Identification of Regulatory Roles for Stress Responsive Transposable Elements in Rice

Transposable elements, or mobile DNA sequences, are known for their structural and functional roles in the rice genome. As sources of genetic variation and drivers of evolution, transposable elements have been extensively studied for their role in regulation of gene expression. In addition, transposable elements are shown to be activated in response to various biotic and abiotic stresses and can possibly serve as a contributor to heat stress adaptation by modification of gene expression. As the global temperature rises, heat stress threatens crop production worldwide by affecting optimal rice growth, development, and yield. Concern for food security amidst a growing population thus calls for development of novel methods to study regulation of gene expression in response to heat stress. Two rice varieties, Cypress and LaGrue, are known to perform well and poorly, respectively, under high night temperatures (HNT) based on their ability to withstand heat stress during growth and development. Using these two contrasting genotypes and their varied response to HNT conditions, we aim to explore the role of stress-induced transposable elements in regulating gene expression underH heat stress. We have identified 139 unique transposable elements that are differentially expressed in response to heat stress. A comprehensive genomic analysis aims to identify Gene-associated Transposable Elements (GaTEs) and understand their regulatory roles in stress response. This information will be leveraged in Machine Learning algorithms to develop predictive models for manipulating genes, enhancing rice plants' resilience to HNT and ultimately contributing to the overall adaptability of rice crops to heat stress conditions.