Transcriptional response to warm temperatures is confounded by organ-specificity

Climate change is causing increases in global average temperatures with detrimental consequences to food security, in part because most plants are sensitive to increases of even 1-2 degrees Celsius. Our molecular understanding of how plants perceive and acclimatise to mild increases in temperature (aka thermomorphogenesis) have largely been built upon transcriptomic analyses of whole seedling using the plant model Arabidopsis thaliana. In this work, we demonstrate that this widely used approach has significant limitations that may have skewed our understanding of gene regulation in thermomorphogenesis.We found a surprisingly poor consensus among published whole seedling transcriptomic datasets. On average, nearly 60% of reported differentially expressed genes (DEGs) are unique to a single study. To investigate the source of this variability, we performed a controlled comparison of RNA sequencing data from whole seedlings versus dissected organs (root, hypocotyl, and cotyledon), which revealed strong organ-specific transcriptional responses to warmth. Critically, we found that ~70% of DEGs identified in whole seedlings were not differentially expressed in any of the individual organs, suggesting that whole seedling data is confounded by the pooling of distinct, and sometimes opposing, organ-level responses. These findings are further supported by proteomic analysis. Our work provides a word of caution and clear guidance for the field to advance when producing and interpreting RNA sequencing data for plant response to warm temperatures.