Discipline: Ecology Environmental and Earth Sciences
Subcategory: Plant Research
Phillip W. Prince - Savannah State University
Co-Author(s): David C. Haak, Virginia Tech, Blacksburg, VA
For agricultural production to keep pace with a growing population in a changing climate, we need to understand the physiological and genetic mechanisms underlying plant responses to the environment. Barbara McClintock’s discovery of Transposable Elements (TEs) indicated that genomes are quite dynamic and inextricably linked to physiological tolerance. TEs are genomic elements that can move throughout the genome sequence changing the expression pattern of genes. Under stress (e.g., drought) these elements can induce mutations by altering gene structure (insertion near active genes), modifying gene activation (altering the expression of regulatory RNA), or retrotransposition (replication of the repetitive element), which causes genome expansion. This process is assessed through the study of whole genome sequencing and transcriptomics the complete set of gene transcripts that are coded by the genome.
This study characterizes TEs among wild tomato species using Next Generation Sequencing (NGS) approaches to generate genomic and transcriptomic data. I used experimental transcriptomics to describe the comparative suite of TEs across the entire clade of wild tomatoes, Solanum spp. section Lycopersicon. Then, I screened whole genome sequence data from public repositories 30 accessions from S. pimpinellifolium, a species widely used for improving the cultivated tomato (S. lycopersicum). Our results demonstrated a variety of prevalence’s within certain phylogenetic relatives. Understanding the role of TEs in plant stress responses has important implications for the agricultural industry. By focusing on wild crop relatives, this research will uncover novel sources of stress resistance traits, which can be directly transferred to high yielding cultivars. (Keywords: Transposable Elements, Bioinformatics, Next Generation Sequencing (NGS), Transcriptomics, Global, Biodiversity, Farming, Agriculture, Government, Distribution).
Funder Acknowledgement(s): National Science Foundation (NSF) / Multicultural Academic Opportunities Program (MAOP)
Faculty Advisor: Devi Chellu,