University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 12-2015 Applying Molecular and Phenotypic Tools to Characterize Flesh Texture and Acidity Traits in the Arkansas Peach Breeding Program and Understanding the Crispy Texture in the Arkansas Blackberry Breeding Program Alejandra Andrea Salgado Rojas University of Arkansas, Fayetteville Follow this and additional works at: http://scholarworks.uark.edu/etd Part of the Fruit Science Commons, and the Plant Breeding and Genetics Commons Recommended Citation Salgado Rojas, Alejandra Andrea, "Applying Molecular and Phenotypic Tools to Characterize Flesh Texture and Acidity Traits in the Arkansas Peach Breeding Program and Understanding the Crispy Texture in the Arkansas Blackberry Breeding Program" (2015). Theses and Dissertations. 1346. http://scholarworks.uark.edu/etd/1346 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. Applying Molecular and Phenotypic Tools to Characterize Flesh Texture and Acidity Traits in the Arkansas Peach Breeding Program and Understanding the Crispy Texture in the Arkansas Blackberry Breeding Program A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Science by Alejandra Salgado Rojas Pontificia Universidad Catolica de Chile Bachelor in Agricultural Science and Natural Resources, 2008 Pontificia Universidad Catolica de Chile Master in Agricultural Science, 2011 December 2015 University of Arkansas This dissertation is approved for recommendation to the Graduate Council. ______________________________ Dr. John R. Clark Dissertation Director ______________________________ ______________________________ Dr. M. Elena Garcia Dr. Richard E. Mason Committee Member Committee Member ______________________________ ______________________________ Dr. Craig S. Rothrock Dr. Allen L. Szalanski Committee Member Committee Member ABSTRACT Quantitative trait loci (QTL) utilizing a pedigree-based analysis (PBA) approach was performed in the peach breeding program for the first time. The pedigree consisted of seven-F1 populations, their parents, ancestors, and cultivars. Flesh firmness and titratable acidity (TA) were examined in 2011, 2012, and 2013. For TA, a consistent and strong QTL was identified on the proximal end of linkage group (LG) 5 of the peach genome. For flesh firmness, two QTLs were located on LG 4. The first QTL was located on the chromosomal region where the slow- melting flesh (SMF) DNA test was identified, and the second QTL was identified in the region of the endopolygalacturonase (endoPG) gene. However, the QTLs on LG 4 were not always consistent. These results indicate that PBA approach for QTL analysis can be applied with success in this mature and ongoing peach breeding program with the aim to find molecular markers associated with relevant quality traits, which is the first step to apply marker-assisted breeding (MAB). Also, DNA tests associated with TA and flesh firmness were analyzed with data taken in 2013 and 2014 on this pedigree and other seedlings, selections, and cultivars to predict acidity levels and flesh texture with the final goal to validate these DNA tests and apply MAB. These tests were able to predict correctly the expected acidity levels and flesh textures of the tested individuals. Firmness and texture are critical traits in blackberry for breeders, growers, and consumers. Crispy and extremely firm fruits were characterized for two blackberry selections which had been observed to have low color reversion (a postharvest disorder). Firmness of these selections and its seedlings were tested in 2013 and 2014. Results indicated that crispy selections had superior firmness and a higher postharvest storage potential compared to cultivars and other selections in the program. These results are important, because firmness will be increased and color reversion will be reduced by use of this germplasm. This research also contributed to better understanding of the physical aspects of crispy and non-crispy genotypes, providing more information about this aspect of blackberries. ACKNOWLEDGEMENTS I would like to thank Dr. John R. Clark, for giving me the opportunity to be part of the fruit breeding family at the University of Arkansas and for expanding my passion in fruit breeding. Dr. Clark‟s advice and friendship throughout my studies have been invaluable and will continue to guide me in my future career. Also, I would like to thank my committee, Dr. M. Elena Garcia, Dr. Richard E. Mason, Dr. Craig S. Rothrock, and Dr. Allen L. Szalanski for their assistance, guidance, and advice. Thanks to Dr. Eduard Gbur for his statistical advice and support. Many thanks to Dr. Ksenija Gasic at Clemson University and Dr. Cameron Peace at Washington State University for their advice and guidance on the molecular components of my dissertation. Thanks to the RosBREED project and its members for giving me the opportunity to be a “Rosbreedling” and learn more on molecular breeding as part of a collective team. Also, I would like to thank Pawel Wolinski and Jeff F. Pummill of the Arkansas High Performance Computing Center for their help in establishing a platform to operate FlexQTLTM. Special thanks to the staff at the University of Arkansas Fruit Research Station in Clarksville, their continuous help made my research possible. Also, special thanks to my colleagues and great friends Terrence J. Frett and Paul J. Sandefur, for their advice and friendship all these years, we sure make a great “peach team”. Also, thanks to Sujeet Verma and Jonathan Fresnedo, members of RosBREED, for their advice with FlexQTLTM. Thanks to the undergrad students who helped with several activities during summers, especially to Lesley Smith, and to Dr. Clark for making this possible. Finally, thanks to my entire family, their support during my graduate studies made my career goals easier to pursue. TABLE OF CONTENTS ABSTRACT ACKNOWLEDGEMENTS INTRODUCTION .......................................................................................................................... 1 LITERATURE REVIEW ............................................................................................................... 6 PEACH ........................................................................................................................................ 6 Origin and Botany of Peach [Prunus persica (L.) Batsch] ...................................................... 6 Peach Production and its Economic Importance ..................................................................... 8 Peach and Nectarine Breeding ............................................................................................... 10 Important Traits of Improvement in Breeding Programs ...................................................... 14 Major Trait Inheritance .......................................................................................................... 15 Molecular Genetics of Peach ................................................................................................. 20 The Diversity of Flesh Types of Peach ................................................................................. 24 Freestone – Melting Locus and the Endopolygalacturonase Enzyme ................................... 29 Other Enzymes and Proteins Involved in the Peach Softening and Ripening Processes ...... 32 Ethylene Cycle and its Role in Ripening and Softening ....................................................... 34 Destructive and Non-Destructive Texture Measurements ..................................................... 38 Molecular Advances in Peach Breeding ................................................................................ 40 Molecular Markers and Application of MAB in Peach ......................................................... 43 RosBREED Project................................................................................................................ 46 BLACKBERRY ........................................................................................................................ 49 Economic Importance and Use of Blackberries .................................................................... 49 Origin of Blackberry .............................................................................................................. 51 Taxonomy and Morphology .................................................................................................. 53 University of Arkansas Blackberry Breeding Program ......................................................... 56 Blackberry Breeding Programs Worldwide .......................................................................... 57 Blackberry Postharvest and its Importance for the Fresh-Market Industry........................... 59 Blackberry Texture and Fruit Firmness ................................................................................. 61 Other Traits Improved in Blackberry Breeding Programs .................................................... 64 Literature Cited ...................................................................................................................... 68 Chapter 1 ....................................................................................................................................... 85