Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 A next generation of studies: Heterosis and inbreeding depression Shreyartha Mukherjee Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agriculture Commons, Bioinformatics Commons, and the Statistics and Probability Commons Recommended Citation Mukherjee, Shreyartha, "A next generation of studies: Heterosis and inbreeding depression" (2014). Graduate Theses and Dissertations. 13878. https://lib.dr.iastate.edu/etd/13878 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 contact [email protected]. A next generation of studies: Heterosis and inbreeding depression by Shreyartha Mukherjee A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Bioinformatics and Computational Biology Program of Study Committee: William Beavis, Co-Major Professor Julie Dickerson, Co-Major Professor Paul Scott Peng Liu Thomas Lubberstedt Iowa State University Ames, Iowa 2013 Copyright © Shreyartha Mukherjee, 2013.All rights reserved. ii DEDICATION I dedicate this dissertation to my father Siddhartha, my mother Alpana, my sister Shreeja and my friend Chandni without whose support I would not have been able to complete this work. iii TABLE OF CONTENTS DEDICATION............................................................................................................................................................ ii ACKNOWLEDGEMENTS ....................................................................................................................................vi ABSTRACT ............................................................................................................................................................. vii CHAPTER 1 ............................................................................................................................................................... 1 INTRODUCTION AND LITERATURE REVIEW ......................................................................................... 1 Heterosis and Production Agriculture.......................................................................................................... 1 Heterotic Biological Systems ........................................................................................................................... 4 Maize as the Model to Study Heterosis......................................................................................................... 7 A Next Generation of Heterosis Investigations ....................................................................................... 11 Connecting grain yield and transcript levels ........................................................................................... 12 Organization of thesis ..................................................................................................................................... 13 Difference in transcript counts (differential gene expression) .................................................... 13 Abundance of sequence variants (Allele-specific expression)...................................................... 14 Abundance of splice variants (alternatively spliced isoform expression) ................................ 14 Statement of Relevance .................................................................................................................................. 15 Author affiliations ............................................................................................................................................ 16 References .......................................................................................................................................................... 17 CHAPTER 2 ............................................................................................................................................................ 26 TRANSCRIPTOMIC ANALYSIS OF FIELD GROWN ELITE MAIZE INBREDS AND THEIR HYBRIDS.................................................................................................. 26 Abstract ............................................................................................................................................................... 26 Introduction ....................................................................................................................................................... 27 Materials and Methods ................................................................................................................................... 32 Experimental Design .................................................................................................................................. 32 Tissue sampling ........................................................................................................................................... 33 RNA Extraction............................................................................................................................................. 34 Sequencing and Bioinformatic Analyses .............................................................................................. 34 Normalization of expression data and assessment of over-dispersion ..................................... 35 Modeling and analyses of gene expression counts ........................................................................... 36 Assessment of gene expression models ............................................................................................... 37 Modeling and analyses of ear traits ....................................................................................................... 40 Data Analyses................................................................................................................................................ 41 Implementation of Data Analyses .......................................................................................................... 41 Results.................................................................................................................................................................. 42 Model Implementation .............................................................................................................................. 42 Goodness of Fit ............................................................................................................................................. 42 Comparisons of Expression in Hybrids vs Mid Parent values....................................................... 43 Genetic Distance and Differential Expression .................................................................................... 47 Functional Analysis of Gene Enrichment Categories for Differentially Expressed Genes ............................................................................................................... 48 Evaluation of whole ear phenotypes for Mid-parent and High-parent heterosis ................................................................................................................................ 53 Discussions ......................................................................................................................................................... 55 iv Mapping reads to AgpV2 ........................................................................................................................... 55 Normalization and modeling of biological variability ..................................................................... 55 Association between genetic diversity and transcriptional variation........................................ 56 Modes of gene action .................................................................................................................................. 56 Functional annotation of differentially expressed genes ............................................................... 58 References .......................................................................................................................................................... 60 CHAPTER 3 ............................................................................................................................................................ 66 ALLELE-SPECIFIC EXPRESSION IS CONSERVED IN MAIZE HYBRIDS...................................... 66 Abstract ............................................................................................................................................................... 66 Introduction ....................................................................................................................................................... 67 Materials and Methods ................................................................................................................................... 73 Genotypic Materials .................................................................................................................................... 73 Field Plot Design 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