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University of Florida Thesis Or Dissertation Formatting ESTIMATION OF GENETIC PARAMETERS FOR ECONOMICALLY IMPORTANT TRAITS IN SOUTHERN HIGHBUSH BLUEBERRIES By CATHERINE CELLON 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 2015 1 © 2015 Catherine Cellon 2 To my parents and friends, thanks for always being there for me 3 ACKNOWLEDGMENTS I would like to sincerely thank my main advisors, Dr. Jim Olmstead and Dr. Patricio Munoz, for all their help and patience. I know you are both incredibly busy and I really appreciate the time you took to answer all my questions and listen to my concerns. Thank you Dr. Matias Kirst for your knowledge and input on the project. Thank you Werner Collante and David Norden for all your help in the field and the lab. I would like to thank all the undergraduate students who helped with my project, especially Allison Bechtloff, Kaitlin Quincy, Ashley Leonard, Elliot Norden, and Micah Weiss. I know the work was incredibly tedious, but I appreciate all your positive attitudes and attention to detail. Thank you Rodrigo for always answering my software questions and developing the packages I used throughout my project. Finally, I would like to acknowledge the blueberries. If those tiny blue guys weren’t so popular, I would not have had a fantastic research project. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 7 LIST OF FIGURES .......................................................................................................... 8 LIST OF ABBREVIATIONS ............................................................................................. 9 ABSTRACT ................................................................................................................... 10 CHAPTER 1 LITERATURE REVIEW .......................................................................................... 12 Economic Importance ............................................................................................. 12 Taxonomy and Description ..................................................................................... 13 Primary Blueberry Species ..................................................................................... 15 Blueberry Breeding ................................................................................................. 16 Early Cultivation ............................................................................................... 16 Breeding Southern Highbush Blueberries for Florida’s Climate ........................ 16 Importance of 2n Gametes in Blueberry Breeding ............................................ 17 Recurrent Selection .......................................................................................... 18 Best Linear Unbiased Prediction ............................................................................. 20 Implications of Autotetraploids ................................................................................ 21 Cytological Behavior ............................................................................................... 24 Current Blueberry Research ................................................................................... 25 2 FOUNDING CLONES, COANCESTRY, AND INBREEDING IN THE UNIVERSITY OF FLORIDA SOUTHERN HIGHBUSH BLUBERRY BREEDING PROGRAM ...... 27 Materials and Methods............................................................................................ 29 Pedigree Information ........................................................................................ 29 Coefficient of Coancestry ................................................................................. 29 Inbreeding Coefficient ...................................................................................... 30 Results and Discussion........................................................................................... 30 Identification of the Founding Clones ............................................................... 30 Genetic Contribution From The Founding Clones ............................................ 33 Inbreeding Coefficient ...................................................................................... 37 Conclusion .............................................................................................................. 39 3 ESTIMATION OF DOUBLE REDUCTION LEVELS FOR SOUTHERN HIGHBUSH BLUEBERRY SELECTION TRAITS ....................................................................... 55 Materials and Methods............................................................................................ 58 5 Blueberry Breeding Population and Pedigree ................................................... 58 Phenotyping ..................................................................................................... 59 Analysis and Model Comparison ...................................................................... 60 Matrix Construction with AGHmatrix ................................................................. 61 Results and Discussion........................................................................................... 63 Double Reduction in Blueberry ......................................................................... 63 Effect of Double Reduction on Inheritance ....................................................... 64 Effect of Double Reductions on the A-matrix Construction ............................... 65 Changes in Depth of Pedigree on Double Reduction Estimates ...................... 66 Conclusions ............................................................................................................ 68 4 ESTIMATION OF GENETIC PARAMETERS IN SOUTHERN HIGHBUSH BLUEBERRIES ....................................................................................................... 73 Materials and Methods............................................................................................ 76 Blueberry Breeding Population ......................................................................... 76 Phenotyping Methods ....................................................................................... 77 Statistical Analysis ............................................................................................ 79 Estimation of Expected Genetic Gain ............................................................... 81 Results and Discussion........................................................................................... 81 Population Distributions .................................................................................... 81 Estimation of Genetic Parameters .................................................................... 82 Breeding Values ............................................................................................... 87 Estimated Genetic Gain ................................................................................... 88 Conclusion .............................................................................................................. 89 5 SUMMARY AND CONCLUSIONS .......................................................................... 97 LIST OF REFERENCES ............................................................................................. 100 BIOGRAPHICAL SKETCH .......................................................................................... 110 6 LIST OF TABLES Table page 2-1 Founding clones from high chilling requirement germplasm used in the University of Florida southern highbush blueberry breeding program ................ 40 2-2 Founding clones from low chilling requirement germplasm used in the University of Florida southern highbush blueberry breeding program ................ 40 2-3 The coefficient of coancestry between the high chilling requirement founders and the southern highbush blueberry cultivars released by the University of Florida ................................................................................................................ 41 2-4 The coefficient of coancestry between the low chilling requirement founders and southern highbush blueberry cultivars released by the University of Florida ................................................................................................................ 42 2-5 Inbreeding coefficients for the southern highbush blueberry cultivars released from the University of Florida .............................................................................. 43 2-6 The coefficient of coancestry between the high chilling requirement founders and the parents of the 2011 southern highbush blueberry breeding population ........................................................................................................... 44 2-7 The coefficient of coancestry between the low chilling requirement founders and the parents of the 2011 southern highbush blueberry breeding population ........................................................................................................... 48 2-8 Inbreeding coefficients for the parents of the 2011 southern highbush blueberry breeding population ............................................................................ 51 3-1 The heritability of five breeding traits calculated assuming disomic and tetrasomic
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