-trait mixed model and PCA ,..140 Chapter Seven: Joint modeling of growth and carcass quality""""' ,..144 ...144 7. 1. lntroduction......... 7,2. Statistical method ...144 7.3. Results................ ...150 7.4. Discussion........... ...r54 7.5. Conclusion .....,.... ...155 Chapter Eight:Conelation between carcass quality and growth characteristics ...t57 ...157 8. 1. lntroduction......... 8.2. Statistical method ....t57 8.3. Results................ ....159 8.4. Discussion.........., ....163 8.4.1. Pre-weaning correlations between body weights and carcass traits """' ....163 8.4.2. Post-weaning correlations between body weights and carcass traits...... ....167 111 8.4.3. Correlations between RGR and carcass quality traits ........169 8.5. Conclusion .......... ........t7r chapter Nine: Predicting carcass quality: testing and critiquing the model ........172 9. 1 . Introduction......... ........172 9.2.The Model ........173 9.3. Implementation of the model ........116 9.5. Evaluation of the model ........180 9.5. 1. Experiment 9. 1....... ........180 9.5.2. Experiment 9.2. ...... ........189 9.6. Discussion........... ........195 9.7. Conclusion .......... ........203 Chapter Ten : Random regression models of growth - Piecewise linear regression .204 I 0. 1. lntroduction......... .................204 1 0.2 Statistical method .................205 1 0.3. Results............... .................209 10.4. Discussion: .,',,....'.....,.2|2 10.5. Conclusion .................2r3 Chapter Eleven : Concluding remarks .................215 1 1. 1. tntroduction....... .................215 1 1.2. Conclusion... .................2r5 1I.2.I. Describing variation in growth .................216 I12.L a) using principal component analysis 2t6 llzJ b) random regression models of growth.... 217 ll.2.l. c) Piecewise random regression model"." .219 112.2. Describing variation in carcass quality .2r9 ll.2.2. a) using principal component analysis.'...'. .2t9 11,2.2. b) using multivariate models... .221 I1.2.3. Joint modeling of growth and carcass quality .22r Reference List ........ 229 Appendices............. 252 IV List of abbreviations o/ /o percentage fuqARG The Association for the Advancement of Animal Breeding and Genetics genetic parameter data base Age First order of age (linear) Ag"' Second order of age (quadratic) Agr' Third order of age (cubic) BW Birth weight c' Maternal heritability (genetic * maternal permanent environmental) CV Coeffi cient of variation d days df Degrees of freedom EMA eye muscle area h2 Additive (direct) heritabilitY HCWt Hot carcass weight (kg) IMF Intramuscular fat (o/o) kg Kilogram Ln Natural logarithm Log Logarithm Mg Management P8 Rump (PS) fat depth (mm) PC1 The first principal comPonent PC2 The second principal comPonent PC3 The third principal component PCA Principal component analYsis PE P ermanent environmental PWG Pre-weaning gain (kg/d) PWG Post-weaning gain (kg/d) I r Correlation coefficient I I f¡,vt¡,,w Correlations between body weight and EMA i REML Restricted Maximum Liklihood I V RGR Relative growth rate (%ld) fHCwt,w Correlations between body weight and HCWt fltr¡r,w Correlations of body weight and IMF fp8,w Correlations of body weight and P8 RRM Random regression model SD Standard deviation Slage Slaughter age V.P. Variance parameters TE Temporary environmental Vr Additive genetic variance Vc Dam genetic variance Vo Dominance genetic variance Vr Epistatic genetic variance Vrrlg Management variance Vp Phenotypic variance Vs Sire variance wr Weight (kg) I ww Weaning weight (kg) YG Yearling (365 d) gain (kg/d) YW Yearling (365 d) weight (kg) { v1 List of Figures Page Figure 2.1Therelationship between climate (rainfall and temperature), herbage mass and digestibility of nutrition þasture growth) at Struan (1994- 1996) (GrassGro, version 2.4.1) 52 Figure 2.2 Boxplot of live body weights of steers (top) and heifers (bottom) at different ages from birth to slaughter 55 Figure 2.3 Scatter plot matrix of live weights of steers (top) and heifers (bottom) at different ages from birth to slaughter 57 Figure 2.4 Scatter plot matrix of age, actual body weights and log body weights of steers (top) and heifers (bottom) 58 Figure 2.5 Points of P8 (left) and eye muscle area (right) measurements 59 Figure 2.6 Box plot of carcass quality traits for steers and heifers 6l Figure 2.7 Scatter plot matrix of carcass quality traits for steers (top) and heifers (bottom) 62 Figure 3.1 The eigenvector plot of PC2 vs PCl for heifers (left) and steers (right) 74 Figure 3.ZManagement gfoups biplot of PC2 vs PCI for heifers (left) and steers (righti, 4 0994),5 (1995), 6 (1996),7 (1,997),w (Wandilo), s (Struan), 1 (post weaning group 1), 2 þost weaning group 2), 3 þost weaning group 3) 76 Figure 3.3 Breed biplot ofPC2 vs PCl for heifers (left) and steers (right) 77 Figure 4.1 The eigenvectors biplot for heifers (left) and steers (righÐ 85 Figure 4.2.Management groups biplot of principal components for heifers (left) and steers (right)' For definition of s¡'mbols see Figure 3'2 89 Figure 4.3 Breed biplot of principal components for heifers (left) and steers (right) 9T Figure 5.1 Scatter plot of fitted vs fitted and fitted vs observed body weights from sire and animal models 105 Figure 5.2 Actual and predicted weight-age curves for heifers (top) and steers (bottom) 106 Figure 5.3 Growth curves (birth to slaughter) for seven crossbreeds derived from the growth model 107 Figure 5.4 Deviation of estimated body weight of six crossbreds from purebred Hereford 108 Figure 5.5 Average growth rate of breeds utilizing first derivatives of estimated coefficients of mean and slopes against time 109 Figure 5.6 Variance components for sire, dam, permanent environmental and management gtoups effects at different ages derived from the sire growth model 111 Figure 5.7 Estimates of additive and matemal heritabilities at different ages r1.2 Figure 5.8 Estimates of additive and dam heritabilities over time 110 Figure 6.1 Median and confidence intervals
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