A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: Derivation of the BXD set. ......................................................... 27 1.6 Indirect genetic effects (IGEs) ................................................................... 28 Figure 1.2: Indirect genetic effects influence phenotypes in interacting individuals.. ................................................................................................. 31 1.7 Parent-of-origin effects (POEs), epigenetics and genomic imprinting ........ 32 Table 1.1: Diseases linked to abnormal genomic imprinting, with their associated features and causative mutations. ............................................. 36 1.8 Parental care ............................................................................................ 37 1.9 Aims of the PhD ........................................................................................ 39 1.10 Alternative format .................................................................................... 40 1.11 References ............................................................................................. 41 Chapter 2: Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease ....................... 56 Chapter 2: Preface.......................................................................................... 57 Abstract .......................................................................................................... 59 2.1 Introduction ............................................................................................... 60 2.2 Materials and methods .............................................................................. 63 2.2.1 Data ................................................................................................... 63 2.2.2 Identification of significant genes for hippocampus size in mouse and human ......................................................................................................... 64 2.2.3 Expression quantitative trait loci ......................................................... 66 2.2.4 Functional analysis ............................................................................. 67 2.2.5 Co-expresion and ‘Guilt-by-association’ ............................................. 67 2.3 Results ..................................................................................................... 70 2 Table of contents 2.3.1 Identification of genes significant in both species ............................... 70 Figure 2.1: Quantile-quantile plot of human homologues of significant mouse genes for hippocampus size.. ...................................................................... 71 2.3.2 Regulation of gene expression ........................................................... 72 Table 2.1: Pearson’s correlations between probes for Mgst3 in adult mouse hippocampus. .............................................................................................. 73 2.3.3 Functional analysis of significant genes .............................................. 73 2.3.4 ‘Guilt-by-association’ .......................................................................... 74 2.4 Discussion ................................................................................................ 76 2.4.1 Conclusion ......................................................................................... 77 2.5 References ............................................................................................... 78 Chapter 3: A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder................................................... 84 Chapter 3: Preface.......................................................................................... 85 Abstract .......................................................................................................... 87 3.1 Introduction ............................................................................................... 88 Figure 3.1: Bipolar disorder traits and analogous mouse phenotypes.. ........ 90 3.2 Materials and methods .............................................................................. 92 3.2.1 Mouse and human data ...................................................................... 92 3.2.2 Evolutionary conservation .................................................................. 94 3.2.3 Identification of areas of expression ................................................... 94 3.2.4 ‘Guilt-by-association’ .......................................................................... 94 3.2.5 Principal component analysis ............................................................. 96 3.2.6 Biological networks ............................................................................. 97 3.3 Results ..................................................................................................... 98 Figure 3.2: Graphical representation of the research method used, providing a summary of the main findings. .................................................................. 98 3.3.1 QTL for bipolar related phenotypes in mice ........................................ 99 Table 3.1: Activity traits in the elevated zero maze which have a significant QTL ........................................................................................................... 101 Figure 3.3: QTL maps showing two QTL within each of the regions we identified ................................................................................................... 102 Table 3.2: Vertical activity traits in the open field which have a significant QTL. .......................................................................................................... 104 3.3.2 Gene expression in the brain ............................................................ 106 3.3.3 ‘Guilt-by-association’ ........................................................................ 106 3.3.4 Co-expression analysis .................................................................... 107 3 Table of contents 3.3.5 Correlation analysis .......................................................................... 109 3.4 Discussion .............................................................................................. 111 3.4.1 Biological function of candidate genes .............................................. 113 3.4.2 RXRG ............................................................................................... 113 3.4.3 MCTP1 ............................................................................................. 114 3.4.4 TNR.................................................................................................. 114 3.4.5 Role of striatum ................................................................................ 115 3.4.6 Conclusion ....................................................................................... 116 3.5 References ............................................................................................. 115 Chapter 4: Genetic variation in offspring indirectly influences the quality of maternal behaviour in mice ........................................................................... 129 Chapter 4: Preface........................................................................................ 130 Abstract ........................................................................................................ 132 4.1 Introduction ............................................................................................. 133 Figure 4.1: Experimental cross-foster design ............................................ 134 4.2. Materials and methods ........................................................................... 136 4.2.1 Experimental animals ....................................................................... 136 4.2.2 Husbandry and mating protocol .......................................................