Alternative splicing is an important mechanism of gene regulation that contributes to transcriptome and proteome diversity. Large scale EST/cDNA based studies suggest that alternative splicing affects at least 20% of the genes in Arabidopsis thaliana, and its frequency in other plant species may be even higher. However, in the vast majority of cases, we do not know where and when splice variants are expressed, or if they have a biological function. Several recent reviews suggest the importance of alternative splicing in plants as a mechanism for controlling both development and stress adaptation. The goal of the proposed project is to further investigate this hypothesis by measuring the extent and functional significance of alternative splicing in Arabidopsis thaliana during its defense against the bacterial pathogen Pseudomonas syringae pv tomato. The investigators will employ high-throughput sequencing to query the expression of alternatively spliced genes, determine the impact of alternative splicing on protein structure and gene function, validate selected splice isoforms, and perform functional analysis of selected genes. A critical component of this project will be the development of new computational tools to detect and quantify alternative splicing in high-throughput sequencing data. So far, researchers might have avoided investigating alternative splicing due to technical challenges during data analysis; the tools developed during the course of this project will help to overcome these difficulties. The end-results of this study will contribute to a mechanistic understanding of alternative splicing, and help to conceive new strategies for stress tolerance improvement in crop plants. This project will provide trans-disciplinary training for two junior scientists. The PIs will also partner with the NCSU Science House to offer research opportunities to underrepresented and rural high school students.
