Impact of alternative splicing on rice (Oryza sativa L.) heat stress response

Abstract

The future of food security is being threatened by climate change. Rice is a major food crop, but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of heat stress tolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defense in plants, but it has been, to our knowledge, completely overlooked in rice genome-wide heat-stress studies. Our project aims at understanding the complexity of dynamic regulation of gene expression in response to heat stress by integrating AS responses to identify key genes regulating heat tolerance. For this, we will perform a high-resolution time-series transcriptome analysis of rice plants exposed to high temperatures. We will use state-of-the-art analysis methods developed for our analysis of the Arabidopsis cold response (Calixto et al., 2018), which identified rapid and major changes in AS and expression and identified novel regulatory genes including transcription factors and splicing factors in the cold response. Through application of advanced computational analysis methods, we will generate robust differential expression analysis that not only provides a systematic view of regulation at the transcriptional levels, but also addresses the unanswered question of the extent and dynamics of AS regulation upon heat stress in rice. From this information, we will investigate the sensitivity and speed of expression/AS behavior of key heat-sensitive genes in different heat stress conditions, as well as its regulation in rice cultivars with contrasting heat tolerance/sensitivity. Lastly, we will investigate putative heat-affected regulators of AS by generating over-expression and loss-of-function (non-transgenic CRISPR-Cas9) lines in candidate genes, which will be monitored for heat stress phenotypes. The resulting knowledge will provide insight and strategies to rapidly advance rice breeding in response to changing environments. (AU)