Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2013 The effects of biotic and abiotic stressors on gene expression in chickens Derrick Jamaal Coble Iowa State University Follow this and additional works at:https://lib.dr.iastate.edu/etd Part of theGenetics Commons Recommended Citation Coble, Derrick Jamaal, "The effects of biotic and abiotic stressors on gene expression in chickens" (2013).Graduate Theses and Dissertations. 13346. https://lib.dr.iastate.edu/etd/13346 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please [email protected]. The effects of biotic and abiotic stressors on gene expression in chickens by Derrick Jamaal Coble A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Genetics Program of Study Committee: Susan J. Lamont, Major Professor Max F. Rothschild Michael E. Persia Christopher K. Tuggle Dan Nettleton Iowa State University Ames, Iowa 2013 Copyright © Derrick Jamaal Coble, 2013. All rights reserved. ii DEDICATION This dissertation is dedicated to my parents, my grandparents, and God for providing me with more love and care than any person could image. Thanks Mom for the care packages that you sent from time to time, they really helped me to make my home here in Iowa. Dad and Papa, thanks for all the time and work you’ve dedicated to my car. I’m sure sending my car back home has saved me thousands. I guess I will have to put gas in the boat now. Thanks Grandma Annie for the great meals that you prepare when I come back in North Carolina, highlighting the fact that there is no place like home. Thanks Grandma Jessie for the good conversations that we have when I come to your home. You always keep me in tune to what is going on at home. Finally, I would like to thank God for the guidance that you have provided me throughout life. iii TABLE OF CONTENTS Page LIST OF FIGURES v LIST OF TABLES vii NOMENCLATURE ix ACKNOWLEDGEMENTS x ABSTRACT xi CHAPTER 1. GENERAL INTRODUCTION 1 Introduction 1 Organization of Dissertation 2 Literature Review 3 References 29 CHAPTER 2. DISTINCT LINES OF CHICKENS EXPRESS DIFFERENT SPLENIC CYTOKINE PROFILES IN RESPONSE TO SALMONELLA ENTERITIDIS 50 Abstract 50 Introduction 51 Materials and Methods 53 Results 55 iv Discussion 56 Acknowledgements 59 References 59 CHAPTER 3. IMPACTS OF SALMONELLA ENTERITIDIS INFECTION ON LIVER TRANSCRIPTOME IN BROILERS 68 Summary 68 Introduction 69 Results 71 Discussion 73 Methods 78 Acknowledgements 81 Literature Cited 82 CHAPTER 4. RNA-SEQ ANALYSIS OF BROILER LIVER TRANSCRIPTOME REVEALS NOVEL RESPONSES TO HEAT STRESS 94 Abstract 94 Background 96 Results 97 Discussion 100 Conclusion 115 Methods 115 v Acknowlegdements 118 References 119 CHAPTER 5. GENERAL DISCUSSION, CONCLUSIONS, AND FUTURE DIRECTIONS 143 References 152 vi LIST OF FIGURES CHAPTER 2. Figure 1A. 66 Mean IL-18 mRNA expression levels by genetic line, in the spleen of hens either non-challenged or challenged with SE Figure 1B 67 Means of adjusted Ct values for IL-6 mRNA expression by genetic line in the spleen of hens either non-challenged or challenged with SE CHAPTER 3. Figure 1. 92 Pathway analysis of cell cycle functions in broiler liver transcriptome in response to S. Enteritidis Figure 2 93 Pathway analysis of metabolic functions in broiler liver transcriptome in response to S. Enteritidis infection CHAPTER 4. Figure 1. 140 Cell Signaling, Molecular Transport, Small Molecule Biochemistry Network Figure 2. 141 Endocrine System Development and Function, Small Molecule vii Biochemistry, Cell Signaling Network Figure 3. 142 Significance levels of functions associated with DE genes in broiler liver in response to chronic, cyclic heat stress viii LIST OF TABLES CHAPTER 2. Table 1. 65 Genetic line, challenge, and line-by-challenge interaction effects on spleen mRNA expression Table 2. 65 Splenic IFN-γ and RANTES mRNA expression of hens from different genetic lines CHAPTER 3. Table 1. 88 List of genes that belong to Cell Cycle and Metabolism networks Table 2. 89 Log fold change of hepatocyte gene expression between S. Enteritidis 2 challenged and non-challenged birds Table 3. 89 Forward and reverse primer sequences used for qPCR Supporting Information Table 1. 90 List of genes, P-values, GO annotations, directions of differential expression and fold changes ix CHAPTER 4. Table 1. 138 Forward and reverse primers used for qPCR Table 2. 138 P-value of hepatocyte gene expression between heat stressed- and non- heat stressed-broilers Supporting Information Table 1. 139 P-values, fold changes, and q-values for DE genes