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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #322511

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: Analysis of petunia hybrida in response to salt stress using high throughput RNA sequencing

item VILLARINO, GONZALLO - Cornell University - New York
item BOMBARELY, AURELIANO - Boyce Thompson Institute
item Giovannoni, James
item SCANLON, MICHAEL - Cornell University - New York
item MATTSON, NEIL - Cornell University - New York

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2014
Publication Date: 12/3/2014
Citation: Villarino, G., Bombarely, A., Giovannoni, J.J., Scanlon, M., Mattson, N. 2014. Analysis of petunia hybrida in response to salt stress using high throughput RNA sequencing. PLoS One. 9(4):e94651.

Interpretive Summary: Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.

Technical Abstract: Salt and drought are among the greatest challenges to crop and native plants in meeting their yield and reproductive potentials. DNA sequencing-enabled transcriptome profiling provides a means of assessing what genes are responding to salt or drought stress so as to better understand the molecular approaches that plants under stress are taking in order to promote survival under such challenging conditions. A better understanding of how plants cope with yield limiting stresses can suggest possible solutions to these problems and genetic strategies to increase plant/crop performance toward increased crop yield and downstream food security. Here we performed a controlled salt stress test on petunia plants, performed transcriptome profiling and highlighted numerous genes suggestive of biochemical pathways deployed as part of the salt stress response. We also refined the transcriptome analysis protocol to show that a costly step could be eliminated with no detectable consequence.