DARLENE ANA SOUZA DUARTE DEPICTING RESIDUAL FEED INTAKE IN NELLORE CATTLE THROUGH GENE EXPRESSION, LIPIDOMIC PROFILING AND PATHWAY-BASED META-ANALYSIS Thesis presented to the Animal Science Graduate Program of the Universidade Federal de Viçosa, in partial fulfillment of the requirements for degree of Doctor Scientiae. VIÇOSA MINAS GERAIS – BRASIL 2018 Ficha catalográfica preparada pela Biblioteca Central da Universidade Federal de Viçosa - Câmpus Viçosa T Duarte, Darlene Ana Souza, 1990- D812d Depicting residual feed intake in Nellore cattle through 2019 gene expression, lipidomic profiling and pathway-based meta-analysis / Darlene Ana Souza Duarte. – Viçosa, MG, 2019. viii, 90 f. : il. (algumas color.) ; 29 cm. Texto em inglês. Inclui apêndices. Orientador: Fabyano Fonseca e Silva. Tese (doutorado) - Universidade Federal de Viçosa. Inclui bibliografia. 1. Bovinos - Melhoramento genético. 2. Eficiência alimentar. I. Universidade Federal de Viçosa. Departamento de Zootecnia. Programa de Pós-Graduação Zootecnia. II. Título. CDD 22. ed. 636.20821 ACKNOWLEDGMENTS I am grateful to Universidade Federal de Viçosa for have been my home since undergraduation, to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for the scholarship. I would like to thank my advisor Fabyano Fonseca e Silva for his patience and for believe in me, since undergraduation, when you became my advisor, until the PhD defense. You are a very special person and I have learned a lot from you, thank you very much for everything. I would especially like to thank Marcio de Souza Duarte for the advices and support during my PhD. Thank you for the patience with which you listened to me and helped me in the many doubts I had. I also thank Prof. Paulo Sávio Lopes and Renata Veroneze for their contributions and wisdom, especially Renata for listening and advising me on all my problems, for give me a place to stay in her office and mainly for the friendship and “lanchinhos”. I would also like to thank all professors and staff of the DZO. A big thank you to all friends from LABTEC, Haniel, Ingrid, Karine, Margareth, Pam, Susana, Lucas and Diego for the talks and laughs, a special thanks to Carol, Dani, Walmir, Ivan and Lets for being such dear friends and always being ready to help me. A special thanks to all friends from the “salinha” and GDMA for the good conversations and discussions, and for the volleyball games, especially Alessandra, Delvan, Téo, Hinayah and Hugo. A big thank you to my friends Candida and André who, even far away, are always taking care of me. A big thank you to my whole family, especially my parents and my sister for all their support, for the many advices and for being an example for me. ii SUMMARY ABSTRACT ..................................................................................................... v RESUMO ...................................................................................................... vii Chapter 1 ....................................................................................................... 1 1.1 General Introduction ............................................................................. 1 1.1.1 Feed efficiency .................................................................................. 1 1.1.2 Physiological basis for residual feed intake ...................................... 2 1.1.3 Molecular basis for residual feed intake ............................................ 3 1.1.4 AMPK signaling pathway .................................................................. 4 1.2 Objectives ............................................................................................ 7 1.3 References ........................................................................................... 8 Chapter 2 ..................................................................................................... 14 Genome-wide association studies pathway-based meta-analysis for residual feed intake in beef cattle1 ............................................................................. 14 2.1 Main text ............................................................................................ 15 2.2 Acknowledgements ............................................................................ 19 2.3 References ......................................................................................... 20 2.4 Supporting information ....................................................................... 23 Chapter 3 ..................................................................................................... 24 High residual feed intake Nellore beef cattle exhibited higher levels of fatty acids and triglycerides in skeletal muscle and liver ...................................... 24 3.1 Introduction ........................................................................................ 25 3.2 Materials and methods ....................................................................... 26 3.2.1 Animals and phenotyping ................................................................ 26 3.2.3 Genes from the AMP-activated protein kinase (AMPK) signaling pathway ....................................................................................................... 27 3.2.4 Transcription Factors Analysis ........................................................ 27 3.2.5 RNA isolation and cDNA synthesis ................................................. 30 3.2.6 RT-qPCR ........................................................................................ 31 3.2.7 Statistical analysis of RT-qPCR data ............................................. 31 3.2.8 Lipidomics analysis ......................................................................... 31 3.2.8.1 Lipid extraction and mass spectrometric analyses .......................... 31 3.2.8.2 Lipids Identification ......................................................................... 32 iii 3.3 Results ............................................................................................... 32 3.3.1 RT-qPCR ........................................................................................ 32 3.3.2 Lipidomics analysis ......................................................................... 35 3.3.2.1 Discrimination analysis to detect metabolites associated with RFI . 35 3.3.2.2 Selection of features explaining the differences in RFI ................... 37 3.3.2.3 Muscle tissue .................................................................................. 37 3.3.2.4 Liver tissue ...................................................................................... 39 3.4 Discussion .......................................................................................... 41 3.5 Conclusion ......................................................................................... 44 3.6 References ......................................................................................... 46 Chapter 4 ..................................................................................................... 50 4.1 General conclusions ........................................................................... 50 5. Appendices ............................................................................................ 52 5.1 Appendix 1 ......................................................................................... 52 5.2 Apendix 2 ........................................................................................... 58 5.3 Appendix 3 ......................................................................................... 65 5.4 Appendix 4 ......................................................................................... 70 5.5 Appendix 5 ......................................................................................... 71 5.6 Appendix 6 ......................................................................................... 80 iv ABSTRACT DUARTE, Darlene Ana Souza, D.Sc., Universidade Federal de Viçosa, February, 2019. Depicting residual feed intake in Nellore cattle through gene expression, lipidomic profiling and pathway-based meta-analysis. Adviser: Fabyano Fonseca e Silva. Increase in feed efficiency result in decrease in feed costs. Thus, to improve profitability in beef cattle production system is necessary to select animals more efficient in the use of feed sources. The residual feed intake (RFI) has become the preferable measure for feed efficiency, once that RFI is not correlated with growth rate or other production trait. Researchers have demonstrated that many physiological mechanisms contribute to variation in RFI, among them are protein turnover, tissue metabolism, synthesis and transportation of fatty acid, inflammatory response, glucose absorption and fatty acid oxidation. Even so, the molecular bases controlling this trait are not well elucidate yet. Thus, we aimed to investigate the biological bases that could be responsible for differences in animals classified for RFI. For that, we performed a pathway meta-analysis approach using several genome association studies results to search for significant pathways that may explain the genetic mechanism underlying this trait. We used an efficient permutation hypothesis test that takes into account the linkage disequilibrium patterns between SNPs. One significant pathway (valine, leucine and isoleucine degradation) related to RFI was found. This pathway is related to protein