UNCOVERING THE GENETIC BASIS AND CHARACTERS ASSOCIATION OF WHEAT SPIKE- RELATED, AGRONOMIC AND QUALITY TRAITS A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Morgan Echeverry-Solarte In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Department: Plant Sciences March 2014 Fargo, North Dakota North Dakota State University Graduate School Title UNCOVERING THE GENETIC BASIS AND CHARACTERS ASSOCIATION OF WHEAT SPIKE-RELATED, AGRONOMIC AND QUALITY TRAITS By Morgan Echeverry-Solarte The Supervisory Committee certifies that this disquisition complies with North Dakota State University‟s regulations and meets the accepted standards for the degree of DOCTOR OF PHILOSOPHY SUPERVISORY COMMITTEE: Dr. Mohamed Mergoum Chair Dr. Elias Elias Dr. Phillip McClean Dr. Mohammed Alamri Dr. Jack Rasmussen Dr. Edward Deckard Approved: 3/26/2014 Richard D. Horsley Date Department Chair ABSTRACT Modern wheat (Triticum aestivum L.) cultivars are characterized by having spikes with fusiform architecture and rachis nodes with one spikelet. However, genotypes with supernumerary spikelets (SS) in which rachis nodes have more than one spikelet exist in nature. Although this may be a promising trait that increases yield components, detailed knowledge about the molecular basis of SS trait and their influence on other wheat traits is still lacking. In the present study, a population of 163 recombinant inbred lines (RILs) derived from an elite line and an exotic line with SS was used to identify QTL for SS and other wheat traits. The RILs, seven checks and the two parents were evaluated for seven SS-related, 10 spike-related, 10 agronomic, and eight quality traits over four to six environments in North Dakota. A genetic map of 3,114.2 cM of length with an average distance of 4.6 cM between any two marker loci was developed using 159 RIL and 939 DArT markers. Composite interval mapping identified 221 QTL, out of which 29% were consistent QTL and 19% were major QTL. Most of the QTL were located on the B- genome (44%) followed by the A-genome (37%) and D-genome (19%). The exotic parent with SS contributed 48% of alleles that increased phenotypic values of the traits suggesting the possibility of enriching the breeding germplasm with genes from this genotype. Seven consistent QTL with epistatic interaction were associated to the SS. QSS.ndsu-2D, a major QTL for SS, was co-located in a cluster of QTL on 2DS demonstrating either pleiotropic effect or closely linkage with 19 QTL for other wheat traits. Similarly, a major QTL associated with glume pubescences (QPP.ndsu-1A.1) was co-located on 1AS with seven QTL for other wheat traits. Major and consistent QTL are targets for further marker assisted selection in wheat breeding programs and/or for research projects aiming of gene cloning. iii ACKNOWLEDGEMENTS I wish to express my gratitude to my advisor, Dr. Mohamed Mergoum for his support, advices, guidance, and patience during the completion of my doctoral studies and research. I also thanks to my graduate committee, Drs. Ed Deckard, Elias Elias, Phil McClean, Mohamed Alamri, and Jack Rasmussen. My gratitude is also extended to Dr. Shahryar Kianian and Dr. Gary Secor initial member of my graduate committee. Special thanks to Dr. Senay Simsek for her support during the quality analysis. Likewise, I would like express my sincere gratitude to Dr. Ajay Kumar for his advices, professionalism, dedication, and commitment during the data analysis and preparation of this document. I thanks to the members and students of the NDSU Hard Red Spring Breeding and Genetics project, Wheat Quality Program, and Wheat Germplasm Enhancement Project: Jesse Underdahl, Matthew Abdallah, DeLane Olsen, Kelly McMonagle, Justin Hegstad, Allen Peckrul, Daniel Liane, Eder Mantovani, Ahmed El-Fatih ElDolfey, Hisam Rabbi, Sepher Mohajeri, Monalisa Almeida and Vishwajeet Chhikara. Special thanks to my friends and classmates Eder, Ana Maria, Andre, Fabio, Jimmi, Roberto, Renata, Angela, Wesam, Magan, Juan Calle, Ali, Samira, Mona, Ronald, Atena, Osvaldo, Adriana, Rosham for their friendship and good moments. I also thanks to Johanna Villamizar-Ruiz, my wife, girlfriend and colleague for unconditional love, support and patience. Also I extend my gratitude to my parents, Jairo and Mireya, and my brother, Stuart, for their love, support and patience during this almost 8 years of absence. I would like also thanks to Juan Manuel, Judith (Yuyis), Juan Esteban, Melissa and Nicholas for their love, kindness, support and for open us the doors of their holy home during these wonderful years in Fargo. I gratefully acknowledge to Dr. Richard Horsley and Dr. Linda Wessel-Beaver to encourage me to be a plant breeder! There are men who struggle for a day, and they are good. There are others who struggle for a year, and they are better. There are some who struggle many years, and they are better still. But there are those who struggle all their lives, and these are the indispensable ones.” Bertol Brecht iv DEDICATION Dedicated to my loved one… Johanna, “La Incondicional”, my wife. Jairo “El Indispensable”, my father. Mireya “Mástil de Hogar”, my mother. Stuart “El Sensato”, my brother. All my loved family v PREFACE This dissertation consists of five chapters. Chapter 1 includes a general introduction about the dissertation research, along with the objectives, literature review and references. Chapters 2, 3 and 4 are written as three papers to be submitted for publication to the appropriate scientific journals. Therefore, these chapters each include an abstract, introduction, material and methods, results, discussion, conclusions and references. Chapter 5 is the general conclusion. Appendices are included after the end of chapter five. vi TABLE OF CONTENTS ABSTRACT ................................................................................................................................................... iii ACKNOWLEDGEMENTS ............................................................................................................................ iv DEDICATION ................................................................................................................................................ v PREFACE .................................................................................................................................................... vi LIST OF TABLES ......................................................................................................................................... xii LIST OF FIGURES ...................................................................................................................................... xiii LIST OF ABBREVIATIONS......................................................................................................................... xiv LIST OF APPENDIX TABLES..................................................................................................................... xvi LIST OF APPENDIX FIGURES ................................................................................................................. xvii CHAPTER 1. INTRODUCTION .................................................................................................................... 1 1.1. General Introduction ........................................................................................................................ 1 1.2. Objectives ........................................................................................................................................ 3 1.2.1. General Objective ........................................................................................................ 3 1.2.2. Specific Objectives ...................................................................................................... 3 1.3. Literature Review ............................................................................................................................. 4 1.3.1. Branched spikes .......................................................................................................... 4 1.3.1.1. Natural variation for branched spikes ............................................................ 4 1.3.1.2. Associations between branched spikes and other wheat characteristics ................................................................................................ 6 1.3.1.3. Genetics of branched spikes .......................................................................... 8 1.3.2. Spike size traits.......................................................................................................... 14 1.3.2.1. Natural variation for spike architecture ........................................................ 14 vii 1.3.2.2. Associations among spike architecture and other wheat traits .................... 15 1.3.2.3. Genetics of spike architecture ...................................................................... 17 1.3.3. Spike awnedness ...................................................................................................... 22 1.3.3.1. Natural variation of spike awnedness .......................................................... 22 1.3.3.2. Associations between spike awnedness and other wheat traits .................. 23 1.3.3.3. Genetics of awnedness ................................................................................ 24 1.3.4. Variations in glume pubescences .............................................................................