Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance

Abstract

To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant’s inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.

Identification of candidate regulators of the response to early heat stress in climate-adapted wheat landraces via transcriptomic and co-expression network analyses

“…A handful of studies have examined the effect of heat stress on the transcriptome of wheat during vegetative development ( Qin et al., 2008 ; Liu et al., 2015 ; Jin et al., 2020 ); however, this type of analysis paired with subsequent network analysis is less common, despite this approach enabling the identification of a small number of promising candidate genes potentially playing large regulatory roles in the stress response, reducing the time spent laboriously screening all of the identified stress-responsive genes. Similar combined approaches have been used in other contexts, however, such as to identify regulators of thermotolerance during vegetative development in wheat ( Girousse et al., 2018 ; Mishra et al., 2021 ); response to heat and cold stresses, and basal thermotolerance in rice ( Wang et al., 2022 ; Zeng et al., 2022 ; Boulanger et al., 2023 ); response to combined heat, drought, and salinity stresses in Brachypodium ( Shaar-Moshe et al., 2017 ); and drought stress response in sugarcane ( Tang et al., 2023 ), whilst we have previously used this combined approach to study the drought stress response in wheat ( Barratt et al., 2023b ). However, there are no similarly exploratory examples of this approach being used to study the heat stress response in wheat, as yet.…”