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Epistatic Interactions Associated with Fatty Acid

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Epistatic Interactions Associated with Fatty Acid FACULDADE DE CIÊNCIAS AGRÁRIAS E VETERINÁRIAS UNIVERSIDADE ESTADUAL PAULISTA CÂMPUS DE JABOTICABAL EPISTATIC INTERACTIONS ASSOCIATED WITH FATTY ACID PROFILE OF BEEF FROM NELLORE CATTLE Sabrina Thaise Amorim Zootecnista 2020 FACULDADE DE CIÊNCIAS AGRÁRIAS E VETERINÁRIAS UNIVERSIDADE ESTADUAL PAULISTA CÂMPUS DE JABOTICABAL EPISTATIC INTERACTIONS ASSOCIATED WITH FATTY ACID PROFILE OF BEEF FROM NELLORE CATTLE Sabrina Thaise Amorim Orientador: Prof. Dr. Fernando Sebastián Baldi Rey Co-orientador: Dr. Fernando Brito Lopes Co-orientadora: Dra. Nedenia Bonvino Stafuzza Dissertação apresentada à Faculdade de Ciências Agrárias e Veterinárias – Unesp, Campus de Jaboticabal, como parte das exigências para a obtenção do título de Mestre em Genética e Melhoramento Animal. 2020 Amorim, Sabrina Thaise A524e Epistatic interactions associated with fatty acid profile of beef from Nellore cattle / Sabrina Thaise Amorim. -- Jaboticabal, 2020 173 p. Dissertação (mestrado) - Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal Orientador: Fernando Sebastián Baldi Rey Coorientador: Fernando Brito Lopes 1. Genética. 2. Melhoramento Animal. 3. Genômica. I. Título. Sistema de geração automática de fichas catalográficas da Unesp. Biblioteca da Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal. Dados fornecidos pelo autor(a). Essa ficha não pode ser modificada. DADOS CURRICULARES DO AUTOR Sabrina Thaise Amorim, nascida em 02 de julho de 1995 na cidade de Brusque – Santa Catarina, filha de Alexandre Adriano Amorim e Liliane RaQuel Pavesi Amorim. Iniciou em março de 2013 o curso de graduação em Zootecnia na Universidade Federal de Santa Catarina, obtendo o título de Zootecnista em dezembro de 2017. Durante a graduação foi bolsista de Iniciação Científica do CNPq, monitora da disciplina “Genética Aplicada à Zootecnia”, integrante do Grupo de Pesquisa em Produção Animal e integrante do Laboratório de Pesquisa e Ensino em Genética Animal (LEPGA) da mesma instituição de fomento, sob a orientação do Prof. Dr. André Luís Ferreira Lima. Em março de 2018, ingressou no Programa de Pós-graduação em Genética e Melhoramento Animal da Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista “Júlio de Mesquita Filho”, campus de Jaboticabal, sob a orientação do Prof. Dr. Fernando Sebastián Baldi Rey, inicialmente como bolsista CAPES e posteriormente como bolsista FAPESP (Processo FAPESP 2018/19463-4). Realizou Estágio de Pesquisa no Exterior (BEPE-MS, Processo FAPESP:2019/04929-0) na Virginia Polytechnic Institute and State University sob supervisão do Dr. Gota Morota. “It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of light, it was the season of darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us” (…). (Charles Dickens - A Tale of Two Cities) Dedico Àquelas Que não medem esforços para realizar meus sonhos, Que sempre estarão ao meu lado e com suas mãos sempre estendidas, minha avó Dorandina Pavesi, minha mãe Liliane RaQuel Pavesi Amorim e as minhas irmãs Sara e Sayuri. AGRADECIMENTOS À minha família Que sempre apoiou minhas escolhas e Que sempre compreendeu minha ausência. Minha avó Dorandina e minha mãe Liliane por sempre me encorajarem a seguir em frente e por toda dedicação em me oferecer a melhor educação possível. Minhas irmãs, Sara e Sayuri por serem os amores da minha vida. Ao meu orientador e amigo, Prof. Dr. Fernando Sebastián Baldi Rey pela disponibilidade em me orientar e por me receber no seu grupo de pesquisa desde Que eu era apenas uma estudante da graduação. Agradeço a confiança em mim depositada na execução desse e de outros trabalhos, por me encorajar a sempre ir além, e por todos os ensinamentos profissionais e pessoais, Que com certeza, moldaram a profissional Que sou hoje. Aos meus coorientadores, Fernando Brito Lopes, e Nedenia Bonvino Stafuzza, pelo auxílio e prontidão no decorrer do desenvolvimento deste trabalho. À Associação Nacional de Criadores e Pesquisadores (ANCP, Ribeirão Preto) pelo fornecimento dos dados. Aos meus amigos Que pós-graduação me deu, Laura Prados, Renata Thaysa, André Mauric, Diogo Silva, Willian Galena, Ana Fabrícia, e Samuel, Que me enturmaram e fizeram minha estadia em Jaboticabal ainda mais enriQuecedora e leve. Aos meus “hermanitos” e “hermanitas”, Sabrina Kluska, Elisa Peripolli, Bianca Olivieri, Mariana Berton, Rafael Tonussi, e Juan Diego por me aturarem, pela parceria, pelas risadas, todos os cafés, todas as cocas-zero compartilhadas, pelos incentivos e por todo apoio dentro de fora da salinha. Às melhores amigas Que alguém pode ter no mundo, Patrícia