Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Genetic basis of lactation and lactation efficiency in pigs Dinesh Moorkattukara Thekkoot Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agriculture Commons, and the Animal Sciences Commons Recommended Citation Moorkattukara Thekkoot, Dinesh, "Genetic basis of lactation and lactation efficiency in pigs" (2014). Graduate Theses and Dissertations. 14217. https://lib.dr.iastate.edu/etd/14217 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genetic basis of lactation and lactation efficiency in pigs by Dinesh Moorkattukara Thekkoot A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Animal Breeding and Genetics (Quantitative Genetics) Program of Study Committee: Jack C. M. Dekkers, Major Professor Max F. Rothschild Dorian J. Garrick Kenneth J. Stalder Kenneth J. Koehler Iowa State University Ames, Iowa 2014 Copyright © Dinesh Moorkattukara Thekkoot, 2014. All rights reserved. ii TABLE OF CONTENTS Page LIST OF FIGURES iv LIST OF TABLES vii ACKNOWLEDGEMENTS xii ABSTRACT xiii CHAPTER 1. GENERAL INTRODUCTION 1 Introduction 1 Dissertation Organization 4 Review of Literature 5 Conclusion 16 Literature Cited 17 CHAPTER 2. ESTIMATION OF GENETIC PARAMETERS FOR TRAITS ASSOCIATED WITH REPRODUCTION, LACTATION AND EFFICIENCY IN SOWS 22 Abstract 22 Introduction 23 Materials and Methods 24 Results 36 Discussion 50 Conclusion 66 Literature Cited 67 Supplementary Materials 72 CHAPTER 3. GENOME WIDE ASSOCIATION ANALYSIS OF SOW LACTATION PERFORMANCE TRAITS IN LINES OF YORKSHIRE PIGS DIVERGENTLY SELECTED FOR RESIDUAL FEED INTAKE DURING GROW-FINISH 84 Abstract 84 Introduction 85 Materials and Methods 86 Results 96 Discussion 106 Conclusion 119 Literature Cited 120 iii Page CHAPTER 4. A GENOME WIDE ASSOCIATION ANALYSIS FOR SOW LACTATION TRAITS IN YORKSHIRE AND LANDRACE SOWS 125 Abstract 125 Introduction 127 Materials and Methods 128 Results 139 Discussion 160 Conclusion 174 Literature Cited 176 Supplementary Material 183 CHAPTER 5. GENOMIC PREDICTION OF TRAITS ASSOCIATED WITH LACTATION IN YORKSHIRE AND LANDRACE SOWS 186 Abstract 186 Introduction 187 Materials and Methods 189 Results 198 Discussion 207 Conclusion 218 Literature Cited 219 Supplementary Material 223 CHAPTER 6. GENERAL DISCUSSION AND CONCLUSIONS 226 Literature Cited 249 iv LIST OF FIGURES Page Figure 2.1. Schematic flow chart of the energy metabolism of sows during lactation (Bergsma et al., 2008; 2009) 31 Figure 3.1. Percentage of genetic variance explained by the top 10 associated windows for pre farrow traits 101 Figure 3.2. Percentage of genetic variance explained by the top 10 associated windows for input traits 101 Figure 3.3. Percentage of genetic variance explained by the top 10 associated windows for output traits 102 Figure 3.4. Percentage of genetic variance explained by the top 10 associated windows for output traits 102 Figure 4.1.Percentage of genetic variance explained by the top 10 associated windows for pre farrow traits in Yorkshire sows 144 Figure 4.2. Percentage of genetic variance explained by the top 10 associated windows for pre farrow traits in Landrace sows (X Chromosome indicated as chromosome19) 144 Figure 4.3. Percentage of genetic variance explained by the top 10 associated windows for input traits in Yorkshire sows 145 Figure 4.4. Percentage of genetic variance explained by the top 10 associated windows for input traits in Landrace sows 145 Figure 4.5. Percentage of genetic variance explained by the top 10 associated windows for output traits in Yorkshire sows 146 v Page Figure 4.6. Percentage of genetic variance explained by the top 10 associated windows for output traits in Landrace sows 146 Figure 4.7. Percentage of genetic variance explained by the top 10 associated windows for efficiency traits in Yorkshire sows 147 Figure 4.8. Percentage of genetic variance explained by the top 10 associated windows for efficiency traits in Landrace sows 147 Figure 4.9. Scatter plot of genomic estimated breeding values from the Bayes B method for Litter weight gain (LWG) estimated for parity 2 Yorkshire sows using information from the 1 Mb window located at 44 Mb on chromosome 2 152 Figure 4.10. LSmeans by parity for sow pre-farrow traits for genotypes of the tag SNP on chromosome 2 for Yorkshire and Landrace sows; within parity, bars with different letters are significantly different at P < 0.05 154 Figure 4.11. LSmeans by parity for sow input traits for genotypes of the tag SNP on chromosome 2 for Yorkshire and Landrace sows; within parity, bars with different letters are significantly different at P < 0.05 154 Figure 4.12. LSmeans by parity for sow output traits for genotypes of the tag SNP on chromosome 2 for Yorkshire and Landrace sows; within