Genome-Wide Analysis of Gene Expression Provides New Insights into Cold Responses in Thellungiella salsuginea

Abstract

Low temperature is one of the major environmental stresses that affects plant growth and development, and leads to decrease in crop yield and quality. <i>Thellungiella salsuginea</i> (salt cress) exhibits high tolerance to chilling, is an appropriate model to investigate the molecular mechanisms of cold tolerance. Here, we compared transcription changes in the roots and leaves of <i>T. salsuginea</i> under cold stress using RNA-seq. We identified 2,782 and 1,430 differentially expressed genes (DEGs) in leaves and roots upon cold treatment, respectively. The expression levels of some genes were validated by quantitative real-time-PCR (qRT-PCR). Among these DEGs, 159 (11.1%) genes in roots and 232 (8.3%) genes in leaves were annotated as various types of transcription factors. We found that five aquaporin genes (three <i>TIPs</i>, one <i>PIPs</i>, and one <i>NIPs)</i> responded to cold treatment. In addition, the expression of <i>COR47, ICE1, and CBF1</i> genes of <i>DREB1/CBF</i>-dependent cold signaling pathway genes altered in response to low temperature. KEGG pathway analysis indicated that these cold regulated genes were enriched in metabolism, photosynthesis, circadian rhythm, and transcriptional regulation. Our findings provided a complete picture of the regulatory network of cold stress response in <i>T. salsuginea</i>. These cold-responsive genes could be targeted for detail functional study and utilization in crop cold tolerance improvement.