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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.

Yang YW, Chen HC, Jen WF, Liu LY, Chang MC - PLoS ONE (2015)

Bottom Line: 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.The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, No. 1, Section 4, Taipei, Taiwan.

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.

No MeSH data available.


Related in: MedlinePlus

MapMan overview of changes in the expression of genes involved in the secondary metabolism of rice roots in response to cold treatment for (A) 3 hr and (B) 24 hr and (C) following recovery for 24 hr after cold treatment.Genes involved in different metabolic processes are shown in the main panel in dark green, while putatively associated genes are shown in light green. Blue indicates that gene expression was induced and red indicates that gene expression was repressed compared with the control.
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pone.0131391.g005: MapMan overview of changes in the expression of genes involved in the secondary metabolism of rice roots in response to cold treatment for (A) 3 hr and (B) 24 hr and (C) following recovery for 24 hr after cold treatment.Genes involved in different metabolic processes are shown in the main panel in dark green, while putatively associated genes are shown in light green. Blue indicates that gene expression was induced and red indicates that gene expression was repressed compared with the control.

Mentions: In roots, the secondary metabolism map generated by MapMan analysis showed a tendency toward the increased activities of the phenylpropanoid and lignin biosynthesis (S6 Table) pathways in TNG67. Expression of the genes in these two pathways was greater in TNG67 than in TCN1 after 3 hr of cold stress. Additional genes were upregulated after 24 compared with those upregulated after 3 hr of cold stress in both cultivars; however, more genes were repressed in TCN1. In contrast, more genes were repressed in TNG67 after recovery compared with those repressed after 24 hr of cold stress (Fig 5).


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.

Yang YW, Chen HC, Jen WF, Liu LY, Chang MC - PLoS ONE (2015)

MapMan overview of changes in the expression of genes involved in the secondary metabolism of rice roots in response to cold treatment for (A) 3 hr and (B) 24 hr and (C) following recovery for 24 hr after cold treatment.Genes involved in different metabolic processes are shown in the main panel in dark green, while putatively associated genes are shown in light green. Blue indicates that gene expression was induced and red indicates that gene expression was repressed compared with the control.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489882&req=5

pone.0131391.g005: MapMan overview of changes in the expression of genes involved in the secondary metabolism of rice roots in response to cold treatment for (A) 3 hr and (B) 24 hr and (C) following recovery for 24 hr after cold treatment.Genes involved in different metabolic processes are shown in the main panel in dark green, while putatively associated genes are shown in light green. Blue indicates that gene expression was induced and red indicates that gene expression was repressed compared with the control.
Mentions: In roots, the secondary metabolism map generated by MapMan analysis showed a tendency toward the increased activities of the phenylpropanoid and lignin biosynthesis (S6 Table) pathways in TNG67. Expression of the genes in these two pathways was greater in TNG67 than in TCN1 after 3 hr of cold stress. Additional genes were upregulated after 24 compared with those upregulated after 3 hr of cold stress in both cultivars; however, more genes were repressed in TCN1. In contrast, more genes were repressed in TNG67 after recovery compared with those repressed after 24 hr of cold stress (Fig 5).

Bottom Line: 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.The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, No. 1, Section 4, Taipei, Taiwan.

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.

No MeSH data available.


Related in: MedlinePlus