HINAYAH ROJAS DE OLIVEIRA GENETIC AND GENOMIC ANALYSES OF LONGITUDINAL TRAITS IN DAIRY CATTLE Thesis presented to the Animal Science Program of the Universidade Federal de Viçosa, in partial fulfillment of the requirements for degree of Doctor Scientiae. VIÇOSA MINAS GERAIS – BRAZIL 2018 Ficha catalográfica preparada pela Biblioteca Central da Universidade Federal de Viçosa - Câmpus Viçosa T Oliveira, Hinayah Rojas de, 1989- O48g Genetic and genomic analyses of longitudinal traits in dairy 2018 cattle / Hinayah Rojas de Oliveira. – Viçosa, MG, 2018. xvii, 250f. : il. (algumas color.) ; 29 cm. Texto em inglês. Inclui apêndice. Orientador: Fabyano Fonseca e Silva. Tese (doutorado) - Universidade Federal de Viçosa. Inclui bibliografia. 1. Bovinos de leite - Genética. 2. Expressão gênica. 3. Leite - Produção. 4. Lactação. 5. Análise de regressão. I. Universidade Federal de Viçosa. Departamento de Zootecnia. Programa de Pós-Graduação em Zootecnia. II. Título. CDD 22. ed. 636.2142 To all people from the “coca-cola” generation. I dedicate. ii ACKNOWLEDGEMENTS I believe that each person appear in our life for a reason. They always teach us something important and, when they leave, we are no longer the same people that we were before. I was very lucky during my PhD. I met (and re-met) very special people, which did not only teach me about genetics and genomics, but also taught me how to be a better person and chase my dreams. They helped me to not give up, even when I was scared and did not believe in myself. I could have never done half of what I did in my PhD if I have not met them at some point of my path. Thus, I would like to show here my thanks to some of the people that were part of these three wonderful years of my life. First of all, I would like to say a very big thank you to my advisor, Dr. Fabyano Fonseca e Silva, for all support that he has given me since my Master’s degree. Fabyano, you gave me a lot of opportunities that I could have never imagined. You were always there ready to help me in everything that I needed. You always helped me to achieve my dreams as if they were yours, and you believed in my potential even when I did not. With your “crazy” and “science-passionate” way of being you taught me how to like science, and how to be happy by helping others. You are the best advisor that I could have asked for, and I am very proud of being your student. Thank you very much for everything that you have done for me. Dr. Flavio Schenkel, I could have never imagined that someone important like you would be so nice and kind. You showed to me that we do not need to give up on things that we like to achieve our professional dreams, and how important is to have a balance between our professional and personal life. Without even realizing it, you taught me how discipline, time and organization are important to keep us going in the right direction. With your paternal heart and kind words you made me realize that we do not need to rush, and that we always can make things better. You are an example of professional and person for me. Thank you very much for all opportunities that you gave me and, especially, thank you for making me feel welcome in your research group and in your house. Dr. Daniela Lourenco, who could imagine that someone so young could be so smart and have achieved so much in life! Your exciting way of seeing things, your willingness to help everybody, and your efforts to make Georgia’s research group united and happy had a great impact in my life. Thank you for always being so accessible to me, and for all hours that you spent with me trying to make things work and explaining concepts. You have no idea how much I have learned iii from you! I am very happy to have meet you and I really hope that we can work together again in the future. You are an amazing person and professional. If it is true that guardian angels sometimes appear in our lives as friends, I think you are mine, Dr. Luiz Fernando Brito. You have been by my side since my undergrad, helping, teaching and cheering for me. I have never met someone that is so benevolent and so enthusiastic to see other people’s achievements. You proved to me how far we can go if we work hard, and how life bring us good surprises when we do our best. But especially, you taught me how much easier our life is when we have someone that we can always count on. All our discussions/partnerships/projects/travels/beers/parties were fundamental in making me who I am today. So, thank you for always believing in my ideas, encouraging me and doing your best to help me in everything