University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Winter 2018 POPULATION GENETICS AND DESICCATION STRESS OF PORPHYRA UMBILICALIS KÜTZING IN THE GULF OF MAINE Yuanyu Cao University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Cao, Yuanyu, "POPULATION GENETICS AND DESICCATION STRESS OF PORPHYRA UMBILICALIS KÜTZING IN THE GULF OF MAINE" (2018). Doctoral Dissertations. 2429. https://scholars.unh.edu/dissertation/2429 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. POPULATION GENETICS AND DESICCATION STRESS OF PORPHYRA UMBILICALIS KÜTZING IN THE GULF OF MAINE BY YUANYU CAO B.A., Jimei University, Xiamen, Fujian, Peoples Republic of China, 2008 M. S., Jimei University, Xiamen, Fujian, Peoples Republic of China, 2013 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Genetics December 2018 This dissertation has been examined and approved in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Genetics by: Dissertation Dir. Anita S. Klein, Assoc. Professor of Biological Sciences Estelle M. Hrabak, Assoc. Professor of Molecular, Cellular, & Biomedical Sci. Matthew D. MacManes, Asst. Professor of Molecular, Cellular, & Biomedical Sci. Arthur Mathieson, Professor of Plant Biology W. Kelley Thomas, Professor of Molecular, Cellular, & Biomedical Sci. On September 13, 2018 ii DEDICATION To my husband, Mengmeng. To my parents, Heming Cao and Chenmei Wu, and to Meng’s parents. iii ACKNOWLEDGEMENTS I would like to thank my committee for their financial, technical, and manuscript support: Drs Anita S. Klein, W. Kelley Thomas, Estelle M. Hrabak, Arthur Mathieson, and Matthew D. MacManes. I owe many thanks to a number of people who helped me during my Ph.D years. Dr. David J Ashlin and Dr. Andy Hanneman from the Glycomics Center, UNH, provided valuable technical support and manuscript advice for the GC-MS study. Dr. Vernon Reinhold from the Glycomics Center for access to the GC-MS equipment. Dr. Elizabeth Ficko-Blean from Sorbonne Universités provided technical support and manuscript advice for the phylogenetic tree. Dr. Renée L. Eriksen and Dr. Lindsay A. Green-Gavrielidis provided valuable tissue samples, RNA-Seq data and manuscript suggestions for the population study. Dr. Paul C. Tsang and Joseph Miseirvitch provided technical support and equipment for real-time PCR analysis. Dr. Matthew D. MacManes, Anthony S. Westbrook and Dr. Feseha Abebe-Akele for software installation, bioinformatic support and server usage guidance. Dr. Subhash Minocha provided RNA extraction equipment and RNA extraction technical suggestions. Dr. Christopher Neefus provided lab space for DNA extraction. Jobriah Anderson performed some Sanger sequencing and Stephen Simpson at Hubbard Center for Genome Studies at UNH performed the RNA seq library preparation and sequencing. The Porphyra RCN provided access to the Porphyra umbilicalis genome database prior to publication, and was funded by NSF 05CH11231 (to Susan H. Brawley, Elizabeth Gantt, Arthur R. Grossman and John Stiller). I also want to thank undergraduates David Macomber and Anna Haber for help with DNA extraction and PCR amplification. Financial support was provided by by the USDA National Institute of Food and Agriculture Hatch Project accession 1004051. Additional support also was provided by the iv Leslie S. Hubbard Marine Program Endowment (to L. Green-Gavrielidis) NOAA contract NA060AR4170108 (to SHB) and by the Joint Genome Institute (U. S. Dept. of Energy) under a Community Science Program award from the Office of Science of the U. S. Dept. of Energy under Contract No. DE-AC02-05CH11231 (to Susan H. Brawley, Elizabeth Gantt, Arthur R. Grossman and John Stiller). v TABLE OF CONTENTS DEDICATION ............................................................................................................................. iii ACKNOWLEDGEMENTS ........................................................................................................ iv LIST OF TABLES ........................................................................................................................ x LIST OF FIGURES ..................................................................................................................... xi ABSTRACT ................................................................................................................................ xiii INTRODUCTION ........................................................................................................................ 1 Porphyra umbilicalis Kützing .................................................................................................. 2 Stress tolerance mechanisms .................................................................................................... 4 Molecular studies ...................................................................................................................... 5 Aquaculture ............................................................................................................................... 6 Algae and microbe interaction ................................................................................................. 8 Abiotic stress ............................................................................................................................ 10 Morphological and cellular alteration ................................................................................... 10 Photosynthesis ...................................................................................................................... 12 Accumulation of organic osmolytes ..................................................................................... 15 Reactive Oxygen Species ...................................................................................................... 18 Plant hormones ...................................................................................................................... 21 Transcriptome analysis under desiccation ............................................................................ 23 Goals ......................................................................................................................................... 24 CHAPTER I ................................................................................................................................ 27 vi A pilot study of genetic structure of Porphyra umbilicalis Kützing in the Gulf of Maine using SNP markers from RNA-Seq ........................................................................................... 27 Abstract .................................................................................................................................... 27 Introduction ............................................................................................................................. 28 Material and Methods ............................................................................................................ 31 Species identification, gametophyte culture, RNA isolation and sequencing ...................... 31 Reference transcriptomes construction ................................................................................. 32 Single nucleotide polymorphism markers detection ............................................................. 33 SNP markers validation ........................................................................................................ 33 Genetic diversity and population structure ........................................................................... 34 Results ...................................................................................................................................... 35 Reference Transcriptome ...................................................................................................... 35 SNP calling and functional annotation of library specific SNP-containing genes ............... 35 SNP validation ...................................................................................................................... 36 Pilot population study ........................................................................................................... 36 Population structure .............................................................................................................. 37 Discussion ................................................................................................................................ 37 SNP discovery and validation ............................................................................................... 38 Population genetics analysis ................................................................................................. 39 Limitation and Future Directions .......................................................................................... 44 Tables ......................................................................................................................................