University of Massachusetts Amherst ScholarWorks@UMass Amherst Masters Theses 1911 - February 2014 January 2008 Self-Incompatibility in African Lycium (Solanaceae) Natalie M. Feliciano University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/theses Feliciano, Natalie M., "Self-Incompatibility in African Lycium (Solanaceae)" (2008). Masters Theses 1911 - February 2014. 133. Retrieved from https://scholarworks.umass.edu/theses/133 This thesis is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Masters Theses 1911 - February 2014 by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. SELF-INCOMPATIBILITY IN AFRICAN LYCIUM (SOLANACEAE) A Thesis Presented by NATALIE M. FELICIANO Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 2008 Plant Biology SELF-INCOMPATIBILITY IN AFRICAN LYCIUM (SOLANACEAE) A Thesis Presented by NATALIE M. FELICIANO Approved as to style and content by: __________________________________________ Jill S. Miller, Chair __________________________________________ Lynn Adler, Member __________________________________________ Ana Caicedo, Member ________________________________________ Elsbeth Walker, Department Head Plant Biology Graduate Program DEDICATION To my brother, David Feliciano, for all your kind words, support and love. Without you, I truly believe that I would not have survived graduate school. ACKNOWLEDGMENTS I would like to give an extremely warm and heartfelt thank you to my thesis advisor, Dr. Jill S. Miller. Thank you for the time and energy that you put into helping me with my work and our research. You are an amazing advisor, role model and friend. Thank you to the North East Alliance for Graduate Education and Professoriate (NEAGEP) for awarding me a graduate fellowship. Thank you to the Dr. Albert L. Delisle Scholarship Fund for awarding me a research grant that helped fund my research travels to South Africa. Thank you to the Botanical Society of America for awarding me a graduate student research award to fund my studies on isolating the SLF self- incompatibility gene in Lycium. Thank you to the following southern African permitting agencies: Western Cape Nature Conservation Board, the Free State Department of Tourism, Environmental and Economic Affairs, the Namibian Ministry of Environment and Tourism, the Northern Cape Nature Conservation Service, and the South African National Parks. Additionally, thank you to P. Nel and A. Le Roux for allowing access to the plants used in the pollination experiments. Chapter one of my thesis has been published in the May 2008 issue of the journal Evolution under the title “A TALE OF TWO CONTINENTS: BAKER’S RULE AND THE MAINTENANCE OF SELF-INCOMPATIBILITY IN LYCIUM (SOLANACEAE).” i v ABSTRACT SELF-INCOMPATIBILITY IN AFRICAN LYCIUM (SOLANACEAE) MAY 2008 NATALIE M. FELICIANO, B.S., UNIVERSITY OF ROCHESTER M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Dr. Jill S. Miller Chapter one of my thesis has been published in the May 2008 issue of the journal Evolution under the title “A TALE OF TWO CONTINENTS: BAKER’S RULE AND THE MAINTENANCE OF SELF-INCOMPATIBILITY IN LYCIUM (SOLANACEAE).” This chapter was co-authored by Dr. Jill S. Miller and Dr. Rachel Levin. v TABLE OF CONTENTS Page ACKNOWLEDGMENTS............................................................................................ iv ABSTRACT ................................................................................................................. v LIST OF TABLES....................................................................................................... ix LIST OF FIGURES ..................................................................................................... xi CHAPTER 1. A TALE OF TWO CONTINENTS: BAKER’S RULE AND THE MAINTENANCE OF SELF-INCOMPATIBILITY IN LYCIUM (SOLANACEAE).................................................................................. 1 1.1 Introduction................................................................................................. 1 1.2 Materials and Methods ................................................................................ 5 1.2.1 Study System ................................................................................ 5 1.2.2 Controlled Pollinations.................................................................. 5 1.2.3 S-RNase Diversity ........................................................................ 7 1.2.4 Selection Analyses of the S-RNase Gene..................................... 10 1.3 Results....................................................................................................... 11 1.3.1 Controlled Pollinations................................................................ 11 1.3.2 S-RNase Diversity ...................................................................... 13 1.3.3 Selection Analyses of the S-RNase Gene..................................... 14 1.3 Discussion................................................................................................. 15 1.3.1 Controlled Pollinations................................................................ 15 1.3.2 S-RNase Diversity ...................................................................... 17 1.3.3 Trans-generic Evolution.............................................................. 18 1.3.4 Selection Analyses of the S-RNase Gene..................................... 20 1.4 Conclusions............................................................................................... 22 2. ALLELIC DIVERSITY AND SEQUENCE SIMILARITY AMONG S-RNASE ALLELES FROM NINE SPECIES OF OLD WORLD LYCIUM......... 31 2.1 Introduction............................................................................................... 31 vi 2.1.1 Gametophytic Self-Incompatibility ............................................. 31 2.1.2 Study System .............................................................................. 35 2.1.3 Self-incompatibility in Old World Lycium................................... 36 2.1.4 Current Study.............................................................................. 38 2.2 Methods .................................................................................................... 41 2.2.1 Isolation of S-RNase Alleles from Style Tissue ........................... 41 2.2.2 Genomic PCR ............................................................................. 43 2.2.3 Genealogy and Phylogeny Construction Using Maximum Likelihood................................................................................ 44 2.2.3.1 S-RNase Allele Genealogy............................................ 44 2.2.3.2 Lycium Phylogeny ........................................................ 46 2.2.4 Selection and Diversity at the S-RNase Gene............................... 46 2.3 Results....................................................................................................... 48 2.3.1 Isolation of S-RNase Alleles........................................................ 48 2.3.2 S-RNase Genealogy and Lycium Phylogeny ................................ 49 2.3.3 Selection and Diversity at the S-RNase Gene............................... 49 2.4 Discussion................................................................................................. 51 2.4.1 S-RNase Genealogy .................................................................... 51 2.4.2 Selection on and Diversity of the S-RNase Gene ......................... 53 2.4.3 Identical Partial S-RNase Alleles................................................. 54 2.5 Conclusions............................................................................................... 59 3. ISOLATION OF THE LYCIUM SLF GENE ................................................... 73 3.1 Introduction............................................................................................... 73 3.2 Methods .................................................................................................... 76 3.2.1 Study System .............................................................................. 76 3.2.2 SLF Isolation............................................................................... 77 3.3 Results....................................................................................................... 79 3.4 Discussion................................................................................................. 80 3.5 Conclusions............................................................................................... 81 vi i APPENDIX Raw Data Associated with Fig 1.2................................................................... 89 BIBLIOGRAPHY....................................................................................................... 90 vi ii LIST OF TABLES Table Page 1.1. S-RNase genotypes for individual Lycium sequenced in the present study...... 24 1.2. Likelihood ratio tests comparing models of neutral evolution (M1a and M7) with corresponding models that incorporate positive selection (M2a and M8) for New World and Old World Lycium S-RNases......... 25 2.1. Allele specific primers designed to amplify similar S-RNase sequences among African Lycium species............................................................. 61 2.2. Allele specific