parity, bars with different letters are significantly different at P < 0.05 155 Figure 4.13. LSmeans by parity for sow lactation efficiency traits for genotypes of the tag SNP on chromosome 2 for Yorkshire and Landrace sows; within parity, bars with different letters are significantly different at P < 0.05 155 vi Page Figure 4.14. Progression of body weight, back fat and loin depth from off test date to weaning in third parity for Yorkshire and Landrace sows 157 Figure 4.15. LSmeans by parity for sow reproduction traits for genotypes of the tag SNP on chromosome 2 in Yorkshire and Landrace sows 159 vii LIST OF TABLES Page Table 2.1. Number of farrowing records by breed and parity 25 Table 2.2: Traits studied, abbreviations and measurement units 26 Table 2.3. Imaginary situation to explain piglet load 33 Table 2.4. Descriptive statistics of the traits studied by breed; standard deviations in parentheses 37 Table 2.5. Estimates of heritability (parity1, 2 and overall), permanent environment effects (proportion of phenotypic variance) and genetic correlations for the same trait measured in parity 1 and 2 in Yorkshire sows; Standard errors in parentheses 38 Table 2.6. Estimates of heritability (parity1, 2 and overall), permanent environment effects (proportion of phenotypic variance) and genetic correlations for the same trait measured in parity 1 and 2 in Landrace sows; Standard errors in parentheses 39 Table 2.7. Estimates of correlations between traits for Yorkshire sows; genetic correlations above diagonal, phenotypic correlations below diagonal, SE in parentheses; bold printed correlations differ from zero (p<0.05) 40 Table 2.8. Estimates of correlations between traits for Landrace sows; genetic correlations above diagonal, phenotypic correlations below diagonal, SE in parentheses; bold printed correlations differ from zero (p<0.05) 42 Table 2.9. Estimates of genetic correlations between lactation traits in parity 1 and reproductive traits in parity 2; bold printed correlations differ from zero (p<0.05) 49 viii Page Table 2.10. Estimates of genetic correlations between economically important traits and indicator traits in Yorkshire sows; bold printed correlations differ from zero (p<0.05) 50 Table 2.11. Estimates of genetic correlations between economically important traits (ERTs) and indicator traits in Landrace sows; bold printed correlations differ from zero (p<0.05) 50 Table 3.1. Number of genotyped sows with reproductive records by generation, parity and line 88 Table 3.2. Traits analyzed, abbreviations used and measurement units 89 Table 3.3. Number of observations (n) and means (standard deviation in parenthesis) by parity 97 Table 3.4. Number of observations (n) and LSmeans (SE in parenthesis) by line 98 Table 3.5. Estimates of marker based and pedigree based heritability (SE in parenthesis) 99 Table 3.6. Percentage of genetic variance explained by the 1 Mb window with the largest effect for each trait and parity 100 Table 3.7. Total proportion of genetic variance explained by the selected windows for different traits and parity 103 Table 3.8. 1 Mb windows that explained more than 1.5% of genetic variance within each trait category by parity 104 Table 3.9. Candidate genes and previously reported QTLs for traits associated with growth, feed intake, metabolism and milk production 105 ix Page Table 3.10. 1 Mb windows explaining more than 1.5% of genetic variance within each trait category when line (high and low RFI) was excluded from the model 107 Table 4.1. Number of sows genotyped and farrowing records available by breed and parity 128 Table 4.2: Traits studied, abbreviations and measurement units 133 Table 4.3. Number of observations (n) and means (standard deviation in parenthesis) by breed 140 Table 4.4. LSmeans (SE in parenthesis) by parity for Yorkshire and Landrace sows 141 Table 4.5. Estimates of marker based and pedigree based heritability (SE in parenthesis) 142 Table 4.6. 1 Mb windows that explained the highest percentage of genetic variance within each breed, parity and trait category 150 Table 4.7. Candidate genes and previously reported QTL for traits associated with growth, feed intake, metabolism and milk production 151 Table 4.8. Distribution of the genotype of the tag SNP by breed and parity 151 Table 5.1. Number of sows genotyped and farrowing records available by breed and parity 190 Table 5.2. Traits studied, abbreviations and measurement units 191 x Page Table 5.3. Number of sows genotyped and farrowing records by breed and parity for sows in the training and validation sets 192 Table 5.4. Estimates of heritability (Parity 1 and across three parities) from single trait pedigree based animal model analysis; standard error in parenthesis 199 Table 5.5.