Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana

3 Biotech (2017)7:209 DOI 10.1007/s13205-017-0858-7 ORIGINAL ARTICLE Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana Bong-Gyu Mun1 • Sang-Uk Lee1 • Eung-Jun Park2 • Hyun-Ho Kim1 • Adil Hussain1,3 • Qari Muhammad Imran1 • In-Jung Lee1 • Byung-Wook Yun1 Received: 25 April 2017 / Accepted: 17 June 2017 Ó The Author(s) 2017. This article is an open access publication Abstract Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species. Electronic supplementary material The online version of this article (doi:10.1007/s13205-017-0858-7) contains supplementary material, which is available to authorized users. Keywords Drought stress
Transcriptome
Poplar
Transcription factors Bong-Gyu Mun and Sang-Uk Lee have contributed equally to this work. & Byung-Wook Yun 1 School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea 2 Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 16631, Republic of Korea 3 Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan Introduction Populus davidiana is a plant species native to the Korean Peninsula and is one of the most widely distributed forest trees in Korea. The ubiquity of Populus species is indicative of their ability to adapt to diverse environmental conditions, such as cold (Chen et al. 2012), salt (Gu et al. 2004), and drought (Li et al. 2011b; Tang et al. 2013b). Drought occurs when there is insufficient irrigation or rainfall for a period, such that soil moisture is reduced to an 123 209 Page 2 of 12 extent that ultimately damages or injures plants. This deficiency is typically accompanied by higher evapotranspiration rates from plant surfaces compared to water absorption by the roots (Jordan and Ritchie 1971). Drought stress has also been found to be accompanied by other abiotic stresses such as salinity and high temperature stress. Salt and drought stress signal transduction consists of ionic and osmotic homeostasis, detoxification, and growth regulation. The adverse effects of water stress on plant physiology and the mechanisms associated with water stress tolerance and water-use efficiency have been extensively studied (Osakabe et al. 2014). Although Populus trees have a much deeper root system compared to agricultural corps, they are still affected by persistent drought. Persistent drought can influence the structure and growth of roots which in turn negatively affects water uptake leading to the appearance of initial drought symptoms and permanent damage if drought persists (Coder 1999; Kozlowski and Pallardy 2002). Published researches on the molecular mechanisms underpinning responses to drought stress in various crops, such as maize (Avramova et al. 2014), barley (Bedada et al. 2014), potato (Gong et al. 2015), rice (Huang et al. 2014), wheat (Okay et al. 2014), sugarcane (Kido et al. 2012), and soybean (Le et al. 2012), and many other plants, including forest trees such as poplar, pine, and oak (Dong et al. 2014a; Li et al. 2011a). These studies provide useful information regarding the underlying mechanisms and possible management of the problem. Populus is a promising model of forest trees and/or other woody plants for research on diverse stress responses (Li et al. 2011a; Qiu et al. 2011; Si et al. 2014; Yan et al. 2012). Moderately drought-stressed Populus euphratica trees have been found to regulate stomatal closure to facilitate higher CO2 accumulation and water absorption for normal growth and development. This is typically accompanied by strong transcriptional regulation of various physiological processes such as stress perception, photoreception, and oxidative stress detoxification at the molecular level (Tang et al. 2013a). Several studies have shown that some species of Populus, such as P. euphratica, are extremely sensitive to drought-induced cavitation (Hukin et al. 2005), whereas P. nigra shows tolerance to drought. Plant cellular responses to various biotic and/or abiotic stresses involve highly complex interconnected networks of signaling pathways, and a systematic understanding of these networks is necessary to comprehend the underlying mechanisms of stress tolerance. An efficient approach for examining the complex internal networks initiated in response to drought stress is discovering genes and metabolic pathways involved in drought stress physiology. This approach may provide clues for the production of drought-tolerant plants (Hamanishi and Campbell 2011). 123 3 Biotech (2017)7:209 Recently, high-throughput sequencing technologies have yielded accurate whole-genome sequences on a large scale at low-cost and in a relatively short time. To date, RNA-seq-mediated transcriptome analysis of three Populus species (P. tremula (Paul et a (...truncated)