Transcriptome analysis reveals genes responsive to three low-temperature treatments in Arabidopsis thaliana

Cold stress impedes the growth and development of plants, restricts the geographical distribution of plant species, and impacts crop productivity. In this study, we analyzed the Arabidopsis thali-ana transcriptome to identify genes with differential expression (DEGs) in 14-day-old plantlets exposed to temperatures of 0°C, 4°C, and 10°C for 24 h, compared to the 22°C control group. We found 31 genes shared among three low temperatures, with 9 genes common to 0°C-4°C, 8 genes to 4°C-10°C, and 2 genes to 0°C-10°C among the top 50 cold-induced genes from each tempera-ture. Our data revealed that genes, such as galactinol synthase 3 (Gols3, At1g09350), CIR1 (At5g37260), DnaJ (At1g71000), and At5g05220 (unknown function), exhibited the highest ex-pressions at 0°C and 4°C during the 24, 48, and 72-h intervals. We also studied genes from the UDP-glycosyltransferase (UGT78) family, including At5g17030 (D3), At5g17040 (D4), At5g17050 (D2), and At1g30530 (D1), which showed increased expression at low temperatures compared to plantlets at 22°C for 24 h. Gene ontology analysis revealed that DEGs highly en-riched were found in biological processes including “RNA secondary structure unwinding” and “rRNA processing” induced at the three low temperatures, whereas processes related to photo-synthesis were repressed. Our findings indicated upregulation in the expression of four RNA hel-icases (RH13, RH48, RH32, and RH29), belonging to the “RNA secondary structure unwinding” category, mainly at 0°C and 4°C. This study provides valuable information on the molecular mechanisms that activate Arabidopsis thaliana in its early response to these three low tempera-tures. Overall design: After growing for two weeks, 14-day-old plantlets were subjected to low temperatures of 0ºC, 4ºC, and 10ºC for 24h, 48h, and 72h, respectively. Control plants were maintained in a growth chamber at 22ºC. After the cold treatments, the plants were harvested, rapidly frozen in liquid nitrogen, and stored at -80°C for further analysis. Each temperature condition had three biological replicates (n=3), with each replicate comprising groups of 10 plantlets per Petri plate.