Villarino Pizarro, Gonzalo.
Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.
Degree: PhD, Horticultural Biology, 2014, Cornell University
Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal plant growth and development. Many studies have used both forward and reverse genetic techniques to understand the complex interactions of plant systems with abiotic stress. These approaches have been invaluable in deciphering some mechanisms of plant salt stress tolerance. Salt tolerance research has also been an important part of basic plant biology, increasing the understanding in areas encompassing gene regulation, mineral nutrition, signaling components, ion transport and osmoregulation. To better understand the detrimental effects of NaCl, as well the fundamental questions associated with salt tolerance, transcript regulation in response to NaCl stress was undertaken using ultra-high-throughput RNA sequencing technology (RNA-seq). RNA-seq has quickly become the method of choice to perform transcriptomic analysis owing to many advantages over existing platforms. The transcriptomic research presented here was carried out in Petunia hybrida, a salt resistant Solanaceous plant that has also been an excellent model species in molecular genetic research regarding flower development and senescence, synthesis and regulation of volatiles, and so on. In chapter one, to bypass the absence of an available Petunia genome, a de-novo assembled Petunia transcriptome was reconstructed by assembling over one- hundred million Illumina cDNA reads with Trinity software. The de-novo assembled contigs represents the most in-depth transcriptome ever reported for a Petunia species, which can be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome. The transcriptome has been made publically available on the SOL Genomics Network (SGN) http://solgenomics.net. Using this newly assembled reference transcriptome, more than 7,000 differentially expressed genes were identified within 24 h of acute NaCl stress. Genes related to regulation of reactive oxygen species, transport, and signal transduction as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. Gene ontology analyses revealed that plants by 24 h after acute NaCl undertook many changes occurring at the molecular level including genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. RNA-seq, despite the many advantages it offers, it is a relatively new methodology with developments and improvements to be made. At the end of chapter one a modification to the library preparation protocol is presented whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. This methodological improvement could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments. In chapter two, root and leaf transcriptomic response to salt stress was investigated, utilizing the Petunia…
Advisors/Committee Members: Mattson, Neil S. (chair), Mattson, Neil S. (chair), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member).
Subjects/Keywords: transcriptomics; RNA-seq; Salt stress
to Zotero / EndNote / Reference
APA (6th Edition):
Villarino Pizarro, G. (2014). Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38983
Chicago Manual of Style (16th Edition):
Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Doctoral Dissertation, Cornell University. Accessed November 29, 2020.
MLA Handbook (7th Edition):
Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Web. 29 Nov 2020.
Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2020 Nov 29].
Available from: http://hdl.handle.net/1813/38983.
Council of Science Editors:
Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38983