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Inbreeding and Inbreeding Depression in Linebred Beef Cattle (PDF) INBREEDING AND INBREEDING DEPRESSION IN LINEBRED BEEF CATTLE by Jordan Kelley Hieber A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Science MONTANA STATE UNIVERSITY Bozeman, Montana April 2020 ©COPYRIGHT by Jordan Kelley Hieber 2020 All Rights Reserved ii DEDICATION To my family and close friends for their continuous support and countless words of encouragement. To my great papa, great grandma, and grandpa who I know are watching over me and cheering me on from above. ii ACKNOWLEDGEMENTS First and foremost, I must thank Drs. Jennifer Thomson, Jane Ann Boles, and Rachel Endecott for their constant support and friendship since I moved to Montana, and Dr. Elhamidi Hay for his expertise and being a member of my committee. This project also would not have been possible without the funding provided by the Montana State University Montana Agricultural Experiment Station, the United States Department of Agriculture – Agriculture Research Service, and the Montana State University Graduate School. I would like to thank those at the Northern Agricultural Research Center who helped collect data and work cows for my project, especially Dr. Darrin Boss, Julia Dafoe, and Cory Parsons. To my academic “siblings” and fellow graduate students, thank you for all the laughs, support, and shoulders to lean on. I also cannot forget all the amazing faculty and staff within ABB that have provided guidance and given countless words of encouragement. I owe the largest thank you to my support system over the last four years, my family and friends. Thank you for providing an endless amount of support and reassurance throughout this adventure, I love you all! To my boyfriend, thank you for all of your support! You may be a recent addition to my life, but you have provided limitless encouragement. Staying up with me during the late nights means more to me than you’ll know. I love you more! iii TABLE OF CONTENTS 1. INTRODUCTION AND LITERATURE REVIEW ...................................................... 1 Introduction ..................................................................................................................... 1 Inbreeding and Inbreeding Depression in Linebred Beef Cattle ............................ 1 Genetic Improvement with the Carcass Merit Program ......................................... 2 Linebreeding and Heterosis ............................................................................................ 3 Inbreeding and Inbreeding Depression ........................................................................... 5 Effects of Inbreeding on Production Traits ..................................................................... 9 Line 1 and Line 4 Hereford Histories ........................................................................... 10 Line 1 .................................................................................................................... 10 Line 4 .................................................................................................................... 12 Methodology ................................................................................................................. 12 Runs of Homozygosity ......................................................................................... 12 Genome-Wide Association Studies ...................................................................... 14 Carcass Characteristics and Maternal Performance ...................................................... 17 2. INBREEDING LEVELS OF THE LINE 4 HEREFORD CATTLE POPULATION ............................................................................................................. 21 Introduction ................................................................................................................... 21 Materials and Methods .................................................................................................. 22 Results and Discussion ................................................................................................. 26 Conclusions ................................................................................................................... 31 3. INBREEDING LEVELS OF THE LINE 1 HEREFORD CATTLE POPULATION ............................................................................................................. 45 Introduction ................................................................................................................... 45 Materials and Methods .................................................................................................. 46 Results and Discussion ................................................................................................. 50 Conclusions ................................................................................................................... 55 4. IDENTIFICATION OF GENETIC MARKERS AND QTL FOR CARCASS QUALITY TRAITS WITHIN THE AMERICAN SIMMENTAL ASSOCIATION CARCASS MERIT PROGRAM ...................................................... 71 Introduction ................................................................................................................... 71 Materials and Methods .................................................................................................. 72 Results and Discussion ................................................................................................. 75 Single-locus Model ............................................................................................... 75 Multi-locus Model ................................................................................................ 77 Genetic Correlations ............................................................................................. 78 iv TABLE OF CONTENTS CONTINUED Conclusions ................................................................................................................... 79 5. CONCLUDING REMARKS ........................................................................................ 83 REFERENCES CITED ..................................................................................................... 87 APPENDICES ................................................................................................................ 105 APPENDIX A: Line 4 Supplementary Tables and Figures ................................ 106 APPENDIX B: Line 1 Supplementary Tables and Figures ................................ 211 APPENDIX C: American Simmental Association Carcass Merit Program Single-Locus Model Supplementary Tables and Figures ................................................................................ 276 APPENDIX D: American Simmental Association Carcass Merit Program Multi-Locus Model Supplementary Tables and Figures ................................................................................ 319 v LIST OF TABLES Table Page 1. Runs of homozygosity (ROH) locations and number of significant single nucleotide polymorphism (SNP) for each trait in each location ............ 33 2. Strongly significant single nucleotide polymorphism (SNP; located above -log10(p-value) of 5 x 10-4) on a Manhattan plot ................................... 35 3. Runs of homozygosity (ROH) locations and number of significant single nucleotide polymorphism (SNP) for each trait in each location ............ 57 4. Strongly significant single nucleotide polymorphism (SNP; located above -log10(p-value) of 5 x 10-4) on a Manhattan plot ................................... 59 5. Genome-wide association significant markers (located above -log10(p-value) of 5 x 10-8) on a Manhattan plot ............................................. 80 6. Genetic correlations between carcass and maternal traits ................................. 81 vi LIST OF FIGURES Figure Page 1. A heatmap showing relatedness of individuals within the Line 4 population. The dark blue line diagonal line is individuals plotted against themselves and the darkest blue boxes above or below the diagonal represent individuals that are more related ........................................ 36 2. A principle component analysis (PCA) plot containing a scatter plot for individual animals on the first and second principle components .............. 37 3. Number of animals by year of birth between 1964 and 2018, and trend of average pedigree inbreeding (blue line) .............................................. 38 4. Manhattan plot for birth weight (BW). Genome-wide significance threshold was -log10(p-value) of 5 x 10-4 and vertical clusters of markers indicate suggestive QTL ..................................................................... 39 5. Regions of the genome with runs of homozygosity (ROH) on an individual chromosome basis (left side of chromosomes, blue lines) and significant single nucleotide polymorphism (SNP; p < 0.005) for birth weight (BW) identified by regression analysis (right side of chromosomes, red arrows). Height of arrow corresponds to number of consecutive significant SNP ......................................................................... 40 6. Regions of the genome with runs of homozygosity (ROH) on an individual chromosome basis (left side of chromosomes, blue lines) and significant single nucleotide polymorphism (SNP; p < 0.005) for weaning weight (WW) identified by regression analysis (right side of chromosomes, red arrows). Height of arrow corresponds to number of consecutive significant SNP ........................................................................
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