Research Article Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize Nepolean Thirunavukkarasu, 1 Rinku Sharma, 1 Nidhi Singh, 1 Kaliyugam Shiriga, 1 Sweta Mohan, 1 Swati Mittal, 1 Shikha Mittal, 1 Mallana Gowdra Mallikarjuna, 1 Atmakuri Ramakrishna Rao, 2 Prasanta Kumar Dash, 3 Firoz Hossain, 1 and Hari Shanker Gupta 1,4 1 Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India 2 Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa, Library Avenue, New Delhi 110 012, India 3 National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi 110012, India 4 Borlaug Institute for South Asia (BISA), New Delhi 110012, India Correspondence should be addressed to Nepolean Tirunavukkarasu; tnepolean@gmail.com Received 8 September 2016; Revised 16 December 2016; Accepted 12 January 2017; Published 23 February 2017 Academic Editor: Mohamed Salem Copyright © 2017 Nepolean Tirunavukkarasu et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. Te number of genes expressed diferentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary diferences at the transcriptional level in stress tolerance. Te global coexpression networks of the two genotypes difered signifcantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between diferent adaptive pathways, each cluster of the network representing a specifc biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modifcation and protein and lipid metabolism. Te interaction of genes involved in crucial biological functions during stress was identifed and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail. 1. Introduction Maize, the third most important food crop in the world afer rice and wheat, meets 50–60% of the calorie requirements of people [1]. Considering its importance, increasing maize production under adverse environments has been an active area of research. Drought stress, a major source of environ- mental stress, lowers crop yields throughout the world [2]. Understanding how plants respond to stress generally is a prerequisite to understanding how they respond to drought at molecular and genomic levels, and a number of promising genes have been identifed at the transcriptional level [3]. Abscisic acid (ABA) is the main factor governing stomatal closure, which is afected by regulating guard cell openings [4]. ABA is also an important factor in activating regulatory, enzymatic, and structural genes [5], which play important roles in the perception of stress stimuli, signal transduction, and transcriptional regulatory networks [6]. Transcription factors (TFs) such as MYB, bZIP, C2H2, and NAC were expressed to a greater degree in plants under drought [7]. Expression analysis and characterization of TFs have shown being important genes for stress tolerance [8]. TFs follow either an ABA-dependent pathway, which involves the ABA- responsive element binding factors (ABFs) MYC and MYB, Hindawi International Journal of Genomics Volume 2017, Article ID 2568706, 14 pages https://doi.org/10.1155/2017/2568706