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THE GENETICS of CHILLING REQUIREMENT in APRICOT (PRUNUS ARMENIACA L.) Bode Olukolu Clemson University, [email protected]

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THE GENETICS of CHILLING REQUIREMENT in APRICOT (PRUNUS ARMENIACA L.) Bode Olukolu Clemson University, Bolukol@Clemson.Edu Clemson University TigerPrints All Dissertations Dissertations 5-2010 THE GENETICS OF CHILLING REQUIREMENT IN APRICOT (PRUNUS ARMENIACA L.) Bode Olukolu Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Genetics Commons Recommended Citation Olukolu, Bode, "THE GENETICS OF CHILLING REQUIREMENT IN APRICOT (PRUNUS ARMENIACA L.)" (2010). All Dissertations. 537. https://tigerprints.clemson.edu/all_dissertations/537 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. THE GENETICS OF CHILLING REQUIREMENT IN APRICOT (PRUNUS ARMENIACA L.) ____________________________________________ A Dissertation Presented to The Graduate School of Clemson University ___________________________________________ In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Genetics ____________________________________________ by Bode Adebowale Olukolu May 2010 ____________________________________________ Accepted by: Dr. Albert G. Abbott, Committee Chair Dr. Julia Frugoli Dr. Chin-Fu Chen Dr. Amy Lawton-Rauh ABSTRACT Commercial production of apricot is severely affected by sensitivity to climatic conditions, an adaptive feature essential for cycling between vegetative or floral growth and dormancy. Yield losses are due to either late winter or early spring frosts or inhibited vegetative or floral growth caused by unfulfilled chilling requirement (CR). Studies in this dissertation developed the first high-density apricot linkage map; followed by a comparative mapping strategy to validate conservation of synteny, genome collinearity and stable quantitative trait loci (QTLs) controlling CR and bud break between apricot and peach; and ultimately attempt to identify key candidate genes following a linkage disequilibrium-based association mapping approach to fine map the major CR QTL genomic regions. Following a two-way pseudotestcross mapping strategy, two high-density apricot maps were constructed using a total of 43 SSR (Simple Sequence Repeats) and 994 AFLP (Amplified Fragment Length Polymorphism) markers that span an average of 502.6 cM with an average marker interval of 0.81 cM. Twelve putative CR QTLs were detected using composite interval mapping, a simultaneous multiple regression fit and an additive- by-additive epistatic interaction model without dominance. An average of 62.3% ± 6.3% of the total phenotypic variance was explained. We report QTLs corresponding to map positions of differentially expressed transcripts and suggest candidate genes controlling CR. ii A majority of the QTLs were shown to be stable between both Prunus species, as well as similar trends in their QTL effects, with the allele for increasing the trait value mostly originating from the high chill parents. The denser apricot maps, due to more AFLP marker polymorphisms, provide a higher resolution to delineate QTLs to smaller genomic intervals, as well as splitting each of some of the peach QTLs into two. The comparative QTL mapping strategy presented here reveals the transferability of genetic information between two Prunus species, the characterization of stable QTLs, the utility of the maps to consolidate each other and to further validate previously identified CR QTL loci as a major controlling factor driving floral bud break. The LD-based association mapping was limited to marker dense genomic regions within and around previously detected major QTLs on linkage group (LG) 1 and 7. LD decayed below the centimorgan scale, indicating insufficient marker density averaged at 0.44 and 1.58 cM on LG1 and 7, respectively. Denser marker regions averaged at 0.1 and 0.7 cM on LG1 and 7, respectively, revealed significant LD estimates above the baseline threshold. We report significant marker-trait associations and underlying genes the markers were derived from. Our results demonstrate that an LD-based association mapping can be used for validating QTLs, fine mapping and detecting CGs in Prunus. iii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Albert Abbott, for giving me the opportunity to work with him and for always been there as a mentor and guide. I also extend my gratitude to my committee members: Dr. Julia Frugoli, Dr. Chin-Fu Chen and Dr. Amy Lawton-Rauh, for all their support and advice throughout the program. Thanks to Dr. Doron Holland and Taly Trainin for providing, maintaining and scoring the phentoypes on the apricot mapping population, Dr. William Okie for providing the peach mapping population, Dr. Gregory L. Reighard and Dr. Douglas G. Bielenberg for maintaining the peach mapping population an Dr. Valentina Gorina for maintaining and scoring the phenotypic data on the apricot germplasm used for the association mapping. Special thanks to members of the Abbott‟s lab. Thanks to Dr. Tatyana N. Zhebentyayeva, for establishing the collaboration on the association mapping, providing apricot germplasm DNA samples, designing SSR markers and for her help on several occasions as a senior colleague and friend. Thanks to Dr. Laura L. Georgi, who made life in the lab comfortable and who was always available as a resource person. Thanks to Dr. Renate Horn for all her unrelenting help, Dr. Chittaranjan Kole whose help I can‟t list exhaustively and to graduate students who showed me the ropes: Renea Hardwick, Fan Shenghua and Samuel Forrest. I would also like to thank Sherri Hughes-Murphree, Megan Mosanto and Phullara Kole for their support in the lab and Jeanice Troutman of CUGI for her help with DNA sequencing. iv TABLE OF CONTENTS Page TITLE PAGE ....................................................................................................................... i ABSTRACT ........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv LIST OF TABLES ............................................................................................................. ix LIST OF FIGURES .............................................................................................................x CHAPTER I LITERATURE REVIEW ............................................................................1 Introduction .....................................................................................1 Regulation of growth cycles and dormancy in woody perennials .........................................................................3 Complexity of bud dormancy and its overlap with related biological processes ...................................................10 Dormancy induction.......................................................................14 Bud dormancy maintenance and release ........................................18 Genetic control of endodormancy-related traits in woody perennials ..............................................................22 Summary of chapters .....................................................................26 References ......................................................................................30 II GENETIC LINKAGE MAPPING FOR MOLECULAR DISSECTION OF CHILLING REQUIREMENT AND BUD BREAK IN APRICOT (PRUNUS ARMENIACA L.) ......................................................................47 Abstract ..........................................................................................48 Introduction ....................................................................................49 Materials and methods ...................................................................50 Results ............................................................................................59 Discussion ......................................................................................70 Conclusion .....................................................................................74 Acknowledgement .........................................................................75 References ......................................................................................76 v III COMPARATIVE ANALYSIS OF QTLS UNDERLYING CHILLING REQUIREMENT AND BUD BREAK IN PEACH (PRUNUS PERSICA L.) AND APRICOT (P. ARMENIACA L.) ................................................82 Abstract ..........................................................................................83 Introduction ....................................................................................84 Materials and methods ...................................................................86 Results ............................................................................................90 Discussion ....................................................................................103 Acknowledgement .......................................................................105 References ....................................................................................106 IV ASSOCIATION MAPPING FOR CANDIDATE GENES UNDERLYING FLORAL BUD BREAK IN APRICOT (PRUNUS ARMENIACA L.) ....109 Abstract ........................................................................................110 Introduction ..................................................................................112 Materials and methods
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