ESTIMATION OF PLOIDY LEVELS AND GENETIC PARAMETERS FOR A BERMUDAGRASS COLLECTION By ALEXANDRA RUCKER A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2016 1 © 2016 Alexandra Rucker 2 To my mother, without whom none of this would be possible 3 ACKNOWLEDGMENTS I would like to sincerely thank my main advisor, Dr. Patricio Munoz, for his constant supervision and support. I truly appreciate all of the time he invested in me, and my project. I would like to add additional thanks to Esteban Rios, Lin Xing and Yolanda Lopez for all of the aid they provided in the field and in the lab. I would also like to thank my mother and siblings for their emotional support. Completing this project would have been much harder without them. This has been a long journey, but a worthwhile one. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 7 LIST OF FIGURES .......................................................................................................... 8 LIST OF ABBREVIATIONS ............................................................................................. 9 ABSTRACT ................................................................................................................... 10 CHAPTER 1 INTRODUCTION .................................................................................................... 12 Importance .............................................................................................................. 12 Bermudagrass Cultivars and Forage Breeding ....................................................... 12 New Threat ............................................................................................................. 14 Objectives ............................................................................................................... 15 Cynodon Ploidy ................................................................................................ 15 Cynodon Genetic Parameters for Breeding ...................................................... 17 2 DETERMINATIONS OF BERMUDAGRASS PLOIDY ............................................ 19 Materials and Methods............................................................................................ 19 Germplasm ....................................................................................................... 19 Field Trial .......................................................................................................... 19 Phenotypes ...................................................................................................... 20 Flow Cytometry ................................................................................................ 21 Ploidy-Traits Association Analysis .................................................................... 23 Results and Discussion........................................................................................... 23 Data Overview .................................................................................................. 23 Ploidy Effect on phenotypic traits ..................................................................... 29 3 ESTIMATION OF GENETIC PARAMETERS OF BERMUDAGRASS .................... 45 Materials and Methods............................................................................................ 45 Germplasm ....................................................................................................... 45 Field Trial .......................................................................................................... 45 Phenotypes ...................................................................................................... 46 Genetic Parameter Estimation .......................................................................... 47 Results and Discussion........................................................................................... 49 Heritability ......................................................................................................... 49 Genotype-by-measurement correlation ...................................................... 51 Traits Genetic Correlations ............................................................................... 52 5 Genotype-by-Environment Interaction .............................................................. 54 4 CONCLUSION ........................................................................................................ 63 APPENDIX: SUPPLEMENTARY MATERIAL ................................................................ 67 LIST OF REFERENCES ............................................................................................... 74 BIOGRAPHICAL SKETCH ............................................................................................ 79 6 LIST OF TABLES Table page 2-1 Dates of Data Collection ..................................................................................... 35 2-2 Ploidy level by genome size determined by flow cytometry ................................ 36 2-3 Mean and standard error (in parenthesis) of all phenotypic traits collected in the field experiment by measurement. ................................................................ 37 2-4 P-values of ploidy level effect on dry matter yield for six harvests for all Cynodon species present in collection and for C. dactylon specifically. ............. 38 2-5 P-values provided for all species in collection and for C. dactylon only .............. 39 2-6 Cultivars with the lowest and highest values for measured traits, as well as the average values for the control cultivars. ....................................................... 40 2-7 Lowest and highest yields (kg/ha) per harvest in Citra 2015, as well as the average yields for the control cultivars. Cultivar with highest and lowest yield in parenthesis ..................................................................................................... 40 2-8 Lowest and highest yields (kg/plot) per harvest in Tifton 2015, as well as the average yields for the control cultivars. Cultivar with highest and lowest yield in parenthesis ..................................................................................................... 41 3-1 Trait classification, description and date of its data recorded from the field experiment .......................................................................................................... 55 3-2 Mean and standard error (in parenthesis) of all phenotypic traits collected in the field experiment by measurement. ................................................................ 56 3-3 Broad-sense heritability of traits measured in the bermudagrass field trial ......... 57 3-4 Genetic correlations (below diagonal) among traits measured from the field trial and its respective standard errors (above diagonal). ................................... 58 3-5 Genetic correlations (below diagonal) between Citra yield measurement dates and its respective standard errors (above diagonal) ................................. 59 3-6 Genetic correlations (below diagonal) between Tifton yield measurement dates and its respective standard errors (above diagonal) ................................. 59 A-1 Estimated genome size and ploidy level for whole bermudagrass collection ..... 67 7 LIST OF FIGURES Figure page 2-1 Histograms showing fluorescence intensity. ....................................................... 42 2-2 Bar graphs comparing the average environmental damage ............................... 43 2-3 Bar graphs comparing the average physiological traits ...................................... 44 3-1 Broad-sense heritability for yield by harvest measurement in two location of the southern USA (Citra, FL and Tifton, GA). ..................................................... 60 3-2 Broad-sense heritability accounting for measurement effect for traits measured more than once in the field experiment. ............................................. 61 3-3 Genotype-by-measurement correlation for traits measured more than once in the field trials ...................................................................................................... 62 8 LIST OF ABBREVIATIONS ADF Acid detergent fiber (ADF) BSM Bermudagrass stem maggot (Atherigona reversura Villeneuve), a relatively new bermudagrass pest in the United States. Originally from Asia, the fly was first discovered in Tifton, GA in 2010 (Hancock, 2012). GxE Genotype-by-Environment interaction GxM Genotype-by-Measurement interaction IVTD In vitro true digestibility (IVTD) NDF Neutral detergent fiber (NDF) 9 Abstract of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science ESTIMATION OF PLOIDY LEVELS AND GENETIC PARAMETERS FOR A BERMUDAGRASS COLLECTION By Alexandra Rucker December 2016 Chair: Patricio R. Munoz Major: Agronomy Bermudagrass is the most widely used warm-season perennial forage in the Southeastern United States. There is increased market demand due to the introduction of a new invasive pest, Bermudagrass Stem Maggot (BSM), and the desire for higher quality forage. However in recent years, the development of