TY - JOUR
T1 - Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network
AU - Mohanty, Bijayalaxmi
AU - Kitazumi, Ai
AU - Cheung, C. Y.Maurice
AU - Lakshmanan, Meiyappan
AU - de los Reyes, Benildo G.
AU - Jang, In Cheol
AU - Lee, Dong Yup
N1 - Funding Information:
This work was supported by the National University of Singapore, the National Research Foundation of Singapore (NRF2013-THE001-035), Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore, the Next-Generation BioGreen 21 Program (SSAC, No. PJ01109405), Rural Development Administration, Republic of Korea, and the Maine Agricultural and Forest Experimental Station (Publication 3416).
Publisher Copyright:
© 2015 Elsevier Ireland Ltd.
PY - 2016/1/1
Y1 - 2016/1/1
N2 - In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.
AB - In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.
KW - Cis-elements
KW - Drought
KW - Metabolic network
KW - Physiological adjustment
KW - Plant breeding
KW - Transcription factor
UR - http://www.scopus.com/inward/record.url?scp=84946605712&partnerID=8YFLogxK
U2 - 10.1016/j.plantsci.2015.09.018
DO - 10.1016/j.plantsci.2015.09.018
M3 - Article
C2 - 26566840
AN - SCOPUS:84946605712
VL - 242
SP - 224
EP - 239
JO - Plant Science
JF - Plant Science
SN - 0168-9452
ER -