Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Investigations into nutritional quality, commercial productivity, and genetic purity of maize grain for organic production systems Ryan Huffman Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Huffman, Ryan, "Investigations into nutritional quality, commercial productivity, and genetic purity of maize grain for organic production systems" (2017). Graduate Theses and Dissertations. 15322. https://lib.dr.iastate.edu/etd/15322 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]. Investigations into nutritional quality, commercial productivity, and genetic purity of maize grain for organic production systems by Ryan D. Huffman A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Molecular, Cellular, and Developmental Biology Program of Study Committee: M. Paul Scott, Co-Major Professor Phil Becraft, Co-Major Professor Marna D. Nelson Jode W. Edwards Alan Myers The student author and the program of study committee are solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2017 Copyright © Ryan D. Huffman, 2017. All rights reserved. ii DEDICATION I dedicate my dissertation work to all my family and friends. A special gratitude to my parents, Dave and Elise, whose constant support and words of encouragement pushed me during my pursuit of higher education. No words are sufficient to describe my late mother’s impact on the completion of this degree. I wholeheartedly dedicate this entire dissertation to her memory. My sister and brother-in-law, Ashley and Aaron, were pivotal to my success and highly supportive. I also dedicate this dissertation to my late grandfather, Arthur Sturtz, who introduced farming to me at a very young age. He instilled many of my core values and passion for agriculture. Lastly, I dedicate this work to my best friend and wife, Amanda, for her love, support and patience throughout the entire doctorate program. You all are very much appreciated. iii TABLE OF CONTENTS Page LIST OF FIGURES ................................................................................................... v LIST OF TABLES ..................................................................................................... vi NOMENCLATURE .................................................................................................. viii ABSTRACT………………………………. .............................................................. ix CHAPTER 1. GENERAL INTRODUCTION .......................................................... 1 Dissertation Organization .................................................................................... 1 Brief Literature Review ....................................................................................... 1 Maize grain quality ........................................................................................ 1 Organic hybrid productivity and adaptation .................................................. 4 Gametophytic cross-incompatibility .............................................................. 6 References ............................................................................................................ 11 CHAPTER 2. INTERACTION OF GENETIC MECHANISMS REGULATING METHIONINE CONCENTRATION IN MAIZE GRAIN ....................................... 17 Abstract ................................................................................................................ 17 Introduction .......................................................................................................... 18 Material and Methods .......................................................................................... 21 Results .................................................................................................................. 24 Discussion ............................................................................................................ 30 Acknowledgements .............................................................................................. 35 References ............................................................................................................ 35 CHAPTER 3. COMBINING ABILITY AND ENVIRONMENTAL INVESTIGATION OF MAIZE TESTCROSSES IN DIVERSE ORGANIC PRODUCTION SYSTEMS……………………………………………………… ... 47 Abstract ................................................................................................................ 47 Introduction ......................................................................................................... 48 Material and Methods .......................................................................................... 52 Results .................................................................................................................. 55 Discussion ............................................................................................................ 59 Acknowledgements .............................................................................................. 64 References ............................................................................................................ 64 CHAPTER 4. PROTEOMIC ANALYSIS OF THE GAMETOPHYTE FACTOR1-STRONG (GA1-S) SYSTEM IN MAIZE .............................................. 78 Abstract ................................................................................................................ 78 Introduction .......................................................................................................... 79 Material and Methods .......................................................................................... 83 Results .................................................................................................................. 86 iv Discussion ............................................................................................................ 96 Acknowledgements .............................................................................................. 101 References ............................................................................................................ 101 CHAPTER 5. GENERAL CONCLUSIONS ............................................................. 110 ACKNOWLEDGMENTS ......................................................................................... 112 LIST OF SUPPLEMENTARY INFORMATION TABLES ..................................... 113 v LIST OF FIGURES Chapter 1 Page Figure 1 Principle of gametophytic cross-incompatibility ....................................... 16 Chapter 3 Figure 1 ‘Which-won-where’ view of the GGE-biplot showing all 49 maize hybrids and 10 environments ..................................................................... 74 Figure 2 ‘Discrimitiveness vs. representativeness’ view of the GGE-biplot comparing all 10 environments .................................................................. 75 Figure 3 ‘Mean vs. stability’ view of the GGE-biplot comparing all 49 hybrids .... 76 Figure 4 Ranking environments view of the GGE-biplot comparing all 10 environments based on both discriminating ability and representativeness ...................................................................................... 77 Chapter 4 Figure 1 1-D gel electrophoresis analysis for all 18 protein extracts ....................... 105 Figure 2 Venn diagram summary of proteins identified in each tissue involved in either a compatible or incompatible pollination .................................... 106 Figure 3 Hierarchical clustering and heat map analysis for the 628 proteins expressed across the six treatments fixed for either the Ga1-s or ga1 allele ................................................................................................... 107 Figure 4 Hierarchical clustering and heat map analysis for the 683 proteins expressed across 18 different treatments ................................................... 109 vi LIST OF TABLES Chapter 2 Page Table 1 Inbred lines used in the seven-by-seven diallel study ................................ 38 Table 2 Mean methionine (Met) concentration (g 100 g−1 dry wt.), starch, protein, and oil concentration (% dry matter) for all 49 entries produced in the diallel study. ..................................................................... 39 Table 3 Analysis of variance (ANOVA) for the methionine (g 100 g−1 dry wt.), oil, protein, and starch concentration (% dry matter) linear model. .......... 40 Table 4 Estimates for the genetic effects for methionine (Met) (g 100 g−1 dry wt.), starch, protein, and oil concentration (% dry matter) ..................................................................... 41 Table 5 Methionine concentration (g 100 g−1 dry wt.) comparisons for hybrid