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The Evolution and Domestication Genetics of the Mango Genus Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 4-27-2018 The volutE ion and Domestication Genetics of the Mango Genus, Mangifera (Anacardiaceae) Emily Warschefsky Florida International University, [email protected] DOI: 10.25148/etd.FIDC006564 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Biodiversity Commons, Biology Commons, Botany Commons, Genetics and Genomics Commons, and the Plant Breeding and Genetics Commons Recommended Citation Warschefsky, Emily, "The vE olution and Domestication Genetics of the Mango Genus, Mangifera (Anacardiaceae)" (2018). FIU Electronic Theses and Dissertations. 3824. https://digitalcommons.fiu.edu/etd/3824 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida EVOLUTION AND DOMESTICATION GENETICS OF THE MANGO GENUS, MANGIFERA (ANACARDIACEAE) A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Emily Warschefsky 2018 To: Dean Michael R. Heithaus College of Arts, Sciences and Education This dissertation, written by Emily Warschefsky, and entitled Evolution and Domestication Genetics of the Mango Genus, Mangifera (Anacardiaceae), having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. _______________________________________ Carl Lewis _______________________________________ Joel Trexler _______________________________________ Giri Narasimhan _______________________________________ Heather Bracken-Grissom _______________________________________ Maureen Donnelly, Co-Major Professor _______________________________________ Eric von Wettberg, Co-Major Professor Date of Defense: April 27, 2018 The dissertation of Emily Warschefsky is approved. _______________________________________ Dean Michael R. Heithaus College of Arts, Sciences and Education _______________________________________ Andrés G. Gil Vice President for Research and Economic Development and Dean of the University Graduate School Florida International University, 2018 ii COPYRIGHT PAGE The following chapters have been published in their entirety in peer-reviewed journals. According to the stated policy of each journal, they can be included here without obtaining formal copyright permission by using a proper citation. CHAPTER II Back to the Wilds: Tapping Evolutionary Adaptations for Resilient Crops Through Systematic Hybridization With Crop Wild Relatives. Warschefsky, E. R.V. Penmetsa, D.R. Cook, and E.J.B. von Wettberg. American Journal of Botany 101 (10): 1791–1800, 2014. doi:10.3732/ajb.1400116 CHAPTER III Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes. Warschefsky, E.J., L.L. Klein , M.H. Frank, D.H. Chitwood, J.P. Londo, E.J.B. von Wettberg, and A.J. Miller. Trends in Plant Science 21(5): 418–437. doi 10.1016/j.tplants.2015.11.008. ALL OTHER WORK © Copyright 2018 by Emily Warschefsky All rights reserved. iii DEDICATION To my parents, who instilled in me a love of questions and a yearning to answer them. iv ACKNOWLEDGMENTS First, thank you to my committee members (past and present) for sharing their expertise: Dr. Richard Campbell for his devotion to the mango and its wild relatives and for putting together a magnificent germplasm collection at Fairchild Tropical Botanic Garden (FTBG), Dr. Carl Lewis for the introduction to Indonesia and support in the lab at FTBG, Dr. Giri Narasimhan for his advice in bioinformatic endeavors, and Dr. Joel Trexler for his ecological and evolutionary insights. I want to extend a special thank you to Dr. Heather Bracken-Grissom for welcoming me into her laboratory space and community along with providing expertise and guidance on phylogenomics. Thank you to my co-advisor Dr. Maureen Donnelly for her spirited reassurance, support, and editing skills during the final stages of my dissertation. And finally, thank you to my co-advisor, Dr. Eric von Wettberg, for his boundless enthusiasm and for encouraging me to pursue my own research interests. I am also grateful for the amazing community of labmates I have had the pleasure of working with over the years and who enriched my graduate school experience: Tonya Fotinos, Klara Scharnagl, Vanessa Sanchez, Damien Nesbeth, Seth Manthey, Eddie Marques, Jorge Pérez-Moreno, and Kelsey Reider. I also want to say a huge thank you to Laura Timm, my labmate and partner in navigating RADseq library preparation and data analysis. Thank you also to Danielle Coogan and Rachel Matthews who performed countless DNA extractions for my project. I would like to acknowledge the following support that I have received from many