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Open Phd Dissertation Wanyan Wang

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Open Phd Dissertation Wanyan Wang The Pennsylvania State University The Graduate School The Huck Institutes of the Life Sciences GENOMICS OF GENOTYPE-BY-ENVIRONMENT INTERACTIONS IN SHRUB WILLOW (SALIX SPP.): INSECT HERBIVORY AND SOIL MICROBIOMES A Dissertation in Plant Biology by Wanyan Wang 2018 Wanyan Wang Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2018 The dissertation of Wanyan Wang was reviewed and approved* by the following: John E. Carlson Professor of Molecular Genetics Dissertation Advisor Chair of Committee Yinong Yang Professor of Plant Pathology Mary Ann Victoria Bruns Associate Professor of Soil Science and Microbial Ecology Surinder Chopra Professor of Maize Genetics Teh-hui Kao Distinguished Professor of Biochemistry and Molecular Biology Chair of the Plant Biology Graduate Program *Signatures are on file in the Graduate School ii ABSTRACT The growth of perennial shrub willow (Salix spp.), as a short rotation woody biomass crop, has superior properties for bioenergy production: short harvest cycle, high yield and adaptability to a wide range of site conditions, high net energy ratio, low demand for fertilizer and management and favorable environmental impact, like soil conservation and biodiversity. The aim of my research is to use advanced, genomics-based techniques to facilitate the breeding of new willow cultivars with improved and consistent yield across a wide variety of sites in the northeastern region, as well as resistance to pests and diseases. Understanding the interactions between environmental factors and shrub willow will be important for optimizing willow growth conditions and will also aid in developing improved cultivars that adapt better to particular environments. There are two overall objectives for this thesis study: 1. Using RNA-Seq technique to capture the transcriptome dynamics of both resistant and susceptible willow species under insect herbivore - potato leafhopper infestation, and ultimately elucidate the defensive mechanism(s) and resistant genes/pathways of shrub willow against this pest. 2. Via comparison among the rhizosphere microbial communities originated from different geographic location and willow genotypes, to identify which factors shape the rhizosphere microbiome structure and how microbiome impact willow biomass yield. iii Table of Contents LIST OF FIGURES ....................................................................................................................................................vi LIST OF TABLES ................................................................................................................................................... viii ACKNOWLEDGEMENTS .......................................................................................................................................ix CHAPTER 1 Introduction to the Shrub Willow and Related Research ................................................................ 1 1.1 INTRODUCTION TO ENERGY CROP ............................................................................................................ 2 1.1.1 Global energy crisis and bioenergy market ................................................................................................. 2 1.1.2 Biomass as “carbon neutral” energy source ............................................................................................... 2 1.1.3 Dedicated energy crops ............................................................................................................................... 3 1.2 BIOLOGY OF THE SHRUB WILLOW ............................................................................................................ 4 1.2.1 Ecology, population and genetic Structure .................................................................................................. 4 1.2.2 Commonly studied Salix species .................................................................................................................. 5 1.2.3 Genomics studies on willows ....................................................................................................................... 5 1.3 USE OF THE SHRUB WILLOW IN ENERGY INDUSTRY ................................................................................. 7 1.4 USE OF SHRUB WILLOW IN OTHER ENVIRONMENTAL PROJECTS .............................................................. 8 CHAPTER 2 Transcriptome Analysis of Contrasting Resistance to Herbivory by Empoasca fabae in Two Shrub Willow Species and Their Hybrid Progeny .............................................................................. 9 ABSTRACT ............................................................................................................................................................... 10 ABBREVIATIONS ...................................................................................................................................................... 10 INTRODUCTION ........................................................................................................................................................ 11 RESULTS .................................................................................................................................................................. 13 Phenotypic responses of shrub willow to PLH attack in greenhouse and field trials ......................................... 13 RNA Sequencing and quality assessment ............................................................................................................ 13 Differentiation of parent transcriptomes based on genotype and defense-response timing ............................... 14 Identification of differentially expressed genes between parents from RNA-Seq data ........................................ 14 Weighted gene correlation network analysis (WGCNA) identified three clusters of genes associated with specific resistance mechanisms in the parents and hybrid progeny .......................................................... 15 Functional annotation enrichment analysis of gene cluster I (darkgreen) ......................................................... 16 Functional annotation enrichment analysis of gene cluster II (magenta)........................................................... 17 Functional annotation enrichment analysis of gene cluster III (black) .............................................................. 18 PLH-resistance associated transcription factor genes and their regulatory networks ....................................... 18 Pair-wise comparison of parents’ Time-0 transcriptomes .................................................................................. 19 Dominance accounts for a large majority of the differential expression among F1 progeny ............................. 20 DISCUSSION ............................................................................................................................................................. 21 Biosynthesis of secondary cell wall compounds as compensation for PLH injury ............................................. 21 Constitutive resistance or priming effects? ......................................................................................................... 22 High correlations between NBS-LRR R genes and PLH-resistance and sex ...................................................... 23 CONCLUSION ............................................................................................................................................................ 24 METHODS................................................................................................................................................................. 25 Plant and pest materials ..................................................................................................................................... 25 Greenhouse no-choice feeding experiment ......................................................................................................... 25 Phenotype measurements .................................................................................................................................... 26 RNA extraction and sequencing .......................................................................................................................... 26 Calculation and quantification of gene expression abundance .......................................................................... 27 iv Differential gene expression analysis ................................................................................................................. 27 Weighted gene correlation network analysis (WGCNA) ..................................................................................... 27 Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis ................... 28 Inheritance of Gene Expression .......................................................................................................................... 28 TABLES .................................................................................................................................................................... 29 FIGURES ................................................................................................................................................................... 31 SUPPLEMENTARY TABLE AND FIGURES ...................................................................................................................
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