Pereira e Tatiane Schmitt, Que mesmo longe, mesmo cada uma em um estado (ou país) diferente, sempre estão e estiveram presentes para um desabafo, uma risada, ou simplesmente um “estou feliz por ser sua amiga”. Aos amigos e amigas Que fiz durante meu estágio na Virginia Tech, Francisco Novais, Barbara RoQueto, Nicholas Dias, Deraldo Andrade, Álvaro Sales, Juan Morales, Con-Ning Yen, Jing Zhou, Claire Gleason, Beth Durham, Skylar Southard, Andrea Dixon, Jasmine Shah, Renata Carneiro, Renata Sutherland. Vocês são as melhores pessoas com Quem eu poderia ter convivido durante um período tão desafiador. Agradeço cada convite, cada churrasco, cada risada, toda a ajuda Que recebi desde meu primeiro dia nos Estados Unidos. Em especial agradeço ao meu irmão de outra mãe Francisco pela cumplicidade, e a minha host-family Skylar e Andrea. Aos meus colegas do Morota Lab, Haipeng Yu, Mehdi Momen, Toshimi Baba, e Malachy Campbell pelos ensinamentos, pelos donuts, e aos pratos de comida chinesa surpresas nos jantares do grupo. Ao Prof. Dr. Gota Morota, por ter me aceito no seu grupo de pesquisa, pelas extensas horas Que passamos juntos enQuanto ele me ensinava truQues de programação, pelo apoio incondicional durante as fases mais difíceis do estágio. Aos meus professores da UFSC, Lucelia Hauptli e Renato Irgang por serem uma inspiração desde a graduação, e por sempre estarem disponíveis. Tenho muito orgulho de ter sido orientada pelos dois. Aos membros da banca do Exame Geral de Qualificação, Prof. Danísio e Prof. Dr. HenriQue, pelas sugestões Que muito contribuíram e acrescentaram a esse trabalho, e pela amizade dentro e fora da sala de aula. À Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias – Campus de Jaboticabal, por oferecer os melhores professores, funcionários e conhecimentos necessários para minha evolução profissional e também pessoal. O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Código de Financiamento 001. À Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) pela concessão da bolsa de mestrado (Processo FAPESP 2018/19463-4), e pela concessão da Bolsa Estágio de Pesquisa no Exterior (BEPE-MS, Processo FAPESP: 2019/04929- 0). i SUMÁRIO CHAPTER 1 – State of the Art .................................................................................. 16 1.0 Lipids in Human Diet ........................................................................................... 16 1.1 Classification of Dietary Lipids ............................................................................ 17 1.2 Fatty Acids ........................................................................................................... 18 1.2.1 Saturated Fatty Acids ....................................................................................... 18 1.2.2 Unsaturated Fatty Acids ................................................................................... 19 1.2.3 Phospholipids and Cholesterol ......................................................................... 20 1.3 Meat Composition ............................................................................................... 21 1.3.1 Lipids in beef .................................................................................................... 22 1.4 Effects of fatty acid composition on human health .............................................. 23 1.5 Genetic Variation for beef fatty acid profile and genomic selection ..................... 25 1.6 Genome-Wide Association Studies and Epistasis .............................................. 28 1.6.1 Genetic variants ............................................................................................... 28 1.6.2 Linkage and association analysis ..................................................................... 29 1.6.3 Heritability and the case of missing heritability ................................................. 30 1.7 Epistasis .............................................................................................................. 31 1.7.1 Concepts of Epistasis ....................................................................................... 31 1.7.2 Epistatic Interactions ........................................................................................ 33 1.8 Analysis Challenge .............................................................................................. 34 1.8.1 Computational challenge .................................................................................. 34 1.8.2 Allele FreQuencies and Genotype Call Rate .................................................... 36 1.8.3 Linkage DiseQuilibrium ....................................................................................
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