grants, travel awards, and fellowships throughout my time as a PhD student: NSF Doctoral Dissertation Improvement Grant, USDA National Institute of Food and v Agriculture AFRI Fellowship, Fairchild Graduate Studies Dissertation Grant, Singapore Botanic Gardens Fellowship, Kelly Foundation Graduate Award for Tropical Botany, American Society of Plant Taxonomists Graduate Student Research Grant, Botanical Society of America Graduate Student Research Award, International Center for Tropical Botany Travel Award, Society for the Study of Evolution Graduate Student Travel Award, Botanical Society of America International Botanical Congress Travel Award, International Botanical Congress Travel Award, FIU Tropics Travel Award. I would also like to acknowledge funding for research assistantships and graduate fellowships provided by: Dr. Eric von Wettberg (Feed the Future Innovation Lab), USDA Project Grow, Fairchild Graduate Student Fellowship Program, FIU Dissertation Evidence Acquisition Fellowship, and FIU Dissertation Year Fellowship. I am extremely grateful to the many institutions, colleagues, and collaborators that have helped me collect samples and hosted me during my travels – without them my research would not have been possible. Thank you to all of the staff who helped me at Fairchild Tropical Botanic Garden, Miami Dade Fruit and Spice Park, and the USDA's Chapman Field Station. Thank you to the many staff members at Bogor Botanic Garden, Purwodadi Botanic Garden, Singapore Botanic Garden, Pasoh Forest, and the Forestry Research Institute of Malaysia for their kindness and hospitality during my field trips. I would especially like to thank my Anacardiaceae collaborators, John D. Mitchell of the New York Botanic Garden, Susan Pell of the U.S. Botanic Garden, and Allison Miller of St. Louis University, who have so kindly provided their expertise throughout my graduate career. vi Finally, thank you to my collaborators and coauthors on Chapters I and II for their contributions to these impactful reviews: Dan Chitwood, Doug Cook, Margaret Frank, Laura Klein, Jason Londo, Allison Miller, R. Varma Penmetsa, and Eric von Wettberg. vii ABSTRACT OF THE DISSERTATION EVOLUTION AND DOMESTICATION GENETICS OF THE MANGO GENUS, MANGIFERA (ANACARDIACEAE) by Emily Warschefsky Florida International University, 2018 Miami, Florida Professor Eric von Wettberg, Co-Major Professor Professor Maureen Donnelly, Co-Major Professor Domesticated species are vital to global food security and have also been foundational to the formulation and advancement of evolutionary theory. My dissertation employs emerging molecular genomic tools to provide an evolutionary context for crop improvement. I begin by providing a contemporary perspective on two components of domestication biology that have long been used to improve crop production: wild relatives of crop species and grafted rootstocks. First, I propose a method to systematically introgress diversity from crop wild relatives into crop breeding programs. Then, I explore rootstocks, the lesser-known half of the perennial crop equation, documenting prevalence and diversity, cataloging rootstock traits under selection, and discussing recent advances in rootstock biology. Both crop wild relatives and rootstocks remain largely underutilized resources and hold great promise for agricultural innovation. While humans have domesticated thousands of plant species, research has largely focused on annual crops, to the exclusion of perennials. To improve our understanding of viii how tree species respond to domestication, I examine the evolution and domestication of one of the world’s most important perennial tropical fruit crops, the mango, Mangifera indica, and its wild and semi-domesticated relatives. I generated a dataset suitable for studying Mangifera across evolutionary time using double digest restriction site associated DNA sequencing. I present a multilocus phylogeny that informs the classification of Mangifera and reveals, for the first time, the evolutionary relationships of wild, semi-domesticated, and domesticated species in the genus. Narrowing my focus to the intraspecific level, I examine how the introduction of M. indica into regions of the world impacted its genetic diversity. My results show M. indica maintained high levels of genetic diversity during its introduction into the Americas. However, the novel diversity I detect in Southeast Asian mango cultivars suggests that M. indica has a more complex domestication history than previously assumed.
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