that I needed. For sure you were my “right hand” in this journey. Dr. Marcos Vinícius Gualberto, it was a pleasure to have the opportunity of working and learning from you again, after my undergrad. I admire you a lot for everything that you have been doing for the improvement of the dairy cattle industry in Brazil, especially for the Gyr and Girolando breeds. Thank you very much for all your teachings, suggestions and help during my PhD, especially in the begging of my thesis. Some people arrive without any intension and end up becoming a fundamental part of our history. And you are one of them, Dr. Janusz Jamrozik. Thank you very much for all your prompt replies, patience, and for always answering my e-mails with “1,000 questions” in the best way possible. In addition, thank you very much for all your great suggestions and comments in our studies and, mainly, for all your intriguing questions that made me think a lot from a different perspective. Dr. John Cant, thank you very much for believing in my ideas and in this project, even without knowing me. Your support and knowledge were fundamental to finalize this thesis. Moreover, thank you for all your great suggestions and comments in our manuscripts, especially in the last chapters of my thesis. I also would like to say thank you to Dr. Camila Ferreira Azevedo and Dr. Domingos Sávio Queiroz, for accepting being part of my defense committee, and for all their contributions to this thesis. During my short stay in Uberaba, I made some very special friends that were very important in the begging of my PhD. Even though our study was not very well related to my thesis, I really appreciated the fact that I could learn more about different things, and I really enjoyed the time that iv we spent together. Thus, I would like to manifest here my sincere thank you to Dr. Henrique Torres Ventura (especially for the great opportunity), Dr. Edson Vinícius Costa (for all conversations and friendship), Dr. Renata Veroneze (for being amazing), and to Mariana Alencar, Gleida Marques, Valeria Castro and Jacqueline Araujo for the great weekends. I had a super fun time with you, guys! I hope we can repeat it in the future. Of course I also have to thanks all my friends from the “vicious city” (Vicosa), where all dreams start. Over these 10 years living in Vicosa is impossible do not think about a lot of special people that are/were very important in my life. Thus, to represent all my “old friends” in Vicosa, I would like to say a special thank you to Patrícia Abrahão and Bruno Carvalho. It does not matter how physically far we are, our friendship and affection for each other is always the same. Thank you for being with me since my first year! For the friends from my PhD program, I have to say thanks to people from “Salinha do Melhoramento” and “Labtec”. All conversations/discussions/courses/projects/GDMAmeetings/volleyballGames/barbecues/beers were very important to me. In special, I would like to thanks my good friends José Teodoro Paiva, Hugo Teixeira Silva, Nadson Souza, Vinicius Junqueira, Alessandra Alves, Darlene Duarte, Delvan Alves, Felipe Gomes, Giovani Caetano, Ivan Carvalho, Laene Alcântara, Lais Brito, Leiri Barili, Leonardo Gloria, Pedro Freitas, Renata Henriques, Rodrigo Godinho, Rodrigo Reis, Sirlene Lazaro, Thaís Cristina, and Otavio Henrique Siqueira. Thank you for being such amazing guys! At this point, I would like to emphasise my thank you to Dr. Ricardo Frederico Euclydes, Dr. Robledo de Almeida Torres, Dr. Paulo Sávio Lopes and Dr. Marcelo Teixeira Rodrigues, that have contributed to my training since my undergrad. Discretely I have being learning a lot from you, and I am very glad for the opportunities that you gave me over the years. Thank you very much for your teachings, patience and help. And because life is a sweet surprise, I also had a chance to meet (and re-meet) really nice people during my stay in Guelph. Thus, I would like to show here my thanks to all people from “CGIL” and “Brazilian Mafia”. In special, I would like to say a big thank you to Aline Guarini, Fabieli Feitosa and Ivan Lange (my best surprises!), Adrien Butty, Agnese Balzani, Ana Lúcia Puerro, Aroa Suarez-Vega, Audrey Martin, Bayode Makanjuola, Carolina Reyes, Emhimad Abdalla, Erin Massender, Evert Varela, Gabriele Marras, Gerson Oliveira, Giovana Vargas, Hakimeh Emamgholi, Kristen Alves, Lucas Alcantara, Malane Muniz, Maria Amelia Menck, Pablo Fonseca, Riani Ananda, Samir Lahoucine, Saranya Narayana, Shadi Nayeri, Stephanie Lam, Tatiane Chud, Valdecy Cruz, Victor Pedrosa and Victoria Asselstine.