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Open Diwu Dissertation Summer2018.Pdf The Pennsylvania State University The Graduate School Intercollege Program in Integrative Biosciences INTRASPECIFIC VARIATION IN GREEN ASH RESPONSE TO AN INVASIVE INSECT A Dissertation in Bioinformatics and Genomics by Di Wu © 2018 Di Wu Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2018 The dissertation of Di Wu was reviewed and approved* by the following: John E. Carlson Professor of Molecular Genetics Dissertation Advisor Chair of Committee Jesse R. Lasky Assistant Professor of Biology Majid Foolad Professor of Plant genetics Rongling Wu Professor of Public Health Sciences Cooduvalli Shashikant Associate Professor of Molecular and Developmental Biology Chair of Bioinformatics and Genomics Graduate Program *Signatures are on file in the Graduate School ii ABSTRACT Green ash (Fraxinus pennsylvanica) is a medium-sized, ecologically and economically valuable tree species native to the eastern and central United States. However, the widely distributed green ash species in North America is under severe threat from the rapid invasion of emerald ash borer (Agrilus planipennis; EAB), an Asian wood-boring beetle. To understand the mechanism of the defense response, transcriptomes were prepared for six green ash genotypes exposed to EAB infestation, using an RNA-seq approach. Mapping these reads to the de novo assembled reference of 107,611 transcript contigs, prepared from 98 Gb of RNAseq data from multiple tissues and treatments (www.hardwoodgenomics.org/node/68249), enabled differentially expressed genes to be identified between potentially resistant (trees that survived EAB-infestations, hereafter simply referred to as “resistant”) and susceptible genotypes and between control and EAB egg-treated bark samples. The enrichment analysis showed that most of the overrepresented GO terms were related to stress response in the resistant genotypes. In addition, our results indicate that the response process was associated with induced, rather than suppressed, gene expression. Further network analysis revealed putative hub genes perhaps regulating the EAB resistance. In addition, comparison of metabolic pathways between resistant and susceptible groups provided insight into the mechanism of EAB resistance in green ash. To understand more about this serious forest health issue and to assist in green ash protection and restoration, I have conducted a genetic diversity study, using SSR markers, with 429 green ash accessions collected from 60 provenances across the species’ natural range. Our results revealed three distinct sub- groups of provenances. Northern provenances fell into one group, southern provenances into a second group, and the third sub-group of provenances consisted of admixtures of northern and southern genotypes. We also constructed a DNA-marker based genetic linkage map for a green ash population of full- sib seedlings segregating for EAB-resistance from a controlled cross of EAB-resistant and EAB- susceptible green ash parent trees. The mapping population can be used in future to conduct quantitative trait locus (QTL) analysis to identify genomic regions contributing to different susceptibilities to EAB. Furthermore, a genetic association study identified loci significantly associated with EAB resistance, height, diameter at breast, budburst and foliage coloration using the range-wide selection of green ash trees in the provenance study. We identified candidate genes potentially associated with EAB resistance and foliage coloration in green ash. These results will be confirmed using larger sample size and more genetic markers. I hope that this study will support further research on the basis of apparent low frequency natural EAB resistance in green ash and lead to strategies for eventual restoration of the species. This research iii was supported by a grant to Dr. John Carlson from NSF’s Plant Genome Research Program (IOS- 1025974) and by the USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN04532 and Accession number 1000326. iv Table of Contents LIST OF FIGURES ............................................................................................................ viii LIST OF TABLES ................................................................................................................ ix Chapter 1 Introduction ......................................................................................................... 1 Background ..................................................................................................................................... 1 Interspecies variation of EAB resistance ............................................................................................. 1 Green Ash ............................................................................................................................................ 2 Natural variation within green ash ....................................................................................................... 3 Common garden trial ........................................................................................................................... 4 Transcriptomic comparison ................................................................................................................. 4 Genetic linkage mapping ..................................................................................................................... 5 Marker-trait associations ..................................................................................................................... 6 Objectives ........................................................................................................................................ 7 References ....................................................................................................................................... 9 Chapter 2 Transcriptome profile between resistant and susceptible green ash genotypes .. 12 Abstract ........................................................................................................................................ 12 Introduction .................................................................................................................................. 12 Materials and Methods ................................................................................................................. 13 Plant materials ................................................................................................................................... 13 EAB inoculation treatments and RNA sequencing ............................................................................ 13 Sequence Read mapping and function annotation ............................................................................. 13 Metabolic pathway analysis ............................................................................................................... 14 Protein-protein interaction network analysis ..................................................................................... 14 Results and Discussion .................................................................................................................. 14 Enrichment analysis results ............................................................................................................... 15 Pathway Analysis .............................................................................................................................. 16 Network Analysis .............................................................................................................................. 17 Putative hub genes ............................................................................................................................. 18 Conclusions ................................................................................................................................... 20 References ..................................................................................................................................... 22 Chapter 3 Population structure and genetic diversity of green ash (Fraxinus pennsylvanica) assessed with SSR markers .................................................................................................. 34 Abstract ........................................................................................................................................ 34 Introduction .................................................................................................................................. 34 Materials and Methods ................................................................................................................. 35 Plant Materials ................................................................................................................................... 35 Simple sequence repeats (SSRs) genotyping and data analysis ......................................................... 36 Marker informativeness testing ......................................................................................................... 36 Population structure and clustering .................................................................................................... 36 Genetic diversity and population differentiation ............................................................................... 37 Phenotypic data ................................................................................................................................
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