Research Article: 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

Date Published: July 2, 2015

Publisher: Public Library of Science

Author(s): Yun-Wei Yang, Hung-Chi Chen, Wei-Fu Jen, Li-Yu Liu, Men-Chi Chang, Debasis Chakrabarty.


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.

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Rice is the most important staple food in the world, especially in Asia. Two subspecies of rice, Oryza sativa ssp. japonica (temperate rice) and ssp. indica (tropical rice), are widely grown in different areas. Rice seedlings frequently experience cold injury, which affects their growth and yield. In general, indica rice tends to be more sensitive to low temperatures. Thus, to further improve rice quality and production and to overcome the limiting factor of cold, a thorough understanding of cold stress tolerance mechanisms in rice is needed, especially the differential means of cold stress perception and responses to this type of stress in the indica (e.g., TCN1) and japonica (e.g., TNG67) rice varieties.

Rice, particularly indica subspecies, is susceptible to chilling stress. Low temperatures can affect rice development during the germination, vegetative growth and reproductive stages. The screening of cold-tolerant rice varieties tends to be unsuccessful because of the poor correlation of cold resistance with different developmental periods [37]. In addition, cold stress tolerance is a quantitative trait that is determined by various quantitative trait loci. To understand the cold stress tolerance mechanisms used by rice to cope with cold sensitivity and to develop cold-tolerant rice cultivars, we conducted a comparative transcriptome study to identify changes in gene expression in response to cold and subsequent recovery between the roots and shoots of japonica (TNG67) and indica (TCN1) rice varieties. We aimed to discover some tolerance-related genes, important TFs and pathways that may benefit the breeding of potential rice varieties that are capable of withstanding cold.

Our transcriptome study revealed a preliminary model for the resistance of TNG67 to cold stress (Fig 10). Following exposure to cold, the rapid induction of ABA and JA in TNG67 accelerated stomatal closure to rapidly prevent water loss. These 2 hormones may interact with one another to alter the expression of a specific set of TFs in shoots (mainly NACs). In roots, auxin may participate in cross-talk with these 2 hormones to adjust the expression of other sets of TFs, such as WRKYs, to promote cold stress tolerance in rice. Polyamine is another key component of cold tolerance in TNG67. In response to cold stress, the level of ET was reduced and then elevated after recovery in these seedlings. Ethylene may facilitate the detection of stress relief because it has an antagonistic function to ABA. CK may also be involved in this process through interacting with ET. Additionally, the activation of apoptosis-related genes may be an important signal to trigger cold stress tolerance. This process can eliminate redundant or harmful cells and recycle the constituents of cells, and it is probably a more energy-efficient means of responding to environmental stimuli. In TCN1 under cold stress, the expression of photosynthesis-related genes increased as a consequence of energy starvation. However, this process causes ROS accumulation and leads to oxidative stress with cold-induced water loss. In contrast, the expression levels of TCA cycle- and glycolysis-related genes were greater in TNG67 than in TCN1. TNG67 may compensate for decreased energy production without excessively increasing photosynthetic reactions to avoid oxidative stress. Our study expands upon the current understanding of cold stress tolerance in rice, and our findings may be used to facilitate the breeding of cold-tolerant rice.