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.
Highlights
Rice is the most important staple food in the world, especially in Asia
After recovery from the cold for 24 hr, the Fv/Fm values were low in the TCN1 rice leaves but were similar to those measured under normal growth conditions in the TNG67 leaves (Fig 1A)
With regard to CK degradation, we discovered 2 catabolic enzymes, the Cytokine oxidase (CKX) (CK dehydrogenase)-related genes LOC_Os10g34230 (CKX3) and LOC_Os01g71310 (CKX4), that were expressed at higher levels in the shoots of TNG67 compared with those of TCN1 in response to cold stress
Summary
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. 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. Various physiological and biochemical responses are altered in plants, such as the inhibition of photosynthesis, respiration and protein translation, accumulation of reactive oxygen species (ROS), alterations in metabolite profiles and osmolyte adjustment. Plants can reprogram or reconfigure their primary metabolism to redistribute energy resources for survival [1]. Alterations in primary metabolism involving sugars and sugar alcohols, amino acids and tricarboxylic acid (TCA) cycle intermediates are general trends in abiotic stress responses [2]
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