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Artocarpus Integer, Moraceae), and Its Wild Relative Bangkong (Artocarpus Integer Var

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Artocarpus Integer, Moraceae), and Its Wild Relative Bangkong (Artocarpus Integer Var Diversity and origins of an underutilized tropical fruit tree, cempedak (Artocarpus integer, Moraceae), and its wild relative bangkong (Artocarpus integer var. silvestris) A THESIS SUBMITTED TO THE FACULTY OF THE PROGRAM IN PLANT BIOLOGY AND CONSERVATION BY MARIA WANG MEI HUA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN PLANT BIOLOGY AND CONSERVATION FROM NORTHWESTERN UNIVERSITY AND THE CHICAGO BOTANIC GARDEN November 20, 2014 1 Abstract The underutilized tropical fruit tree, “cempedak” (Artocarpus integer (Thunb.) Merr. , Moraceae), is a major crop in Malaysia but the distribution of genetic diversity in the crop and its putative wild progenitor, “bangkong” (Artocarpus integer var. silvestris Corner), have not been studied. To investigate the diversity and origins of cempedak, we assessed the genetic diversity of cempedak and bangkong, explored geographic patterns in genetic structure and differentiation, and conducted phylogenetic analyses. We also tested whether cempedak cultivars were true-to- type. We used 12 microsatellite loci to genotype 269 cempedak and 187 bangkong individuals from Peninsular Malaysia, 64 cempedak individuals from Borneo, and 12 cempedak samples from other regions. We found that the number of effective alleles (Ne), allelic richness (Ar), Shannon’s Information Index (I), and expected heterozygosity (He) were higher in bangkong populations than cempedak populations, but cempedak populations harbored alleles not found in bangkong populations. In contrast, Borneo cempedak showed overall lower genetic diversity compared to Peninsular cempedak. Both bangkong and cempedak exhibited weak geographic structure within Peninsular Malaysia; but we found evidence for isolation-by-distance among bangkong populations, as well as increased genetic structure in cempedak at a broader geographic scale. Borneo cempedak represented a gene pool distinct from Peninsular cempedak. Results of phylogenetic analyses varied based on the methods used, but indicate that bangkong or Borneo cempedak may be possible progenitors of Peninsular cempedak. Lastly, clonal analysis showed that cempedak cultivar names were not always indicative of genotype, which may be due to multiple reasons such as mislabeling, hybridization, and scoring errors. Although we did not find conclusive evidence regarding the origins of cempedak, this study confirmed that bangkong and Borneo cempedak populations harbor unique genetic variation that should be conserved. We hope that the results of this study will inform further research and conservation strategies for genetic resources of cempedak and other fruit crops in Malaysia and beyond. 3 Acknowledgements This research project was funded by the Plant Biology and Conservation Award from Northwestern University, the Botanical Society of America (BSA) Graduate Student Research Award, and a National Science Foundation grant awarded to my advisor, Nyree Zerega (NSF DEB REVSYS 0919119). My Masters education was funded in part by the Shaw Fellowship in Plant Biology and Conservation. I would like to thank my advisor Nyree Zerega, for being an all-round supportive, fantastic, and super-woman advisor and my thesis committee, Jeremie Fant (for his patience with my endless questions in the lab and during data analysis), and Andrea Kramer (for her kindness and apt advice) for all their valuable advice and help in this project. I would like to sincerely thank my Malaysian collaborators: the Economic Planning Unit (EPU) of Malaysia, Forestry Department of Peninsular Malaysia, Department of Orang Asli Development (JAKOA) for enabling this project; personal thanks to Dr. Richard Chung, Miss Chew Ming Yee, Dr. Lee Soon Leong, Angan, Apok, and others at FRIM; Dr. Abdul Rahman Milan, Dr. Salma Idris, Pn. Noor Baiti, En. Khadzir Darus, En. Mat Nazim, En. Mohd. Noor, En. Ai, En. Mohd. Azram, and others at MARDI; Pn. Zaliza and others at UPM; Dr. Ong Hean Chooi from USM for advice early on in the project; the Orange Asli communities, especially Norli (Sungai Buloh), Insan (Ulu Groh), whose knowledge of the forests is indispensable to forest research and conservation; Orang Asli guides Norli (Sungai Buloh), Insan (Ulu Groh); officers at JAKOA Jeli and Ayer Hitam; all of the cempedak tree/orchard owners and guides (Uncle Lim Boon Huat, Mr. Gan, Mr. Cheng, Aunty Michelle, Mr. James ‘Ah Fook’, Liew brothers, Mr. Lim from Balik Pulau, and others I have not mentioned), friends and family who have provided information, contacts, and assistance with travel/accommodation, with special thanks to my parents and their whole- 4 hearted support that was crucial to the success of this project. With all my heart, I would like to thank all the wonderful members of the Zerega lab who have been awesome in big and little ways, especially Elliot Gardner who deserves a gold star award for his help in various aspects of the project including sequencing, providing R code, and helping obtain additional leaf material from herbarium specimens; members of the CBG genetics lab; members of the Eco-Climate lab at SCBI; CBG folks and the trusty PACE 213 bus for ferrying me to and from CBG; and everyone who have helped in any way to make this project possible – again, Ribuan Terima Kasih!!! 5 Table of Contents Signature page ......................................................................................................................................... 2 Abstract ................................................................................................................................................... 3 Acknowledgements ................................................................................................................................. 4 Table of Contents .................................................................................................................................... 6 List of Figures ......................................................................................................................................... 8 List of Tables ........................................................................................................................................ 10 1. Introduction ....................................................................................................................................... 12 1.1 Malaysia .............................................................................................................................. 14 1.2 Study Species ...................................................................................................................... 17 1.3 Uses of cempedak ............................................................................................................... 19 1.4 Wild relative of cempedak: Bangkong ............................................................................... 21 1.5 Cempedak Research in Malaysia ........................................................................................ 26 1.6 Objectives and Hypotheses ................................................................................................. 27 2. Methods ............................................................................................................................................ 31 2.1 Site selection and sampling ................................................................................................. 31 2.2 Microsatellite amplification and genotyping ...................................................................... 43 2.3 Genetic diversity ................................................................................................................. 46 2.3 Geographic patterns in genetic structure and differentiation .............................................. 46 2.4 Phylogenetic analyses ......................................................................................................... 47 2.5 Analysis of cempedak cultivars .......................................................................................... 48 3. Results .............................................................................................................................................. 49 3.1 Genetic diversity ................................................................................................................. 49 3.1.1 Diversity across loci ..................................................................................................... 49 3.1.2 Diversity of cempedak and bangkong .......................................................................... 50 3.1.3 Diversity of Peninsular and Borneo cempedak ............................................................ 53 3.2 Geographic patterns in genetic structure and differentiation .............................................. 54 3.2.1 Structure analysis ......................................................................................................... 54 3.2.2 Population Differentiation ........................................................................................... 64 3.2.3 Isolation-by-distance .................................................................................................... 69 3.3 Phylogenetic analysis of cempedak and bangkong ............................................................. 70 3.4 Analysis of cempedak cultivars .......................................................................................... 76 3.4.1 Cultivar names, clonal assignment and structure ........................................................
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