Genome-Wide Analysis of Stress-Responsive Genes and Alternative Splice Variants in Arabidopsis Roots under Osmotic Stresses

Plant roots show distinct gene-expression profiles from those of shoots under abiotic stress conditions. In this study, we performed mRNA sequencing (mRNA-Seq) to analyze the transcriptional profiling of Arabidopsis roots under osmotic stress conditions-high salinity (NaCl) and drought (mannitol). The roots demonstrated significantly distinct gene-expression changes from those of the aerial parts under both the NaCl and the mannitol treatment. We identified 68 closely connected transcription-factor genes involved in osmotic stress-signal transduction in roots. Well-known abscisic acid (ABA)-dependent and/or ABA-independent osmotic stress-responsive genes were not considerably upregulated in the roots compared to those in the aerial parts, indicating that the osmotic stress response in the roots may be regulated by other uncharacterized stress pathways. Moreover, we identified 26 osmotic-stress-responsive genes with distinct expressions of alternative splice variants in the roots. The quantitative reverse-transcription polymerase chain reaction further confirmed that alternative splice variants, such as those for ANNAT4, MAGL6, TRM19, and CAD9, were differentially expressed in the roots, suggesting that alternative splicing is an important regulatory mechanism in the osmotic stress response in roots. Altogether, our results suggest that tightly connected transcription-factor families, as well as alternative splicing and the resulting splice variants, are involved in the osmotic stress response in roots.

Automated summary

Plant roots exhibit distinct gene expression patterns compared to shoots under abiotic stress conditions. This study used mRNA sequencing to analyze the gene expression profiles of Arabidopsis roots subjected to osmotic stress caused by high salinity (NaCl) and drought (mannitol). The results showed significant changes in gene expression in the roots compared to the aerial parts under both NaCl and mannitol treatments. The study identified 68 transcription factor genes that are closely involved in osmotic stress signal transduction in roots. Additionally, alternative splice variants of 26 osmotic stress-responsive genes were found in the roots. The findings suggest that transcription factor families, alternative splicing, and resulting splice variants play important roles in the osmotic stress response in roots.