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Investigation of Genomic Regions Affecting Ketosis in Dairy Cattle By Investigation of Genomic Regions Affecting Ketosis in Dairy Cattle by Riani Ananda Nunes Soares A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Animal Biosciences Guelph, Ontario, Canada © Riani Ananda Nunes Soares, September, 2020 ABSTRACT INVESTIGATION OF GENOMIC REGIONS AFFECTING KETOSIS IN DAIRY CATTLE Riani Ananda N. Soares Advisor: University of Guelph, 2020 Dr. E James Squires Co-advisor: Dr. Flavio Schenkel Ketosis is a severe metabolic disease caused by negative energy balance (NEB) that leads to decreased milk production. Thus, the main objectives were to investigate literature information on the genetic background of NEB, subclinical and clinical ketosis through a systematic review and meta-analysis and to identify genomic regions associated with subclinical and clinical ketosis in first and later lactations, and also for subclinical ketosis in two periods in early lactation (5 to 21 DIM and 22 to 45 DIM) by performing genome wide association studies (GWAS). The weighted single-step GBLUP (wssGBLUP) method was used for GWAS to identify genetic regions associated with the traits. The genes identified within the top-20 genomic windows were used for functional analyses. Biological understanding of this metabolic disease will help enhance accuracy of selection in the Canadian dairy cattle breeding programs and help with the development of biomarkers for early diagnosis and prevention of ketosis. iii ACKNOWLEDGEMENTS First, I would like to thank my advisor, Dr. James Squires, who trusted me and gave me the opportunity to pursue my master’s degree in Canada, starting a new chapter of my life. Thank you for always having your door open, for trusting me with new ideas and for making me challenge myself every step of the way. I am tremendous grateful for all your support and for everything I learned from you. I also want to thank the members of my advisory committee, Dr. Flavio Schenkel and Dr. Todd Duffield, for all your help along this journey. I am grateful for having the opportunity to meet Dr. Schenkel. You are an inspiring person and a professional everyone should have as a role model. I appreciate all your support since the first day I went to the Department of Animal Biosciences, even when I needed to have a surgery and your kind words made this process smoother. Thank you for always been available and for being a great person. I can only say thank you one million times to Dr. Giovana Vargas. Without her, I would not be where I am today. You helped me put this thesis together, and you were with me every step of the way, teaching me, giving me advices, cheering for my success, and even sharing our best times in the department. I found an amazing mentor and a great friend. Most of all, thank you for being so patient and for teaching me how to be a better person and a better professional. Dr. Angela Canovas, I am grateful for the opportunity you gave me to be your TA, for making me grow as a researcher, for all the knowledge shared, for the patience, and for helping me to become a better professional. Thank you for the conversations and for the trust placed in me. iv At this time, I can only be grateful, and I can not thank enough the friends I made here and helped me go through the challenges of living abroad. In special, I would like to say thank you to Malane Muniz, Hinayah Rojas, Tatiane Chud, Ivan Campos, Gerson Oliveira, Lucas Alcantara, Pablo Fonseca, Amelia Soares, Samla Marques, Mariana Berton, Bruna Mion, Bianca Kato, Larissa Costa. You were my family in Canada! I also want to express my sincere gratitude to my lab mates, Christine Bone and Jocelyn Cameron, who I had the pleasure of working alongside and to have the best times in the lab and in our trip to Texas. I have learned the best jokes from you! Special thanks to Yanping Lou, for all your help in the lab and for always being available and with a smile on your face. I thank my parents, Rivaldo Soares and Nivani Soares, for all the times they put me first in their lives, abdicating your dreams to give me the opportunity to pursue mine. For allowing me to grow away from you, and even so, to be present even when I was away. You taught me the importance of being an honest person and being tankful for what I have in life. Your trust and love made me get here. I especially thank my mother for always believing in me and for being such a strong woman that makes me want to fight for the best always. To my brothers, Rivaldo Filho and Rian Soares, for forgiving all the absence and for always helping me when I felt lost. Thank you for your unconditional love and support always. It was very difficult to spend so much time away from you. To the Nunes family, for all their understanding and support, believing that one day everything would be all right. You have been my “saudade” for all those years away. Thank you for every encouragement and for every word of motivation, for every time I called crying and you consoled me, for every joke and for every hug in our reunions. With a unique and special way, you helped me on this journey. I know that wherever I go, I will never be alone, because I have you. v I need to acknowledge Shakeel Ashraf for being with me during the best and worst moments of this journey. I am grateful for meeting you here, and for sure you made it more special. Thank you for always encouraging me to seek the best, for rooting for my happiness, for being my best friend and for being my accomplice at all times. To those who were always my companions, Thais Magalhaes, Herbeson Martins, Eden Souza, Jadilson Mariano, Lais Maia, and Verenna Barros, thank you for being part of this achievement. Defying distance, time, and logic, we have become closer than ever. I would also like to thank Felipe Ivo for these seven years of friendship and for never let me feel alone in Canada. It is not possible to give thanks without thanking God. Who gives me the strength to believe and move forward, fighting for my goals and believing in a better future. Thank you for all the opportunities and the signs that made me get where I am, for guiding and protecting me. Finally, I thank all those people who, directly or indirectly, were part of my life during this degree and those who contributed to the accomplishment of this work. vi TABLE OF CONTENTS ABSTRACT .................................................................................................................................... ii2 ACKNOWLEDGEMENTS ............................................................................................................ i3ii TABLE OF CONTENTS ................................................................................................................ v6i LIST OF TABLES .......................................................................................................................... i1x LIST OF FIGURES ........................................................................................................................ x1i LIST OF ABBREVIATIONS ......................................................................................................... xi1 ii CHAPTER ONE: General Considerations ..................................................................................... 1 Introduction ................................................................................................................................. 1 Objectives ................................................................................................................................... 2 Literature Review........................................................................................................................ 3 Overview of Ketosis ............................................................................................................... 3 Ketosis Categorization ............................................................................................................ 4 Etiology and Pathogenesis ...................................................................................................... 5 Epidemiology .......................................................................................................................... 8 Diagnosis and Clinical Findings ............................................................................................. 9 Impact of the disease ............................................................................................................. 11 Treatment .............................................................................................................................. 11 Genetic control of Ketosis .................................................................................................... 14 Genome-wide Association Studies ....................................................................................... 15 Conclusion ................................................................................................................................ 17 References ................................................................................................................................. 17 CHAPTER TWO: Differential gene expression in dairy cows under negative energy balance and ketosis: A systematic review and meta-analysis ........................................................................... 31 Abstract ....................................................................................................................................
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