Comparative Transcriptome Analysis of Shoots and Roots of TNG67 and TCN1 Rice Seedlings under Cold Stress and Following Subsequent Recovery: Insights into Metabolic Pathways, Phytohormones, and Transcription Factors

Abstract

Cold stress affects rice growth, quality and yield. The investigation of genome-wide gene expression is important for understanding cold stress tolerance in rice. We performed comparative transcriptome analysis of the shoots and roots of 2 rice seedlings (TNG67, cold-tolerant; and TCN1, cold-sensitive) in response to low temperatures and restoration of normal temperatures following cold exposure. TNG67 tolerated cold stress via rapid alterations in gene expression and the re-establishment of homeostasis, whereas the opposite was observed in TCN1, especially after subsequent recovery. Gene ontology and pathway analyses revealed that cold stress substantially regulated the expression of genes involved in protein metabolism, modification, translation, stress responses, and cell death. TNG67 takes advantage of energy-saving and recycling resources to more efficiently synthesize metabolites compared with TCN1 during adjustment to cold stress. During recovery, expression of OsRR4 type-A response regulators was upregulated in TNG67 shoots, whereas that of genes involved in oxidative stress, chemical stimuli and carbohydrate metabolic processes was downregulated in TCN1. Expression of genes related to protein metabolism, modification, folding and defense responses was upregulated in TNG67 but not in TCN1 roots. In addition, abscisic acid (ABA)-, polyamine-, auxin- and jasmonic acid (JA)-related genes were preferentially regulated in TNG67 shoots and roots and were closely associated with cold stress tolerance. The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1. The TNG67-preferred TFs which express in shoot or root, such as OsIAA23, SNAC2, OsWRKY1v2, 24, 53, 71, HMGB, OsbHLH and OsMyb, may be good candidates for cold stress tolerance-related genes in rice. Our findings highlight important alterations in the expression of cold-tolerant genes, metabolic pathways, and hormone-related and TF-encoding genes in TNG67 rice during cold stress and recovery. The cross-talk of hormones may play an essential role in the ability of rice plants to cope with cold stress.

Comparative transcriptomics provides insight into the evolution of cold response in Pooideae

“…lipid membranes) [10,12]. Several studies have used transcriptomics to compare cold stress response, however, they focused on closely related taxa or varieties within model species [17,[32][33][34][35][36]. As such, these studies were not able to investigate evolutionary mechanisms underlying adaptation to cold climates of entire clades.…”

Rootstock Sub-Optimal Temperature Tolerance Determines Transcriptomic Responses after Long-Term Root Cooling in Rootstocks and Scions of Grafted Tomato Plants

“…This effect of long-term stress is further supported by the fact that bins for regulation of transcription and protein synthesis were enriched for down-regulated genes, while they were enriched for up-regulated genes after a short-term cold stress in the roots of a tolerant rice cultivar (Yang et al, 2015). …”

Dealing with abiotic stresses: an integrative view of how phytohormones control abiotic stress-induced oxidative stress

“…However, JA signaling appears to involve a more complex hormonal interaction since JA stimulated the expression of crucial enzymes for ABA biosynthesis, as well as alleviated injury by cold because it also induced cellular alkalinization, which occured through increase in intracellular pH in stomatal guard cells and preceded stomatal closure (Hossain et al 2011). Moreover, in a comparative transcriptome analysis of rice seedlings under cold stress, Yang et al (2015) observed increases in the expression of ABA and JA genes and polyamines, which suggested that a coordinated action established the state of rice cold stress tolerance.…”

“…It is not the objective of this review to discuss climate change, although it is a subject that is extremely important, relevant and linked to this sub-section, but it is a subject that is directly linked to plant survival and performance in a changing environment. Low temperatures can reduce enzyme activity by a number of ways, including reduced metabolic rates and operation not in the optimum temperature, hardening of membranes and destabilization of protein complexes, besides the accumulation of ROS, which combined or individually, and depending on the intensity and duration of the stress, may even cause cell death (Gratão et al 2005;Ruelland et al 2009;Yang et al 2015). On the other hand, high temperatures can cause water deficiency in plants by enhancing transpiration and evaporation and change the level and balance of hormone regulation (Nimir et al 2015).…”